Psyllid ID: psy2693

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120--
Protein Sequence
MEILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINNIDSSLAATEHWMMKI
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHccccccEEEcccccccEEEEccccEEEccccccEEccccccEEcccccccccccccEEEEccccccccEEEEccccHHHHHHccHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cHHHHHccccHHHHHHHHHHHHHHccccccEEEEccccccEEEEEccccEcccccccEEcccccccccccccccEcEEEEEEEEcccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
meilakfqiIPVATQARKLLAICnanptdehtidydehnpfqicarsytpiyhgreseacvycgasylpkykgelCAVCTVSVIDTHRNAYGLQICAGLMKSDVINNIDSSLAATEHWMMKI
Flexible Loop (DISEMBL)
meilakfqiiPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINNIDSslaatehwmmki
Low Complexity Region (SEG)
MEILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINNIDSSLAATEHWMMKI
Disordered region (IsUnstruct)
**ILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINNIDSSLAAT*******
Disordered Region (DISOPRED)
MEI************************TDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLM**********SLAATEHWMMKI
Disordered Region (DISEMBL)
MEILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINNIDSSLAATEHWMMKI
Disordered Region (DISPRO)
MEILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINNIDSSLAATEHWMMKI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICAGLMKSDVINNIDSSLAATEHWMMKI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	122	2.2.26 [Sep-21-2011]
Q27954	1224	Coatomer subunit alpha OS	yes	N/A	0.672	0.066	0.5	1e-18
P53621	1224	Coatomer subunit alpha OS	yes	N/A	0.672	0.066	0.5	1e-18
Q8CIE6	1224	Coatomer subunit alpha OS	yes	N/A	0.672	0.066	0.5	6e-18
Q55FR9	1221	Coatomer subunit alpha OS	yes	N/A	0.672	0.067	0.453	2e-15
Q94A40	1216	Coatomer subunit alpha-1	yes	N/A	0.606	0.060	0.402	1e-13
Q9SJT9	1218	Coatomer subunit alpha-2	no	N/A	0.647	0.064	0.419	2e-13
Q9AUR7	1218	Coatomer subunit alpha-2	no	N/A	0.663	0.066	0.352	1e-11
Q9AUR8	1218	Coatomer subunit alpha-1	no	N/A	0.639	0.064	0.358	1e-11
Q0J3D9	1218	Coatomer subunit alpha-3	no	N/A	0.639	0.064	0.358	4e-11
Q96WV5	1207	Putative coatomer subunit	yes	N/A	0.606	0.061	0.378	6e-10

>sp|Q27954|COPA_BOVIN Coatomer subunit alpha OS=Bos taurus GN=COPA PE=1 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/84 (50%), Positives = 56/84 (66%), Gaps = 2/84 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct: 1137 VAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1196

Query: 72   KGELCAVCTVSVIDTHRNAYGLQI 95
            KG++C V TV+ I   ++  GL+I
Sbjct: 1197 KGQICKVTTVTEIG--KDVIGLRI 1218

Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor.
Bos taurus (taxid: 9913)

>sp|P53621|COPA_HUMAN Coatomer subunit alpha OS=Homo sapiens GN=COPA PE=1 SV=2

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 42/84 (50%), Positives = 56/84 (66%), Gaps = 2/84 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct: 1137 VAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1196

Query: 72   KGELCAVCTVSVIDTHRNAYGLQI 95
            KG++C V TV+ I   ++  GL+I
Sbjct: 1197 KGQICRVTTVTEIG--KDVIGLRI 1218

Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor.

Homo sapiens (taxid: 9606)

>sp|Q8CIE6|COPA_MOUSE Coatomer subunit alpha OS=Mus musculus GN=Copa PE=1 SV=2

 Score = 89.4 bits (220), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 42/84 (50%), Positives = 55/84 (65%), Gaps = 2/84 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA Q RK+L+ C  NPTD   ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct: 1137 VAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1196

Query: 72   KGELCAVCTVSVIDTHRNAYGLQI 95
            KG++C V TV+ I   ++  GL+I
Sbjct: 1197 KGQICRVTTVTEIG--KDVIGLRI 1218

Xenin stimulates exocrine pancreatic secretion. It inhibits pentagastrin-stimulated secretion of acid, to induce exocrine pancreatic secretion and to affect small and large intestinal motility. In the gut, xenin interacts with the neurotensin receptor.

Mus musculus (taxid: 10090)

>sp|Q55FR9|COPA_DICDI Coatomer subunit alpha OS=Dictyostelium discoideum GN=copa PE=3 SV=1

 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/86 (45%), Positives = 53/86 (61%), Gaps = 4/86 (4%)

Query: 12   VATQARKLLAICNANPT--DEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLP 69
            +ATQA+K+       PT  D   ++YDE NPF ICA SY PIY G     C YC + YLP
Sbjct: 1133 LATQAKKVFNFAQQTPTPSDIQQLNYDERNPFVICAHSYVPIYKGSPLIKCPYCSSCYLP 1192

Query: 70   KYKGELCAVCTVSVIDTHRNAYGLQI 95
             +KG++C+VC +S I   ++  GLQ+
Sbjct: 1193 THKGKVCSVCQISEIG--KDVQGLQV 1216

The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.

Dictyostelium discoideum (taxid: 44689)

>sp|Q94A40|COPA1_ARATH Coatomer subunit alpha-1 OS=Arabidopsis thaliana GN=At1g62020 PE=1 SV=2

 Score = 75.1 bits (183), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 31/77 (40%), Positives = 48/77 (62%), Gaps = 3/77 (3%)

Query: 11   PVATQA---RKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASY 67
            PV +QA   R+++     N TDE  ++YD  NPF +C  +Y PIY G++  +C YC A +
Sbjct: 1125 PVDSQAKMARQVVQAAERNMTDETKLNYDFRNPFVVCGSTYVPIYRGQKDVSCPYCTARF 1184

Query: 68   LPKYKGELCAVCTVSVI 84
            +P  +G +C VC ++VI
Sbjct: 1185 VPNQEGNICTVCDLAVI 1201

The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SJT9|COPA2_ARATH Coatomer subunit alpha-2 OS=Arabidopsis thaliana GN=At2g21390 PE=2 SV=1

 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 50/81 (61%), Gaps = 2/81 (2%)

Query: 13   ATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYK 72
            A  AR+++     N TD  T++YD  NPF IC  +Y PIY G++  AC YC A ++P  +
Sbjct: 1132 ARTARQVMQAAERNMTDATTLNYDFRNPFVICGSTYVPIYKGQKDVACPYCTARFVPSQE 1191

Query: 73   GELCAVCTVSVIDTHRNAYGL 93
            G +C+VC ++VI    +A GL
Sbjct: 1192 GNICSVCDLAVIGA--DASGL 1210

The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9AUR7|COPA2_ORYSJ Coatomer subunit alpha-2 OS=Oryza sativa subsp. japonica GN=Os03g0711500 PE=2 SV=1

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/85 (35%), Positives = 53/85 (62%), Gaps = 4/85 (4%)

Query: 13   ATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYK 72
            A +AR++   C+    D   ++YD  NPF +C  +Y PIY G++  +C YCG+ ++P  +
Sbjct: 1133 ARRARQVQQQCSGK-KDSSELNYDYRNPFVVCGATYVPIYRGQKDVSCPYCGSRFVPSIE 1191

Query: 73   GELCAVCTVSVIDTHRNAYGLQICA 97
            G+LC +C ++V+    +A GL +C+
Sbjct: 1192 GQLCTICELAVVGA--DASGL-VCS 1213

The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9AUR8|COPA1_ORYSJ Coatomer subunit alpha-1 OS=Oryza sativa subsp. japonica GN=Os03g0711400 PE=2 SV=1

 Score = 68.6 bits (166), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 50/81 (61%), Gaps = 3/81 (3%)

Query: 13   ATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYK 72
            A +AR++   C+    D   ++YD  NPF +C  +Y PIY G++  +C YCG+ ++P  +
Sbjct: 1133 ARRARQVQQQCSGK-KDSSELNYDYRNPFVVCGATYVPIYRGQKDVSCPYCGSRFVPSIE 1191

Query: 73   GELCAVCTVSVIDTHRNAYGL 93
            G+LC +C ++V+    +A GL
Sbjct: 1192 GQLCTICELAVVGA--DASGL 1210

The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q0J3D9|COPA3_ORYSJ Coatomer subunit alpha-3 OS=Oryza sativa subsp. japonica GN=Os09g0127800 PE=2 SV=1

 Score = 67.0 bits (162), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 50/81 (61%), Gaps = 3/81 (3%)

Query: 13   ATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYK 72
            A +AR++   C+    D   ++YD  NPF +C  +Y PIY G++  +C YCG+ ++P  +
Sbjct: 1133 AKRARQVQQQCSGK-KDSCELNYDYRNPFVVCGATYVPIYRGQKDVSCPYCGSRFVPSIE 1191

Query: 73   GELCAVCTVSVIDTHRNAYGL 93
            G+LC +C ++V+    +A GL
Sbjct: 1192 GQLCTICELAVVGA--DASGL 1210

The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q96WV5|COPA_SCHPO Putative coatomer subunit alpha OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBPJ4664.04 PE=1 SV=1

