CmaCh04G019670 (gene) Cucurbita maxima (Rimu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmaCh04G019670
Type	gene
Organism	Cucurbita maxima (Cucurbita maxima (Rimu))
Description	Photosystem II D2 protein
Location	Cma_Chr04 : 11157359 .. 11158389 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDS

Hold the cursor over a type above to highlight its positions in the sequence below.

ATGACTATAGCCGTTGGTAAATTGACCAAAGACTCAAATGATTTCTTCTTCGAGATTATGGATGACTCGTTACGGAGGGACCGGTTCGGTCTTGTAGGTTGGTCCGGTCTATTTCTCTTTCCTTGTGCCTATTTTATTGTCGTAGGAGGTTGGTTTACAGGTACACCCTTTATAACTTAATGGTATATCTAACCGTATGGATTGGCAAGTTCCTATTTGTTTGGAAGGATGCAACTTCTTAACCGCCGCTGTTTCGACTCCTGCTAATAGTTTAGCACACTCTTTCTTTGTTGTTACTATGGGGGCCTGAAGCACAAGGAGATAGATTTGACTCCTTGATGTCCATTACCATTAGGTGGTCTGTGGACTTTTGTTGCTCTCCACAGTTCGGACTAATAGGTTTCATGGTACGTCTAATCTTGCTCGATCCGTTCAATTGCTTTGTTTGTTTCCGTATTCCTGATGATTGATCCACTAGGTCAGTCTGGTTGGTTCTTTGCGCCTAGTTTTGGTGTAGCAGCTATGTTTCGATTCATCCTACTTTTCCCGGGAATGAAATAATTGAACATTGAACCCATTTCATATGATGGGAGTTGGTTGCGGGAGTATTGGGCGTTGCTTGGCTATGGCGCTATTCATGGTGCTACCCTAGAAAATCCCTTATTTGAAGGAAGATGGTGATGATGCTTCAAATACATTCCGTGCTTTTAACCCAACTCAAGCTGAAGGAAGAAACTTATTCAATGGTCACTGCTAACCGCTTTTGGTACCAAATCTTTGGGGTTGCTTTTTCCACTAAAGGTTGGTTACATTTCTTTCTGTTATTTGTACCAGTAACTGCTTTATGGCTGAGTGCTCTTGGAGTAGTTGGTCTGGCCCTGAACCTACGTGTCTATGACTTCGGTTCTCAGGAAATCCGTGCAGTAGGGGAAGATCCTGAATTTGAGACTTTATATACCCTACTATACCCAGAATCTTCTCTTAACCGAAGGTATTCGTGCTTGGATGGCGGCTCAAGATCAGCCTCATGA

mRNA sequence

ATGACTATAGCCGTTGGTAAATTGACCAAAGACTCAAATGATTTCTTCTTCGAGATTATGGATGACTCGTTACGGAGGGACCGGTTCGGTCTTGTAGTAACTGCTTTATGGCTGAGTGCTCTTGGAGTAGTTGGTCTGGCCCTGAACCTACGTGTCTATGACTTCGGTTCTCAGGAAATCCGTGCAGTAGGGGAAGATCCTGAATTTGAGACTTTATATACCCTACTATACCCAGAATCTTCTCTTAACCGAAGGTATTCGTGCTTGGATGGCGGCTCAAGATCAGCCTCATGA

Coding sequence (CDS)

ATGACTATAGCCGTTGGTAAATTGACCAAAGACTCAAATGATTTCTTCTTCGAGATTATGGATGACTCGTTACGGAGGGACCGGTTCGGTCTTGTAGTAACTGCTTTATGGCTGAGTGCTCTTGGAGTAGTTGGTCTGGCCCTGAACCTACGTGTCTATGACTTCGGTTCTCAGGAAATCCGTGCAGTAGGGGAAGATCCTGAATTTGAGACTTTATATACCCTACTATACCCAGAATCTTCTCTTAACCGAAGGTATTCGTGCTTGGATGGCGGCTCAAGATCAGCCTCATGA