 Score = 62.8 bits (151), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 40/74 (54%)

Query: 11   PVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPK 70
            P A  A + + + + NP D   I+YD H   +IC ++ TP+Y G + + C  CGA Y   
Sbjct: 1123 PAAEAANRAITLGDRNPHDAFEIEYDPHVEMRICPKTLTPVYSGDDFDVCSVCGAVYHKG 1182

Query: 71   YKGELCAVCTVSVI 84
            Y  E+C VC V  I
Sbjct: 1183 YVNEVCTVCDVGGI 1196

The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	122
91094941	1220	PREDICTED: similar to coatomer [Triboliu	0.672	0.067	0.547	2e-21
289629216	1230	coatomer protein complex subunit alpha [	0.680	0.067	0.552	5e-21
157108446	1223	coatomer [Aedes aegypti] gi|108868541|gb	0.721	0.071	0.544	5e-21
157134451	1227	coatomer [Aedes aegypti] gi|108870473|gb	0.721	0.071	0.544	5e-21
170050521	1227	coatomer subunit alpha [Culex quinquefas	0.721	0.071	0.544	6e-21
242002678	1018	coatomer, alpha chain, putative [Ixodes	0.672	0.080	0.5	2e-20
156380509	1224	predicted protein [Nematostella vectensi	0.672	0.066	0.511	4e-20
31236603	1231	AGAP010251-PA [Anopheles gambiae str. PE	0.721	0.071	0.511	3e-19
242015300	1222	coatomer alpha subunit, putative [Pedicu	0.688	0.068	0.523	4e-19
393905469	1237	proxenin [Loa loa]	0.680	0.067	0.494	7e-19

>gi|91094941|ref|XP_967472.1| PREDICTED: similar to coatomer [Tribolium castaneum] gi|270016760|gb|EFA13206.1| hypothetical protein TcasGA2_TC016033 [Tribolium castaneum]

 Score =  106 bits (264), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 46/84 (54%), Positives = 61/84 (72%), Gaps = 2/84 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA+Q RK+L +C +N TDE  + YDEHNPF +C  SYTPIY G+  E C +CG SYLPKY
Sbjct: 1133 VASQTRKILQVCESNLTDELQLHYDEHNPFNLCGYSYTPIYRGKAEEKCSFCGTSYLPKY 1192

Query: 72   KGELCAVCTVSVIDTHRNAYGLQI 95
            KG +C +CTV+ I   +++ GL+I
Sbjct: 1193 KGAMCCICTVAEIG--KDSIGLRI 1214

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289629216|ref|NP_001166192.1| coatomer protein complex subunit alpha [Bombyx mori] gi|284027820|gb|ADB66734.1| coatomer protein complex subunit alpha [Bombyx mori]

 Score =  105 bits (261), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 47/85 (55%), Positives = 59/85 (69%), Gaps = 2/85 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA QARK+L  C   PTDEH + YDEHNPF IC  SY PIY G+  E C  C AS++P++
Sbjct: 1142 VAQQARKILQACEKTPTDEHQLLYDEHNPFSICGISYKPIYRGKPEEKCSLCAASFMPEH 1201

Query: 72   KGELCAVCTVSVIDTHRNAYGLQIC 96
            KG+LC VC V+ I   ++A GL+IC
Sbjct: 1202 KGKLCPVCGVAEIG--KDALGLRIC 1224

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157108446|ref|XP_001650231.1| coatomer [Aedes aegypti] gi|108868541|gb|EAT32766.1| AAEL015001-PA [Aedes aegypti]

 Score =  105 bits (261), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 49/90 (54%), Positives = 59/90 (65%), Gaps = 2/90 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA QARK+L  C  N TDEHT+ YDEHNPF +CA +Y PIY G+  E C  C ASYLP Y
Sbjct: 1136 VAQQARKILQACEMNETDEHTLQYDEHNPFTLCAVTYKPIYRGKPEEKCSLCSASYLPPY 1195

Query: 72   KGELCAVCTVSVIDTHRNAYGLQICAGLMK 101
            KG  CAVC V+  +  ++  GL+I A   K
Sbjct: 1196 KGVTCAVCRVA--EVGKDVIGLRISASQFK 1223

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157134451|ref|XP_001663309.1| coatomer [Aedes aegypti] gi|108870473|gb|EAT34698.1| AAEL013098-PA [Aedes aegypti]

 Score =  104 bits (260), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 49/90 (54%), Positives = 59/90 (65%), Gaps = 2/90 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA QARK+L  C  N TDEHT+ YDEHNPF +CA +Y PIY G+  E C  C ASYLP Y
Sbjct: 1140 VAQQARKILQACEMNETDEHTLQYDEHNPFTLCAVTYKPIYRGKPEEKCSLCSASYLPPY 1199

Query: 72   KGELCAVCTVSVIDTHRNAYGLQICAGLMK 101
            KG  CAVC V+  +  ++  GL+I A   K
Sbjct: 1200 KGVTCAVCRVA--EVGKDVIGLRISASQFK 1227

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170050521|ref|XP_001861349.1| coatomer subunit alpha [Culex quinquefasciatus] gi|167872144|gb|EDS35527.1| coatomer subunit alpha [Culex quinquefasciatus]

 Score =  104 bits (260), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 49/90 (54%), Positives = 59/90 (65%), Gaps = 2/90 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA QARK+L  C  N +DEHT+ YDEHNPF +CA SY PIY G+  E C  C ASYLP Y
Sbjct: 1140 VAQQARKILQACEMNESDEHTLQYDEHNPFTLCAVSYRPIYRGKPEEKCSLCSASYLPPY 1199

Query: 72   KGELCAVCTVSVIDTHRNAYGLQICAGLMK 101
            KG  CAVC V+ +   ++  GL+I A   K
Sbjct: 1200 KGVTCAVCRVAEVG--KDVIGLRISASQFK 1227

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242002678|ref|XP_002435982.1| coatomer, alpha chain, putative [Ixodes scapularis] gi|215499318|gb|EEC08812.1| coatomer, alpha chain, putative [Ixodes scapularis]

 Score =  102 bits (255), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 42/84 (50%), Positives = 57/84 (67%), Gaps = 2/84 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA Q RK+L  C+  PTD+H + YDEHNPF +CA+SY PIY G+    C  C ASYLP++
Sbjct: 931  VAAQTRKILQACDKTPTDQHDLRYDEHNPFALCAKSYVPIYRGKPEVKCPLCSASYLPEF 990

Query: 72   KGELCAVCTVSVIDTHRNAYGLQI 95
            KG +C VC  S+ +  ++  GL+I
Sbjct: 991  KGSVCTVC--SIAEVGKDTIGLRI 1012

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156380509|ref|XP_001631811.1| predicted protein [Nematostella vectensis] gi|156218857|gb|EDO39748.1| predicted protein [Nematostella vectensis]

 Score =  101 bits (252), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 43/84 (51%), Positives = 56/84 (66%), Gaps = 2/84 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VATQ RK+L  C+ NPTD H + YDEHNPF IC  SY P+Y G+  E C +C  SY P +
Sbjct: 1137 VATQTRKILQACDKNPTDSHQLKYDEHNPFSICGASYQPLYRGKPQEKCAFCQTSYCPDF 1196

Query: 72   KGELCAVCTVSVIDTHRNAYGLQI 95
            KG LC VC +S  +  +++ GL+I
Sbjct: 1197 KGTLCQVCEIS--EVGKDSIGLRI 1218

Source: Nematostella vectensis

Species: Nematostella vectensis

Genus: Nematostella

Family: Edwardsiidae

Order: Actiniaria

Class: Anthozoa

Phylum: Cnidaria

Superkingdom: Eukaryota

>gi|31236603|ref|XP_319442.1| AGAP010251-PA [Anopheles gambiae str. PEST] gi|21302213|gb|EAA14358.1| AGAP010251-PA [Anopheles gambiae str. PEST]

 Score = 99.4 bits (246), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 46/90 (51%), Positives = 57/90 (63%), Gaps = 2/90 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA QARK+L  C  N +DEHT+ YDEHNPF +CA +Y PIY G+  E C  C ASY P Y
Sbjct: 1144 VAQQARKILQACEMNESDEHTLHYDEHNPFTLCAVTYKPIYRGKPEEKCSLCSASYQPPY 1203

Query: 72   KGELCAVCTVSVIDTHRNAYGLQICAGLMK 101
            KG  C VC V+ +   ++  GL+I A   K
Sbjct: 1204 KGVTCVVCKVAEVG--KDVIGLRISASQFK 1231

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242015300|ref|XP_002428302.1| coatomer alpha subunit, putative [Pediculus humanus corporis] gi|212512887|gb|EEB15564.1| coatomer alpha subunit, putative [Pediculus humanus corporis]

 Score = 99.0 bits (245), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 45/86 (52%), Positives = 57/86 (66%), Gaps = 2/86 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VATQARK+L  C+ N  DEH + YDEHNPF +CAR+Y PIY G+    C  C ASY P++
Sbjct: 1134 VATQARKILQACDKNLVDEHELVYDEHNPFSLCARTYKPIYRGKPEITCPLCEASYFPQF 1193

Query: 72   KGELCAVCTVSVIDTHRNAYGLQICA 97
            KG +C VC VS I   +   GL+I +
Sbjct: 1194 KGSICNVCAVSEIG--KETIGLRISS 1217

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|393905469|gb|EJD73980.1| proxenin [Loa loa]

 Score = 97.8 bits (242), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 42/85 (49%), Positives = 56/85 (65%), Gaps = 2/85 (2%)

Query: 12   VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
            VA Q RK+LA+    P D H ++YDEHNPF IC+R + P+Y G+    C +CGASY P  
Sbjct: 1149 VAAQIRKVLAVVEKEPNDTHELEYDEHNPFVICSRKFKPLYRGKPQVKCPFCGASYSPDI 1208

Query: 72   KGELCAVCTVSVIDTHRNAYGLQIC 96
             GE+C VC V+  +  R+A GL+IC
Sbjct: 1209 TGEICDVCQVA--EVGRDAIGLKIC 1231

Source: Loa loa

Species: Loa loa

Genus: Loa

Family: Onchocercidae

Order: Spirurida

Class: Chromadorea

Phylum: Nematoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	122
ZFIN|ZDB-GENE-020905-2	1226	copa "coatomer protein complex	0.672	0.066	0.523	4.1e-18
UNIPROTKB|F1PU93	1214	COPA "Coatomer subunit alpha"	0.672	0.067	0.511	8.5e-18
RGD|1310525	568	Copa "coatomer protein complex	0.672	0.144	0.5	1.8e-17
UNIPROTKB|Q27954	1224	COPA "Coatomer subunit alpha"	0.672	0.066	0.5	1.8e-17
UNIPROTKB|P53621	1224	COPA "Coatomer subunit alpha"	0.672	0.066	0.5	1.8e-17
UNIPROTKB|F1RJX8	1224	COPA "Uncharacterized protein"	0.672	0.066	0.5	1.8e-17
UNIPROTKB|H9L3L2	1134	LOC100859596 "Uncharacterized	0.672	0.072	0.488	3.4e-17
UNIPROTKB|H9KZL3	1169	LOC100859596 "Uncharacterized	0.672	0.070	0.488	3.5e-17
MGI|MGI:1334462	1224	Copa "coatomer protein complex	0.672	0.066	0.5	6.1e-17
UNIPROTKB|G3V6T1	1224	Copa "Protein Copa" [Rattus no	0.672	0.066	0.5	6.1e-17

ZFIN|ZDB-GENE-020905-2 copa "coatomer protein complex, subunit alpha" [Danio rerio (taxid:7955)]

 Score = 233 (87.1 bits), Expect = 4.1e-18, P = 4.1e-18
 Identities = 44/84 (52%), Positives = 55/84 (65%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+LA C  + TD H ++YD HNPF ICA SYTP+Y GR  E C   GA Y PKY
Sbjct:  1139 VAQQTRKILAACEKSLTDAHQLNYDPHNPFDICAASYTPLYRGRPVEKCPLSGACYCPKY 1198

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             KGE+C V  V+ I   ++  GL++
Sbjct:  1199 KGEVCRVTQVTEIG--KDVIGLRV 1220

GO:0030117 "membrane coat" evidence=IEA

GO:0005198 "structural molecule activity" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0030126 "COPI vesicle coat" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0030903 "notochord development" evidence=IMP

UNIPROTKB|F1PU93 COPA "Coatomer subunit alpha" [Canis lupus familiaris (taxid:9615)]

 Score = 230 (86.0 bits), Expect = 8.5e-18, P = 8.5e-18
 Identities = 43/84 (51%), Positives = 56/84 (66%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:  1127 VAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1186

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             KG++C V TV+ I   R+  GL+I
Sbjct:  1187 KGQICKVTTVTEIG--RDVIGLRI 1208

GO:0030126 "COPI vesicle coat" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0005198 "structural molecule activity" evidence=IEA

RGD|1310525 Copa "coatomer protein complex subunit alpha" [Rattus norvegicus (taxid:10116)]

 Score = 222 (83.2 bits), Expect = 1.8e-17, P = 1.8e-17
 Identities = 42/84 (50%), Positives = 55/84 (65%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD   ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:   481 VAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 540

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             KG++C V TV+ I   ++  GL+I
Sbjct:   541 KGQICRVTTVTEIG--KDVIGLRI 562

GO:0005615 "extracellular space" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0030126 "COPI vesicle coat" evidence=ISO

GO:0030157 "pancreatic juice secretion" evidence=ISO

UNIPROTKB|Q27954 COPA "Coatomer subunit alpha" [Bos taurus (taxid:9913)]

 Score = 227 (85.0 bits), Expect = 1.8e-17, P = 1.8e-17
 Identities = 42/84 (50%), Positives = 56/84 (66%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:  1137 VAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1196

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             KG++C V TV+ I   ++  GL+I
Sbjct:  1197 KGQICKVTTVTEIG--KDVIGLRI 1218

GO:0005515 "protein binding" evidence=IPI

GO:0006890 "retrograde vesicle-mediated transport, Golgi to ER" evidence=TAS

GO:0030126 "COPI vesicle coat" evidence=IDA

GO:0006891 "intra-Golgi vesicle-mediated transport" evidence=TAS

GO:0030157 "pancreatic juice secretion" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005179 "hormone activity" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0005198 "structural molecule activity" evidence=IEA

UNIPROTKB|P53621 COPA "Coatomer subunit alpha" [Homo sapiens (taxid:9606)]

 Score = 227 (85.0 bits), Expect = 1.8e-17, P = 1.8e-17
 Identities = 42/84 (50%), Positives = 56/84 (66%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:  1137 VAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1196

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             KG++C V TV+ I   ++  GL+I
Sbjct:  1197 KGQICRVTTVTEIG--KDVIGLRI 1218

GO:0005198 "structural molecule activity" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0005179 "hormone activity" evidence=IEA

GO:0030126 "COPI vesicle coat" evidence=ISS;IDA

GO:0005615 "extracellular space" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0030157 "pancreatic juice secretion" evidence=IDA

GO:0005829 "cytosol" evidence=TAS

GO:0006890 "retrograde vesicle-mediated transport, Golgi to ER" evidence=TAS

GO:0016044 "cellular membrane organization" evidence=TAS

GO:0048205 "COPI coating of Golgi vesicle" evidence=TAS

UNIPROTKB|F1RJX8 COPA "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 227 (85.0 bits), Expect = 1.8e-17, P = 1.8e-17
 Identities = 42/84 (50%), Positives = 56/84 (66%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:  1137 VAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1196

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             KG++C V TV+ I   ++  GL+I
Sbjct:  1197 KGQICRVTTVTEIG--KDVIGLRI 1218

GO:0030157 "pancreatic juice secretion" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0030126 "COPI vesicle coat" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0005198 "structural molecule activity" evidence=IEA

UNIPROTKB|H9L3L2 LOC100859596 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 224 (83.9 bits), Expect = 3.4e-17, P = 3.4e-17
 Identities = 41/84 (48%), Positives = 56/84 (66%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:  1047 VAQQTRKILSACEKNPTDTYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYCPEF 1106

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             +G++C V TV+ I   ++  GL+I
Sbjct:  1107 QGQICRVTTVTEIG--KDVIGLRI 1128

GO:0005198 "structural molecule activity" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0030126 "COPI vesicle coat" evidence=IEA

UNIPROTKB|H9KZL3 LOC100859596 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 224 (83.9 bits), Expect = 3.5e-17, P = 3.5e-17
 Identities = 41/84 (48%), Positives = 56/84 (66%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:  1082 VAQQTRKILSACEKNPTDTYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYCPEF 1141

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             +G++C V TV+ I   ++  GL+I
Sbjct:  1142 QGQICRVTTVTEIG--KDVIGLRI 1163

GO:0005198 "structural molecule activity" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0030126 "COPI vesicle coat" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0030157 "pancreatic juice secretion" evidence=IEA

MGI|MGI:1334462 Copa "coatomer protein complex subunit alpha" [Mus musculus (taxid:10090)]

 Score = 222 (83.2 bits), Expect = 6.1e-17, P = 6.1e-17
 Identities = 42/84 (50%), Positives = 55/84 (65%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD   ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:  1137 VAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1196

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             KG++C V TV+ I   ++  GL+I
Sbjct:  1197 KGQICRVTTVTEIG--KDVIGLRI 1218

GO:0005179 "hormone activity" evidence=IEA

GO:0005198 "structural molecule activity" evidence=IEA

GO:0005576 "extracellular region" evidence=IEA

GO:0005615 "extracellular space" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0030117 "membrane coat" evidence=IEA

GO:0030126 "COPI vesicle coat" evidence=ISO

GO:0030157 "pancreatic juice secretion" evidence=ISO

GO:0031410 "cytoplasmic vesicle" evidence=IEA

UNIPROTKB|G3V6T1 Copa "Protein Copa" [Rattus norvegicus (taxid:10116)]

 Score = 222 (83.2 bits), Expect = 6.1e-17, P = 6.1e-17
 Identities = 42/84 (50%), Positives = 55/84 (65%)