Protein sequence

MTIAVGKLTKDSNDFFFEIMDDSLRRDRFGLVVTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYTLLYPESSLNRRYSCLDGGSRSAS

Homology

[Close]

BLAST of CmaCh04G019670 vs. Swiss-Prot
Match: PSBD_AETGR (Photosystem II D2 protein OS=Aethionema grandiflorum GN=psbD PE=3 SV=1)

HSP 1 Score: 69.7 bits (169), Expect = 2.0e-11
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

[Close]

BLAST of CmaCh04G019670 vs. Swiss-Prot
Match: PSBD_ARATH (Photosystem II D2 protein OS=Arabidopsis thaliana GN=psbD PE=1 SV=3)

HSP 1 Score: 69.7 bits (169), Expect = 2.0e-11
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

[Close]

BLAST of CmaCh04G019670 vs. Swiss-Prot
Match: PSBD_ATRBE (Photosystem II D2 protein OS=Atropa belladonna GN=psbD PE=3 SV=1)

HSP 1 Score: 69.7 bits (169), Expect = 2.0e-11
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

[Close]

BLAST of CmaCh04G019670 vs. Swiss-Prot
Match: PSBD_BARVE (Photosystem II D2 protein OS=Barbarea verna GN=psbD PE=3 SV=1)

HSP 1 Score: 69.7 bits (169), Expect = 2.0e-11
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

[Close]

BLAST of CmaCh04G019670 vs. Swiss-Prot
Match: PSBD_BIGNA (Photosystem II D2 protein OS=Bigelowiella natans GN=psbD PE=3 SV=1)

HSP 1 Score: 69.7 bits (169), Expect = 2.0e-11
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 276 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 316

[Close]

BLAST of CmaCh04G019670 vs. TrEMBL
Match: S5CK09_9MONI (Photosystem II D2 protein OS=Osmunda vachellii GN=psbD PE=3 SV=1)

HSP 1 Score: 70.5 bits (171), Expect = 1.3e-09
Identity = 35/42 (83.33%), Postives = 37/42 (88.10%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SA+GVVGLALNLR YDF SQEIRA  EDPEFETLYT
Sbjct: 277 VTGLWMSAIGVVGLALNLRAYDFVSQEIRA-AEDPEFETLYT 317

[Close]

BLAST of CmaCh04G019670 vs. TrEMBL
Match: A0A0D2TVP7_GOSRA (Uncharacterized protein (Fragment) OS=Gossypium raimondii GN=B456_009G327700 PE=4 SV=1)

HSP 1 Score: 70.1 bits (170), Expect = 1.7e-09
Identity = 35/42 (83.33%), Postives = 37/42 (88.10%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT+LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 84  VTSLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 124

[Close]

BLAST of CmaCh04G019670 vs. TrEMBL
Match: A0A0K0N7Y1_9LILI (Photosystem II protein D2 OS=Dioscorea nipponica GN=psbD PE=3 SV=1)

HSP 1 Score: 69.7 bits (169), Expect = 2.2e-09
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 151 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 191

[Close]

BLAST of CmaCh04G019670 vs. TrEMBL
Match: A0A0U2EYC8_9BRAS (Photosystem II D2 protein OS=Capsella rubella GN=psbD PE=3 SV=1)

HSP 1 Score: 69.7 bits (169), Expect = 2.2e-09
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

[Close]

BLAST of CmaCh04G019670 vs. TrEMBL
Match: A0A144YUE4_9SOLA (Photosystem II D2 protein OS=Iochroma lehmannii GN=psbD PE=3 SV=1)

HSP 1 Score: 69.7 bits (169), Expect = 2.2e-09
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

[Close]

BLAST of CmaCh04G019670 vs. TAIR10
Match: ATCG00270.1 (ATCG00270.1 photosystem II reaction center protein D)

HSP 1 Score: 69.7 bits (169), Expect = 1.1e-12
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

[Close]