Query:    12 VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
             VA Q RK+L+ C  NPTD   ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct:  1137 VAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 1196

Query:    72 KGELCAVCTVSVIDTHRNAYGLQI 95
             KG++C V TV+ I   ++  GL+I
Sbjct:  1197 KGQICRVTTVTEIG--KDVIGLRI 1218

GO:0005198 "structural molecule activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0016192 "vesicle-mediated transport" evidence=IEA

GO:0030126 "COPI vesicle coat" evidence=IEA

GO:0030157 "pancreatic juice secretion" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	122
pfam06957	421	pfam06957, COPI_C, Coatomer (COPI) alpha subunit C	5e-32

>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus

 Score =  116 bits (291), Expect = 5e-32
 Identities = 44/84 (52%), Positives = 56/84 (66%), Gaps = 2/84 (2%)

Query: 12  VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
           VA QARK+L  C  NPTD H ++YDEHNPF +C  SY PIY G+    C YCGAS+ P +
Sbjct: 334 VAQQARKVLQACEKNPTDAHQLNYDEHNPFVVCGASYVPIYRGKPDVKCPYCGASFSPGF 393

Query: 72  KGELCAVCTVSVIDTHRNAYGLQI 95
           +G LC VC V+ I   ++  GL+I
Sbjct: 394 EGNLCTVCEVAEIG--KDVIGLRI 415

This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport. Note that many family members also contain the pfam04053 domain. Length = 421

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	122
PF06957	422	COPI_C: Coatomer (COPI) alpha subunit C-terminus;	100.0
KOG0292|consensus	1202		99.97
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	92.65
cd00350	33	rubredoxin_like Rubredoxin_like; nonheme iron bind	92.6
PRK12496	164	hypothetical protein; Provisional	92.2
PF05191	36	ADK_lid: Adenylate kinase, active site lid; InterP	91.61
PF10276	40	zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Z	91.35
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	90.26
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	90.0
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	88.81
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	87.31
cd00729	34	rubredoxin_SM Rubredoxin, Small Modular nonheme ir	87.25
PRK05452	479	anaerobic nitric oxide reductase flavorubredoxin;	86.5
PF13248	26	zf-ribbon_3: zinc-ribbon domain	86.18
PF00301	47	Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubred	86.12
TIGR02300	129	FYDLN_acid conserved hypothetical protein TIGR0230	85.08
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	84.84
PRK00420	112	hypothetical protein; Validated	80.61

>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=100.00  E-value=2.1e-43  Score=302.70  Aligned_cols=98  Identities=54%  Similarity=0.981  Sum_probs=72.3

Q ss_pred             cccccCCChHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCCCcccCcccc
Q psy2693           2 EILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTV   81 (122)
Q Consensus         2 ~lLel~p~~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~l   81 (122)
                      +|||++|++++++||||||++|||+|||+|+||||+||||+||++||||||+|+++|+||||||+|+|+|||+||+||+|
T Consensus       325 RLLel~p~~~~a~qArKil~~~e~~~tDa~~i~yD~~npF~ICa~s~tPIY~G~~~v~CP~cgA~y~~~~kG~lC~vC~l  404 (422)
T PF06957_consen  325 RLLELNPSPEVAEQARKILQACERNPTDAHEIDYDERNPFDICAASYTPIYRGSPSVKCPYCGAKYHPEYKGQLCPVCEL  404 (422)
T ss_dssp             HHHCT--SCHHHHHHHHHHHHHCCS--BSS--S--TTS-EEEBTTT--EEETTS-EEE-TTT--EEEGGGTTSB-TTTTT
T ss_pred             HHHHcCCCHHHHHHHHHHHHHHhcCCCCceecCCCCCCCceeeecccccccCCCCCeeCCCCCCccChhhCCCCCCCCcc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCCcccCcceecccch
Q psy2693          82 SVIDTHRNAYGLQICAGLMK  101 (122)
Q Consensus        82 s~IG~~~~a~GLr~~~~~~~  101 (122)
                      ++||  ++++|||++++|+|
T Consensus       405 ~~IG--~~a~GLris~~q~r  422 (422)
T PF06957_consen  405 SEIG--ADASGLRISPSQFR  422 (422)
T ss_dssp             BBTT-----S----SGGG--
T ss_pred             eeeC--CcceeeEecccccC
Confidence            9999  99999999999998

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.

>KOG0292|consensus

Probab=99.97  E-value=3.3e-33  Score=256.73  Aligned_cols=95  Identities=47%  Similarity=0.905  Sum_probs=93.0

Q ss_pred             CcccccCCChHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCCCcccCccc
Q psy2693           1 MEILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCT   80 (122)
Q Consensus         1 ~~lLel~p~~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~   80 (122)
                      |+||++.|++++|+|||||+++||+||+|+++|+||+||||+||++||+|||+|+|.++||||||+|+|.++|++|.||+
T Consensus      1108 ~rLlel~~~~~~A~q~rki~~a~eknp~Da~~l~yd~~n~f~iC~~t~~Piy~g~p~~~cp~cga~y~~~~~g~iCtvc~ 1187 (1202)
T KOG0292|consen 1108 RRLLELAPSPPVAEQARKIKQAAEKNPTDAYELNYDPHNPFVICGATYVPIYRGRPDVSCPYCGACFVPSSKGNICTVCD 1187 (1202)
T ss_pred             HHHHhhCCCChHHHHHHHHHHHhhcCcccccccCcccCCCeeEecccceeeecCCCCcCCCcccceeccccCCceeeeee
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceeecCCCcccCcceec
Q psy2693          81 VSVIDTHRNAYGLQICA   97 (122)
Q Consensus        81 ls~IG~~~~a~GLr~~~   97 (122)
                      |++||  ++++||||++
T Consensus      1188 V~~ig--~~~~Glris~ 1202 (1202)
T KOG0292|consen 1188 VGVIG--ADASGLRISA 1202 (1202)
T ss_pred             eeeec--CcccceeecC
Confidence            99999  9999999964

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=92.65  E-value=0.076  Score=35.98  Aligned_cols=20  Identities=20%  Similarity=0.629  Sum_probs=15.8

Q ss_pred             ceeccCCCcceecCCCCceec
Q psy2693          48 YTPIYHGRESEACVYCGASYL   68 (122)
Q Consensus        48 ~tPIY~G~~~v~CP~CgA~Y~   68 (122)
                      |-+| .-+.+|.|||||.+|.
T Consensus        40 ~L~m-g~~gev~CPYC~t~y~   59 (62)
T COG4391          40 FLDM-GDEGEVVCPYCSTRYR   59 (62)
T ss_pred             EEEc-CCCCcEecCccccEEE
Confidence            4444 4588999999999985

>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center

Probab=92.60  E-value=0.1  Score=30.27  Aligned_cols=26  Identities=27%  Similarity=0.523  Sum_probs=21.9

Q ss_pred             eecCCCCceecCCCCCcccCccccee
Q psy2693          58 EACVYCGASYLPKYKGELCAVCTVSV   83 (122)
Q Consensus        58 v~CP~CgA~Y~p~~kG~lC~VC~ls~   83 (122)
                      -.|+.||-.|.++.....|++|+..+
T Consensus         2 ~~C~~CGy~y~~~~~~~~CP~Cg~~~   27 (33)
T cd00350           2 YVCPVCGYIYDGEEAPWVCPVCGAPK   27 (33)
T ss_pred             EECCCCCCEECCCcCCCcCcCCCCcH
Confidence            36999999999988899999998653

The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PRK12496 hypothetical protein; Provisional

Probab=92.20  E-value=0.091  Score=40.31  Aligned_cols=35  Identities=23%  Similarity=0.660  Sum_probs=26.1

Q ss_pred             ccceecc-CCCcc-----eecCCCCceecCCCCCcccCccc
Q psy2693          46 RSYTPIY-HGRES-----EACVYCGASYLPKYKGELCAVCT   80 (122)
Q Consensus        46 ~S~tPIY-~G~~~-----v~CP~CgA~Y~p~~kG~lC~VC~   80 (122)
                      ..+.+|. +|-..     ..|+-||..|.-.+.+..|++|+
T Consensus       110 i~v~~~~~~~i~~~~~w~~~C~gC~~~~~~~~~~~~C~~CG  150 (164)
T PRK12496        110 IKFENIKTKGIKKVIKWRKVCKGCKKKYPEDYPDDVCEICG  150 (164)
T ss_pred             CeEeccccccchhheeeeEECCCCCccccCCCCCCcCCCCC
Confidence            3445543 45444     35999999998888899999998

>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2

Probab=91.61  E-value=0.13  Score=30.91  Aligned_cols=23  Identities=26%  Similarity=0.713  Sum_probs=19.4

Q ss_pred             ecCCCCceecCCCC----CcccCcccc
Q psy2693          59 ACVYCGASYLPKYK----GELCAVCTV   81 (122)
Q Consensus        59 ~CP~CgA~Y~p~~k----G~lC~VC~l   81 (122)
                      .||-||+.|+-.|+    ..+|.+|+-
T Consensus         3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~   29 (36)
T PF05191_consen    3 ICPKCGRIYHIEFNPPKVEGVCDNCGG   29 (36)
T ss_dssp             EETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred             CcCCCCCccccccCCCCCCCccCCCCC
Confidence            69999999998776    488988874

7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....

>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=91.35  E-value=0.14  Score=31.64  Aligned_cols=21  Identities=29%  Similarity=0.757  Sum_probs=14.0

Q ss_pred             ceeccCCCcceecCCCCceec
Q psy2693          48 YTPIYHGRESEACVYCGASYL   68 (122)
Q Consensus        48 ~tPIY~G~~~v~CP~CgA~Y~   68 (122)
                      |=+|-+....+.|||||..|.
T Consensus        20 yl~l~~~~~~~~CpYCg~~yv   40 (40)
T PF10276_consen   20 YLNLDDEPGPVVCPYCGTRYV   40 (40)
T ss_dssp             EEE-TTTTCEEEETTTTEEEE
T ss_pred             EEecCCCCCeEECCCCCCEEC
Confidence            334433345799999999984

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=90.26  E-value=0.13  Score=28.05  Aligned_cols=20  Identities=30%  Similarity=0.780  Sum_probs=16.6

Q ss_pred             ecCCCCceecCCCCCcccCccc
Q psy2693          59 ACVYCGASYLPKYKGELCAVCT   80 (122)
Q Consensus        59 ~CP~CgA~Y~p~~kG~lC~VC~   80 (122)
                      .||.||+...+.  .+.|+.|+
T Consensus         1 ~Cp~CG~~~~~~--~~fC~~CG   20 (23)
T PF13240_consen    1 YCPNCGAEIEDD--AKFCPNCG   20 (23)
T ss_pred             CCcccCCCCCCc--CcchhhhC
Confidence            489999999876  78898886

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=90.00  E-value=0.17  Score=33.28  Aligned_cols=28  Identities=25%  Similarity=0.711  Sum_probs=21.5

Q ss_pred             eeeecccceeccCCCcceecCCCCceecCCC
Q psy2693          41 FQICARSYTPIYHGRESEACVYCGASYLPKY   71 (122)
Q Consensus        41 F~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~   71 (122)
                      =.+|...|+|   |.+.|.||-|||.||-+-
T Consensus         8 C~~Cg~~~~~---~dDiVvCp~CgapyHR~C   35 (54)
T PF14446_consen    8 CPVCGKKFKD---GDDIVVCPECGAPYHRDC   35 (54)
T ss_pred             ChhhCCcccC---CCCEEECCCCCCcccHHH
Confidence            3456665554   789999999999999763

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.81  E-value=0.21  Score=30.17  Aligned_cols=23  Identities=30%  Similarity=0.866  Sum_probs=15.3

Q ss_pred             ecCCCCceec--CCCCCc-ccCcccc
Q psy2693          59 ACVYCGASYL--PKYKGE-LCAVCTV   81 (122)
Q Consensus        59 ~CP~CgA~Y~--p~~kG~-lC~VC~l   81 (122)
                      +||.||+++.  ....|+ +|+.|+.
T Consensus         2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~   27 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPERGELVCPNCGL   27 (43)
T ss_dssp             SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred             CCcCCcCCceEEcCCCCeEECCCCCC
Confidence            6999999762  233454 8999863

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=87.31  E-value=0.55  Score=28.63  Aligned_cols=12  Identities=42%  Similarity=0.955  Sum_probs=7.3

Q ss_pred             ceecCCCCceec
Q psy2693          57 SEACVYCGASYL   68 (122)
Q Consensus        57 ~v~CP~CgA~Y~   68 (122)
                      ..+||+||+...
T Consensus        21 ~~~Cp~CG~~~~   32 (46)
T PRK00398         21 GVRCPYCGYRIL   32 (46)
T ss_pred             ceECCCCCCeEE
Confidence            566666666554

>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase

Probab=87.25  E-value=0.5  Score=27.77  Aligned_cols=25  Identities=24%  Similarity=0.477  Sum_probs=16.6

Q ss_pred             eecCCCCceecCCCCCcccCcccce
Q psy2693          58 EACVYCGASYLPKYKGELCAVCTVS   82 (122)
Q Consensus        58 v~CP~CgA~Y~p~~kG~lC~VC~ls   82 (122)
                      -.|+.||-.|.-+..-..|++|+..
T Consensus         3 ~~C~~CG~i~~g~~~p~~CP~Cg~~   27 (34)
T cd00729           3 WVCPVCGYIHEGEEAPEKCPICGAP   27 (34)
T ss_pred             EECCCCCCEeECCcCCCcCcCCCCc
Confidence            4677777777655555677777653

In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.

>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional

Probab=86.50  E-value=2  Score=37.72  Aligned_cols=73  Identities=15%  Similarity=0.138  Sum_probs=42.7

Q ss_pred             cCCChHHHHH----HHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCC---------
Q psy2693           6 KFQIIPVATQ----ARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYK---------   72 (122)
Q Consensus         6 l~p~~~va~q----ArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~k---------   72 (122)
                      ..|..+..++    +|++.++-.+.|-++...+=+-..+-..    .+| -......+|+.||-.|.|+.-         
T Consensus       375 ~~P~ee~~~~~~~~g~~la~~~~~~~~~~~~~~~~~~~~~~~----~~~-~~~~~~~~c~~c~~~yd~~~g~~~~~~~~g  449 (479)
T PRK05452        375 WRPDQDALELCREHGREIARQWALAPLPQSTVNTVVKEETSA----TTT-ADLGPRMQCSVCQWIYDPAKGEPMQDVAPG  449 (479)
T ss_pred             ecCCHHHHHHHHHHHHHHHHHHhhCCcccccccccccccccc----ccc-cCCCCeEEECCCCeEECCCCCCcccCCCCC
Confidence            4455444433    5666655545555544333331111111    444 256788899999999999841         


Q ss_pred             --------CcccCccccee
Q psy2693          73 --------GELCAVCTVSV   83 (122)
Q Consensus        73 --------G~lC~VC~ls~   83 (122)
                              .-.||+|+.++
T Consensus       450 t~~~~lp~~~~cp~c~~~k  468 (479)
T PRK05452        450 TPWSEVPDNFLCPECSLGK  468 (479)
T ss_pred             CChhhCCCCCcCcCCCCcH
Confidence                    13899998765

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=86.18  E-value=0.37  Score=26.63  Aligned_cols=22  Identities=32%  Similarity=0.786  Sum_probs=17.3

Q ss_pred             eecCCCCceecCCCCCcccCcccc
Q psy2693          58 EACVYCGASYLPKYKGELCAVCTV   81 (122)
Q Consensus        58 v~CP~CgA~Y~p~~kG~lC~VC~l   81 (122)
                      +.||.||+...++  -+.|+.|+-
T Consensus         3 ~~Cp~Cg~~~~~~--~~fC~~CG~   24 (26)
T PF13248_consen    3 MFCPNCGAEIDPD--AKFCPNCGA   24 (26)
T ss_pred             CCCcccCCcCCcc--cccChhhCC
Confidence            5799999976666  678888874

>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []

Probab=86.12  E-value=0.57  Score=29.69  Aligned_cols=26  Identities=31%  Similarity=0.667  Sum_probs=18.3

Q ss_pred             eecCCCCceecCCCCC-----------------cccCccccee
Q psy2693          58 EACVYCGASYLPKYKG-----------------ELCAVCTVSV   83 (122)
Q Consensus        58 v~CP~CgA~Y~p~~kG-----------------~lC~VC~ls~   83 (122)
                      .+|+.||-.|.|+.-.                 =.|++|+.++
T Consensus         2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~K   44 (47)
T PF00301_consen    2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAPK   44 (47)
T ss_dssp             EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSBG
T ss_pred             cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCcc
Confidence            4789999999988632                 1788888765

The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....

>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300

Probab=85.08  E-value=0.52  Score=35.93  Aligned_cols=33  Identities=21%  Similarity=0.449  Sum_probs=26.4

Q ss_pred             eeeecccceeccC-CCcceecCCCCceecCCCCC
Q psy2693          41 FQICARSYTPIYH-GRESEACVYCGASYLPKYKG   73 (122)
Q Consensus        41 F~ICa~S~tPIY~-G~~~v~CP~CgA~Y~p~~kG   73 (122)
                      ..+|..+=+.-|- ++..+.|||||+.|.+++..
T Consensus         9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~~   42 (129)
T TIGR02300         9 KRICPNTGSKFYDLNRRPAVSPYTGEQFPPEEAL   42 (129)
T ss_pred             cccCCCcCccccccCCCCccCCCcCCccCcchhh
Confidence            4577777777775 78899999999999998543

Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=84.84  E-value=0.51  Score=34.42  Aligned_cols=30  Identities=20%  Similarity=0.625  Sum_probs=22.1

Q ss_pred             eeeecccceeccC-CCcceecCCCCceecCC
Q psy2693          41 FQICARSYTPIYH-GRESEACVYCGASYLPK   70 (122)
Q Consensus        41 F~ICa~S~tPIY~-G~~~v~CP~CgA~Y~p~   70 (122)
                      -.+|..+=+.-|- ++..+.|||||+.|.++
T Consensus         9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~   39 (108)
T PF09538_consen    9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE   39 (108)
T ss_pred             cccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence            3456666666664 55668899999999998

The function of members of this family is unknown.