BLAST of CmaCh04G019670 vs. NCBI nr
Match: gi|521675253|gb|AGQ03792.1| (photosystem II protein D2 (chloroplast) [Osmunda vachellii])

HSP 1 Score: 70.5 bits (171), Expect = 1.9e-09
Identity = 35/42 (83.33%), Postives = 37/42 (88.10%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SA+GVVGLALNLR YDF SQEIRA  EDPEFETLYT
Sbjct: 277 VTGLWMSAIGVVGLALNLRAYDFVSQEIRA-AEDPEFETLYT 317

[Close]

BLAST of CmaCh04G019670 vs. NCBI nr
Match: gi|763793838|gb|KJB60834.1| (hypothetical protein B456_009G327700, partial [Gossypium raimondii])

HSP 1 Score: 70.1 bits (170), Expect = 2.4e-09
Identity = 35/42 (83.33%), Postives = 37/42 (88.10%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT+LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 84  VTSLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 124

[Close]

BLAST of CmaCh04G019670 vs. NCBI nr
Match: gi|984912465|gb|AMC31669.1| (photosystem II protein D2 (chloroplast) [Vicia americana var. minor])

HSP 1 Score: 69.7 bits (169), Expect = 3.2e-09
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

[Close]

BLAST of CmaCh04G019670 vs. NCBI nr
Match: gi|553832083|gb|AGY61452.1| (photosystem II D2 protein (plastid) [Lotharella oceanica])

HSP 1 Score: 69.7 bits (169), Expect = 3.2e-09
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 276 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 316

[Close]

BLAST of CmaCh04G019670 vs. NCBI nr
Match: gi|408899226|gb|AFU94447.1| (PsbD, partial (chloroplast) [Garcinia mangostana])

HSP 1 Score: 69.7 bits (169), Expect = 3.2e-09
Identity = 35/42 (83.33%), Postives = 36/42 (85.71%), Query Frame = 1


Query: 33  VTALWLSALGVVGLALNLRVYDFGSQEIRAVGEDPEFETLYT 75
           VT LW+SALGVVGLALNLR YDF SQEIRA  EDPEFET YT
Sbjct: 277 VTGLWMSALGVVGLALNLRAYDFVSQEIRA-AEDPEFETFYT 317

The following BLAST results are available for this feature:

BLAST of CmaCh04G019670 vs. Swiss-Prot


Match Name	E-value	Identity	Description
PSBD_AETGR	2.0e-11	83.33	Photosystem II D2 protein OS=Aethionema grandiflorum GN=psbD PE=3 SV=1	[more]
PSBD_ARATH	2.0e-11	83.33	Photosystem II D2 protein OS=Arabidopsis thaliana GN=psbD PE=1 SV=3	[more]
PSBD_ATRBE	2.0e-11	83.33	Photosystem II D2 protein OS=Atropa belladonna GN=psbD PE=3 SV=1	[more]
PSBD_BARVE	2.0e-11	83.33	Photosystem II D2 protein OS=Barbarea verna GN=psbD PE=3 SV=1	[more]
PSBD_BIGNA	2.0e-11	83.33	Photosystem II D2 protein OS=Bigelowiella natans GN=psbD PE=3 SV=1	[more]

BLAST of CmaCh04G019670 vs. TrEMBL


Match Name	E-value	Identity	Description
S5CK09_9MONI	1.3e-09	83.33	Photosystem II D2 protein OS=Osmunda vachellii GN=psbD PE=3 SV=1	[more]
A0A0D2TVP7_GOSRA	1.7e-09	83.33	Uncharacterized protein (Fragment) OS=Gossypium raimondii GN=B456_009G327700 PE=...	[more]
A0A0K0N7Y1_9LILI	2.2e-09	83.33	Photosystem II protein D2 OS=Dioscorea nipponica GN=psbD PE=3 SV=1	[more]
A0A0U2EYC8_9BRAS	2.2e-09	83.33	Photosystem II D2 protein OS=Capsella rubella GN=psbD PE=3 SV=1	[more]
A0A144YUE4_9SOLA	2.2e-09	83.33	Photosystem II D2 protein OS=Iochroma lehmannii GN=psbD PE=3 SV=1	[more]