>PRK00420 hypothetical protein; Validated

Probab=80.61  E-value=0.96  Score=33.46  Aligned_cols=27  Identities=26%  Similarity=0.485  Sum_probs=16.5

Q ss_pred             eecCCCCceecC-CCCCcccCcccceee
Q psy2693          58 EACVYCGASYLP-KYKGELCAVCTVSVI   84 (122)
Q Consensus        58 v~CP~CgA~Y~p-~~kG~lC~VC~ls~I   84 (122)
                      ..||.||+...- +---..|++|+-..+
T Consensus        24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~   51 (112)
T PRK00420         24 KHCPVCGLPLFELKDGEVVCPVHGKVYI   51 (112)
T ss_pred             CCCCCCCCcceecCCCceECCCCCCeee
Confidence            467777776665 333346777776544

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	122
3mkr_B	320	Crystal Structure Of Yeast AlphaEPSILON-Cop Subcomp		7e-20
3mv3_A	325	Crystal Structure Of A-Cop In Complex With E-Cop Le		5e-06
3mv2_A	325	Crystal Structure Of A-Cop In Complex With E-Cop Le		6e-06

>pdb|3MKR|B Chain B, Crystal Structure Of Yeast AlphaEPSILON-Cop Subcomplex Of The Copi Vesicular Coat Length = 320

Iteration: 1
 Score = 92.0 bits (227), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 42/84 (50%), Positives = 56/84 (66%), Gaps = 2/84 (2%)
Query: 12  VATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKY 71
           VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C   GA Y P++
Sbjct: 233 VAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEF 292
Query: 72  KGELCAVCTVSVIDTHRNAYGLQI 95
           KG++C V TV+ I   ++  GL+I
Sbjct: 293 KGQICKVTTVTEIG--KDVIGLRI 314

>pdb|3MV3|A Chain A, Crystal Structure Of A-Cop In Complex With E-Cop Length = 325

Iteration: 1
 Score = 46.2 bits (108), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 11  PVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPK 70
           P A QARK+    ++  +D   ID+D +  F ICA +Y PIY    S +    G+ Y+  
Sbjct: 241 PRAEQARKIKNKADSXASDAIPIDFDPYAKFDICAATYKPIYEDTPSVSDPLTGSKYVIT 300
Query: 71  YKGELCAVCTVSVIDTHRNAYGLQI 95
            K ++  +  +S I     A GL+I
Sbjct: 301 EKDKIDRIAXISKIGAP--ASGLRI 323

>pdb|3MV2|A Chain A, Crystal Structure Of A-Cop In Complex With E-Cop Length = 325

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 11  PVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPK 70
           P A QARK+    ++  +D   ID+D +  F ICA +Y PIY    S +    G+ Y+  
Sbjct: 241 PRAEQARKIKNKADSMASDAIPIDFDPYAKFDICAATYKPIYEDTPSVSDPLTGSKYVIT 300
Query: 71  YKGELCAVCTVSVIDTHRNAYGLQI 95
            K ++  +  +S I     A GL+I
Sbjct: 301 EKDKIDRIAMISKIGAP--ASGLRI 323

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	122
3mv2_A	325	Coatomer subunit alpha; vesicular membrane coat CO	5e-31
3mkr_B	320	Coatomer subunit alpha; tetratricopeptide repeats	4e-30

>3mv2_A Coatomer subunit alpha; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_A Length = 325

 Score =  111 bits (278), Expect = 5e-31
 Identities = 30/94 (31%), Positives = 45/94 (47%), Gaps = 2/94 (2%)

Query: 2   EILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACV 61
           E L      P A QARK+    ++  +D   ID+D +  F ICA +Y PIY    S +  
Sbjct: 232 EFLKIISSGPRAEQARKIKNKADSMASDAIPIDFDPYAKFDICAATYKPIYEDTPSVSDP 291

Query: 62  YCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQI 95
             G+ Y+   K ++  +  +S I     A GL+I
Sbjct: 292 LTGSKYVITEKDKIDRIAMISKIG--APASGLRI 323

>3mkr_B Coatomer subunit alpha; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus} Length = 320

 Score =  108 bits (272), Expect = 4e-30
 Identities = 43/96 (44%), Positives = 58/96 (60%), Gaps = 2/96 (2%)

Query: 2   EILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACV 61
            +L       VA Q RK+L+ C  NPTD + ++YD HNPF ICA SY PIY G+  E C 
Sbjct: 223 RLLELGPKPEVAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCP 282

Query: 62  YCGASYLPKYKGELCAVCTVSVIDTHRNAYGLQICA 97
             GA Y P++KG++C V TV+ I   ++  GL+I  
Sbjct: 283 LSGACYSPEFKGQICKVTTVTEIG--KDVIGLRISP 316

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	122
3mkr_B	320	Coatomer subunit alpha; tetratricopeptide repeats	100.0
3mv2_A	325	Coatomer subunit alpha; vesicular membrane coat CO	100.0
6rxn_A	46	Rubredoxin; electron transfer(iron-sulfur protein)	88.99
3pwf_A	170	Rubrerythrin; non heme iron peroxidases, oxidative	87.55
1yk4_A	52	Rubredoxin, RD; electron transport; 0.69A {Pyrococ	85.65
2v3b_B	55	Rubredoxin 2, rubredoxin; alkane degradation, iron	85.58
4rxn_A	54	Rubredoxin; electron transfer(iron-sulfur protein)	84.87
1dx8_A	70	Rubredoxin; electron transport, zinc-substitution;	83.93
2jvm_A	80	Uncharacterized protein; alpha+beta, structural ge	83.16
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	82.66
2kn9_A	81	Rubredoxin; metalloprotein, ssgcid, structural gen	80.98
2jrr_A	67	Uncharacterized protein; solution structure, SIR90	80.72
1yuz_A	202	Nigerythrin; rubrythrin, rubredoxin, hemerythrin,	80.42
2lcq_A	165	Putative toxin VAPC6; PIN domain, Zn ribbon domain	80.31

>3mkr_B Coatomer subunit alpha; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=100.00  E-value=5.7e-43  Score=290.34  Aligned_cols=98  Identities=44%  Similarity=0.821  Sum_probs=96.3

Q ss_pred             cccccCCChHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCCCcccCcccc
Q psy2693           2 EILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTV   81 (122)
Q Consensus         2 ~lLel~p~~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~l   81 (122)
                      +|||++|++++++|||||+++|||+|+|+|+||||++|||+||++||||||+|+++|+||||||+|+|+|||++|+||+|
T Consensus       223 rLLel~p~~~~~~qArkil~~ce~~~~da~eidyD~~~~f~iCa~s~tPIY~g~~~v~Cp~cgA~y~~~~kG~lC~vC~l  302 (320)
T 3mkr_B          223 RLLELGPKPEVAQQTRKILSACEKNPTDAYQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEFKGQICKVTTV  302 (320)
T ss_dssp             HHHHTCCCHHHHHHHHHHHHHHHHSCCBSSCCSCCTTSCCCBBTTTCCBCCTTSCCEECTTTCCEECGGGTTSBCTTTSS
T ss_pred             HHHhcCCCHHHHHHHHHHHHHHhcCCCCccccCCCCCCccceecCCCccccCCCCCccCCCCCCeechhhCCCCCCCCcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCCcccCcceecccch
Q psy2693          82 SVIDTHRNAYGLQICAGLMK  101 (122)
Q Consensus        82 s~IG~~~~a~GLr~~~~~~~  101 (122)
                      ++||  ++++|||++..|+|
T Consensus       303 ~~IG--~~~~GL~~~~~~~~  320 (320)
T 3mkr_B          303 TEIG--KDVIGLRISPLQFR  320 (320)
T ss_dssp             BBSS--CCCCCCCCSGGGCC
T ss_pred             cccC--CcccCccccccccC
Confidence            9999  99999999988886

>3mv2_A Coatomer subunit alpha; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_A

Probab=100.00  E-value=1.7e-41  Score=282.16  Aligned_cols=93  Identities=32%  Similarity=0.467  Sum_probs=91.6

Q ss_pred             cccccCCChHHHHHHHHHHHHHhcCCCCceeecCCCCCCeeeecccceeccCCCcceecCCCCceecCCCCCcccCcccc
Q psy2693           2 EILAKFQIIPVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRESEACVYCGASYLPKYKGELCAVCTV   81 (122)
Q Consensus         2 ~lLel~p~~~va~qArKIl~~ce~~~tDa~eIdYD~~npF~ICa~S~tPIY~G~~~v~CP~CgA~Y~p~~kG~lC~VC~l   81 (122)
                      +||+++|++++++|||||+++|||+|+|+++||||++|||+||++||||||+|+++|+||||||+|+|+|||++|+||+|
T Consensus       232 rLLel~p~~~~a~qArkil~~ce~~~~Da~eidyD~~~~F~iCa~s~tPIY~g~~~v~Cp~cgA~y~~~~kG~lC~vC~l  311 (325)
T 3mv2_A          232 EFLKIISSGPRAEQARKIKNKADSMASDAIPIDFDPYAKFDICAATYKPIYEDTPSVSDPLTGSKYVITEKDKIDRIAMI  311 (325)
T ss_dssp             HHHTTCCSSHHHHHHHHHHHHHHTSCCCSSCCSCCTTSCEEECTTTCCEEESSSCEEECTTTCCEEEGGGTTSBCSSSSC
T ss_pred             HHHhcCCCHHHHHHHHHHHHHHhcCCCCccccCCCCCCCceeecCCcccccCCCCCccCCCCCCeechhhCCCCCCCCcC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCCcccCccee
Q psy2693          82 SVIDTHRNAYGLQIC   96 (122)
Q Consensus        82 s~IG~~~~a~GLr~~   96 (122)
                      ++||  ++++|||++
T Consensus       312 ~~IG--~~a~GL~~~  324 (325)
T 3mv2_A          312 SKIG--APASGLRIR  324 (325)
T ss_dssp             BBTT--CCCCCCCCB
T ss_pred             cccC--CCccceeee
Confidence            9999  999999986

>6rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.50A {Desulfovibrio desulfuricans} SCOP: g.41.5.1

Probab=88.99  E-value=0.17  Score=31.05  Aligned_cols=27  Identities=37%  Similarity=0.673  Sum_probs=19.3

Q ss_pred             ceecCCCCceecCCCCC----------cccCccccee
Q psy2693          57 SEACVYCGASYLPKYKG----------ELCAVCTVSV   83 (122)
Q Consensus        57 ~v~CP~CgA~Y~p~~kG----------~lC~VC~ls~   83 (122)
                      ..+|+.||-.|.|+.-.          -.|++|+..+
T Consensus         4 ~y~C~vCGyvyd~~~Gd~t~f~~lP~dw~CP~Cg~~k   40 (46)
T 6rxn_A            4 KYVCNVCGYEYDPAEHDNVPFDQLPDDWCCPVCGVSK   40 (46)
T ss_dssp             CEEETTTCCEECGGGGTTCCGGGSCTTCBCTTTCCBG
T ss_pred             EEECCCCCeEEeCCcCCCcchhhCCCCCcCcCCCCcH
Confidence            35899999999875311          1799998754

>3pwf_A Rubrerythrin; non heme iron peroxidases, oxidative stress, oxidoreductase; 1.64A {Pyrococcus furiosus} PDB: 3mps_A 3pza_A 3qvd_A 1nnq_A 2hr5_A

Probab=87.55  E-value=0.39  Score=35.83  Aligned_cols=27  Identities=26%  Similarity=0.662  Sum_probs=20.0

Q ss_pred             CcceecCCCCceecCCCCCcccCcccce
Q psy2693          55 RESEACVYCGASYLPKYKGELCAVCTVS   82 (122)
Q Consensus        55 ~~~v~CP~CgA~Y~p~~kG~lC~VC~ls   82 (122)
                      .....|+.||-.|.++ .-..||+|+..
T Consensus       136 ~~~~~C~~CG~i~~~~-~p~~CP~Cg~~  162 (170)
T 3pwf_A          136 KKVYICPICGYTAVDE-APEYCPVCGAP  162 (170)
T ss_dssp             SCEEECTTTCCEEESC-CCSBCTTTCCB
T ss_pred             CCeeEeCCCCCeeCCC-CCCCCCCCCCC
Confidence            4556799999999865 34489999854

>1yk4_A Rubredoxin, RD; electron transport; 0.69A {Pyrococcus abyssi} PDB: 2pya_A 1yk5_A 1bq8_A 1bq9_A* 3kyu_A 3kyv_A 3kyw_A 3kyx_A 3kyy_A 3ryg_A 3rz6_A 3rzt_A 3ss2_A 1brf_A 1caa_A 1cad_A 1vcx_A 1zrp_A 1iu5_A 1iu6_A ...

Probab=85.65  E-value=0.48  Score=29.50  Aligned_cols=13  Identities=31%  Similarity=0.649  Sum_probs=10.6

Q ss_pred             eecCCCCceecCC
Q psy2693          58 EACVYCGASYLPK   70 (122)
Q Consensus        58 v~CP~CgA~Y~p~   70 (122)
                      .+|+.||-.|.|+
T Consensus         3 ~~C~~CGyvYd~~   15 (52)
T 1yk4_A            3 LSCKICGYIYDED   15 (52)
T ss_dssp             EEESSSSCEEETT
T ss_pred             EEeCCCCeEECCC
Confidence            5788899888875

>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur protein, oxidoreductase, ELE transfer, electron transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas aeruginosa}

Probab=85.58  E-value=0.5  Score=29.75  Aligned_cols=27  Identities=30%  Similarity=0.566  Sum_probs=19.1

Q ss_pred             ceecCCCCceecCCC---------------CCc--ccCccccee
Q psy2693          57 SEACVYCGASYLPKY---------------KGE--LCAVCTVSV   83 (122)
Q Consensus        57 ~v~CP~CgA~Y~p~~---------------kG~--lC~VC~ls~   83 (122)
                      ..+|+.||-.|.|+.               --.  .|++|+..+
T Consensus         3 ~y~C~~CGyvYd~~~Gdp~~gi~pGt~f~~lP~dw~CP~Cga~K   46 (55)
T 2v3b_B            3 KWQCVVCGFIYDEALGLPEEGIPAGTRWEDIPADWVCPDCGVGK   46 (55)
T ss_dssp             EEEETTTCCEEETTTCBTTTTBCTTCCGGGSCTTCCCTTTCCCG
T ss_pred             cEEeCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCCCCCCCH
Confidence            357899999998764               112  788888754

>4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A 1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A 1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A 1smw_A 1be7_A 1t9o_A ...

Probab=84.87  E-value=0.54  Score=29.71  Aligned_cols=26  Identities=31%  Similarity=0.703  Sum_probs=19.3

Q ss_pred             eecCCCCceecCCCC-----------------CcccCccccee
Q psy2693          58 EACVYCGASYLPKYK-----------------GELCAVCTVSV   83 (122)
Q Consensus        58 v~CP~CgA~Y~p~~k-----------------G~lC~VC~ls~   83 (122)
                      .+|+.||-.|.|+.-                 .-+|++|+..+
T Consensus         4 y~C~vCGyvYd~~~Gdp~~gi~pGt~fe~lP~dw~CP~Cg~~K   46 (54)
T 4rxn_A            4 YTCTVCGYIYDPEDGDPDDGVNPGTDFKDIPDDWVCPLCGVGK   46 (54)
T ss_dssp             EEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCBG
T ss_pred             eECCCCCeEECCCcCCcccCcCCCCChhHCCCCCcCcCCCCcH
Confidence            579999999988641                 12799998765

>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A

Probab=83.93  E-value=0.63  Score=30.62  Aligned_cols=28  Identities=25%  Similarity=0.649  Sum_probs=20.4

Q ss_pred             cceecCCCCceecCCC---------------CCc--ccCccccee
Q psy2693          56 ESEACVYCGASYLPKY---------------KGE--LCAVCTVSV   83 (122)
Q Consensus        56 ~~v~CP~CgA~Y~p~~---------------kG~--lC~VC~ls~   83 (122)
                      ...+|+.||-.|.|+-               --.  .|++|+..+
T Consensus         6 ~~y~C~vCGyiYd~~~Gdp~~gi~pGT~f~~lPddw~CP~Cga~K   50 (70)
T 1dx8_A            6 GKYECEACGYIYEPEKGDKFAGIPPGTPFVDLSDSFMCPACRSPK   50 (70)
T ss_dssp             SCEEETTTCCEECTTTCCTTTTCCSSCCGGGSCTTCBCTTTCCBG
T ss_pred             ceEEeCCCCEEEcCCCCCcccCcCCCCchhhCCCCCcCCCCCCCH
Confidence            3568999999998764               112  799998754

>2jvm_A Uncharacterized protein; alpha+beta, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Rhodobacter sphaeroides 2}

Probab=83.16  E-value=0.63  Score=31.83  Aligned_cols=16  Identities=25%  Similarity=0.621  Sum_probs=13.1

Q ss_pred             CCcceecCCCCceecC
Q psy2693          54 GRESEACVYCGASYLP   69 (122)
Q Consensus        54 G~~~v~CP~CgA~Y~p   69 (122)
                      ....+.|||||..|.-
T Consensus        50 ~~g~~~CpYCg~~f~l   65 (80)
T 2jvm_A           50 ETGFVECGYCDRRYIH   65 (80)
T ss_dssp             TTCEEECSSSSCEEEE
T ss_pred             CCCeEECCCCCCEEEe
Confidence            3568999999999963

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=82.66  E-value=0.36  Score=30.38  Aligned_cols=14  Identities=29%  Similarity=0.733  Sum_probs=11.2

Q ss_pred             CcceecCCCCceec
Q psy2693          55 RESEACVYCGASYL   68 (122)
Q Consensus        55 ~~~v~CP~CgA~Y~   68 (122)
                      -|.++|||||-+..
T Consensus        21 lP~IrCpyCGyrii   34 (48)
T 4ayb_P           21 LPGVRCPYCGYKII   34 (48)
T ss_dssp             CSSSCCTTTCCSCE
T ss_pred             CCCcccCccCcEEE
Confidence            48899999997643