BLAST of CmaCh04G019670 vs. TAIR10


Match Name	E-value	Identity	Description
ATCG00270.1	1.1e-12	83.33	ATCG00270.1 photosystem II reaction center protein D	[more]

BLAST of CmaCh04G019670 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|521675253\|gb\|AGQ03792.1\|	1.9e-09	83.33	photosystem II protein D2 (chloroplast) [Osmunda vachellii]	[more]
gi\|763793838\|gb\|KJB60834.1\|	2.4e-09	83.33	hypothetical protein B456_009G327700, partial [Gossypium raimondii]	[more]
gi\|984912465\|gb\|AMC31669.1\|	3.2e-09	83.33	photosystem II protein D2 (chloroplast) [Vicia americana var. minor]	[more]
gi\|553832083\|gb\|AGY61452.1\|	3.2e-09	83.33	photosystem II D2 protein (plastid) [Lotharella oceanica]	[more]
gi\|408899226\|gb\|AFU94447.1\|	3.2e-09	83.33	PsbD, partial (chloroplast) [Garcinia mangostana]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR000484	Photo_RC_L/M

Vocabulary: **Biological Process**
Term	Definition
GO:0019684	photosynthesis, light reaction
GO:0009772	photosynthetic electron transport in photosystem II

Vocabulary: **Molecular Function**
Term	Definition
GO:0045156	electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0009772	photosynthetic electron transport in photosystem II
biological_process	GO:0018298	protein-chromophore linkage
biological_process	GO:0019684	photosynthesis, light reaction
cellular_component	GO:0009535	chloroplast thylakoid membrane
cellular_component	GO:0016021	integral component of membrane
cellular_component	GO:0009523	photosystem II
cellular_component	GO:0044425	membrane part
cellular_component	GO:0009536	plastid
molecular_function	GO:0016168	chlorophyll binding
molecular_function	GO:0045156	electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
molecular_function	GO:0005506	iron ion binding
molecular_function	GO:0016491	oxidoreductase activity

Relationships

The following mRNA feature(s) are a part of this gene:


Feature Name	Unique Name	Type
CmaCh04G019670.1	CmaCh04G019670.1	mRNA

InterPro

Analysis Name: InterPro Annotations of Cucurbita maxima
Date Performed: 2017-05-20


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR000484	Photosynthetic reaction centre, L/M	GENE3D	G3DSA:1.20.85.10		coord: 15..64 score: 6.
IPR000484	Photosynthetic reaction centre, L/M	unknown	SSF81483	Bacterial photosystem II reaction centre, L and M subunits	coord: 15..77 score: 8.1
None	No IPR available	PANTHER	PTHR33149	FAMILY NOT NAMED	coord: 33..74 score: 3.0
None	No IPR available	PANTHER	PTHR33149:SF2	SUBFAMILY NOT NAMED	coord: 33..74 score: 3.0

Synteny

The following gene(s) are orthologous to this gene:

None

The following gene(s) are paralogous to this gene:


Gene	Paralogue	Organism	Block
CmaCh04G019670	CmaCh00G001270	Cucurbita maxima (Rimu)	cmacmaB018

The following block(s) are covering this gene:


Gene	Organism	Block
CmaCh04G019670	Watermelon (97103) v2	cmawmbB726
CmaCh04G019670	Cucurbita moschata (Rifu)	cmacmoB679
CmaCh04G019670	Cucurbita moschata (Rifu)	cmacmoB728
CmaCh04G019670	Watermelon (Charleston Gray)	cmawcgB622
CmaCh04G019670	Watermelon (97103) v1	cmawmB739
CmaCh04G019670	Bottle gourd (USVL1VR-Ls)	cmalsiB635
CmaCh04G019670	Cucumber (Gy14) v2	cgybcmaB670
CmaCh04G019670	Melon (DHL92) v3.6.1	cmamedB737