>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle structural genomics center for infectious electron transport, iron; NMR {Mycobacterium tuberculosis}

Probab=80.98  E-value=0.91  Score=30.90  Aligned_cols=29  Identities=21%  Similarity=0.403  Sum_probs=21.7

Q ss_pred             CcceecCCCCceecCCC---------------C--CcccCccccee
Q psy2693          55 RESEACVYCGASYLPKY---------------K--GELCAVCTVSV   83 (122)
Q Consensus        55 ~~~v~CP~CgA~Y~p~~---------------k--G~lC~VC~ls~   83 (122)
                      ....+|+.||-.|.|+.               -  .-.|++|+..+
T Consensus        25 m~~y~C~vCGyvYD~~~Gdp~~gI~pGT~fedlPddW~CPvCga~K   70 (81)
T 2kn9_A           25 YKLFRCIQCGFEYDEALGWPEDGIAAGTRWDDIPDDWSCPDCGAAK   70 (81)
T ss_dssp             CCEEEETTTCCEEETTTCBTTTTBCTTCCTTTSCTTCCCTTTCCCG
T ss_pred             cceEEeCCCCEEEcCCcCCcccCcCCCCChhHCCCCCcCCCCCCCH
Confidence            34689999999999854               1  22799998754

>2jrr_A Uncharacterized protein; solution structure, SIR90, structural genomics, PSI-2, protein structure initiative; NMR {Silicibacter pomeroyi}

Probab=80.72  E-value=0.75  Score=30.39  Aligned_cols=16  Identities=31%  Similarity=0.708  Sum_probs=13.7

Q ss_pred             CcceecCCCCceecCC
Q psy2693          55 RESEACVYCGASYLPK   70 (122)
Q Consensus        55 ~~~v~CP~CgA~Y~p~   70 (122)
                      ...+.|||||..|.-+
T Consensus        38 ~g~~~CpYCg~~f~l~   53 (67)
T 2jrr_A           38 TGWVECPYCDCKYVLK   53 (67)
T ss_dssp             TSEEEETTTTEEEEET
T ss_pred             CCeEECCCCCCEEEEC
Confidence            5789999999999755

>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIR center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_A

Probab=80.42  E-value=1.2  Score=33.97  Aligned_cols=26  Identities=23%  Similarity=0.405  Sum_probs=17.5

Q ss_pred             cceecCCCCceecCCCCCcccCcccce
Q psy2693          56 ESEACVYCGASYLPKYKGELCAVCTVS   82 (122)
Q Consensus        56 ~~v~CP~CgA~Y~p~~kG~lC~VC~ls   82 (122)
                      ....|+.||-.|.. -.-..||+|+..
T Consensus       170 ~~~~C~~CG~i~~g-~~p~~CP~C~~~  195 (202)
T 1yuz_A          170 KFHLCPICGYIHKG-EDFEKCPICFRP  195 (202)
T ss_dssp             CEEECSSSCCEEES-SCCSBCTTTCCB
T ss_pred             cEEEECCCCCEEcC-cCCCCCCCCCCC
Confidence            45678888888765 223578888754

>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}

Probab=80.31  E-value=0.84  Score=32.85  Aligned_cols=25  Identities=24%  Similarity=0.648  Sum_probs=21.4

Q ss_pred             ceecCCCCceecCCCCCcccCcccc
Q psy2693          57 SEACVYCGASYLPKYKGELCAVCTV   81 (122)
Q Consensus        57 ~v~CP~CgA~Y~p~~kG~lC~VC~l   81 (122)
                      ..+|+-||..|.....+..|+.|+-
T Consensus       132 ~y~C~~Cg~~~~~~~~~~~Cp~CG~  156 (165)
T 2lcq_A          132 RYVCIGCGRKFSTLPPGGVCPDCGS  156 (165)
T ss_dssp             CEEESSSCCEESSCCGGGBCTTTCC
T ss_pred             EEECCCCCCcccCCCCCCcCCCCCC
Confidence            5789999999987766789999984

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	122
d1akya2	38	Microbial and mitochondrial ADK, insert "zinc fing	89.96
d2ak3a2	37	Microbial and mitochondrial ADK, insert "zinc fing	87.22
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	84.76
d1e4va2	35	Microbial and mitochondrial ADK, insert "zinc fing	83.99
d1s3ga2	35	Microbial and mitochondrial ADK, insert "zinc fing	83.36
d1zina2	35	Microbial and mitochondrial ADK, insert "zinc fing	82.02
d2dsxa1	52	Rubredoxin {Desulfovibrio gigas [TaxId: 879]}	81.82
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	80.36

>d1akya2 g.41.2.1 (A:131-168) Microbial and mitochondrial ADK, insert "zinc finger" domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.96  E-value=0.085  Score=29.96  Aligned_cols=23  Identities=17%  Similarity=0.043  Sum_probs=16.7

Q ss_pred             eecCCCCceecCCCC----CcccCccc
Q psy2693          58 EACVYCGASYLPKYK----GELCAVCT   80 (122)
Q Consensus        58 v~CP~CgA~Y~p~~k----G~lC~VC~   80 (122)
                      -.||-||+.|+-.|+    ..+|.+|+
T Consensus         3 r~C~~cG~~Yh~~~~ppk~~g~CD~cg   29 (38)
T d1akya2           3 LIHPASGRSYHKIFNPPKEDMKDDVTG   29 (38)
T ss_dssp             EECTTTCCEEETTTBCCSSTTBCTTTC
T ss_pred             cCCcCccchhhhhccCcCcCCccCCCC
Confidence            369999999984443    34788776

>d2ak3a2 g.41.2.1 (A:125-161) Microbial and mitochondrial ADK, insert "zinc finger" domain {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=87.22  E-value=0.13  Score=29.06  Aligned_cols=23  Identities=9%  Similarity=-0.035  Sum_probs=18.0

Q ss_pred             eecCCCCceecCCCC----CcccCccc
Q psy2693          58 EACVYCGASYLPKYK----GELCAVCT   80 (122)
Q Consensus        58 v~CP~CgA~Y~p~~k----G~lC~VC~   80 (122)
                      -.||-||+.|+-.|+    ..+|.+|+
T Consensus         3 ~vc~~cG~~Yh~~~~pPk~~g~CD~cg   29 (37)
T d2ak3a2           3 WIHPGSGRVYNIEFNPPKTMGIDDLTG   29 (37)
T ss_dssp             EEETTTTEEEETTTBCCSSTTBCTTTC
T ss_pred             eeeCCcCChhhhccCCccccCCccCCC
Confidence            369999999986654    56788887

>d1yuza2 g.41.5.1 (A:167-202) Nigerythrin, C-terminal domain {Desulfovibrio vulgaris [TaxId: 881]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Nigerythrin, C-terminal domain
species: Desulfovibrio vulgaris [TaxId: 881]

Probab=84.76  E-value=0.13  Score=29.04  Aligned_cols=23  Identities=26%  Similarity=0.519  Sum_probs=11.1

Q ss_pred             ceecCCCCceecCCCCCcccCccc
Q psy2693          57 SEACVYCGASYLPKYKGELCAVCT   80 (122)
Q Consensus        57 ~v~CP~CgA~Y~p~~kG~lC~VC~   80 (122)
                      .-.|+.||-.+.-+ .-..|+||+
T Consensus         5 ~~vC~vCGyi~~g~-~Pe~CPvCg   27 (36)
T d1yuza2           5 FHLCPICGYIHKGE-DFEKCPICF   27 (36)
T ss_dssp             EEECSSSCCEEESS-CCSBCTTTC
T ss_pred             EEECCCCCCEeeCC-CCCcCCCCC
Confidence            34455555555432 334455554

>d1e4va2 g.41.2.1 (A:122-156) Microbial and mitochondrial ADK, insert "zinc finger" domain {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Escherichia coli [TaxId: 562]

Probab=83.99  E-value=0.27  Score=27.25  Aligned_cols=23  Identities=17%  Similarity=0.065  Sum_probs=17.6

Q ss_pred             ecCCCCceecCCC----CCcccCcccc
Q psy2693          59 ACVYCGASYLPKY----KGELCAVCTV   81 (122)
Q Consensus        59 ~CP~CgA~Y~p~~----kG~lC~VC~l   81 (122)
                      .||-||+.|+-.|    +..+|.+|+-
T Consensus         4 ~c~~cG~~Yh~~~~PPk~~g~CD~cg~   30 (35)
T d1e4va2           4 VHAPSGRVYHVKFNPPKVEGKDDVTGE   30 (35)
T ss_dssp             EETTTTEEEETTTBCCSSTTBCTTTCC
T ss_pred             CCcCcCChhhhccCccccCCcccCCCC
Confidence            6999999998555    4567888864

>d1s3ga2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus globisporus [TaxId: 1459]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus globisporus [TaxId: 1459]

Probab=83.36  E-value=0.31  Score=27.01  Aligned_cols=23  Identities=26%  Similarity=0.499  Sum_probs=17.7

Q ss_pred             ecCCCCceecCCCC----CcccCcccc
Q psy2693          59 ACVYCGASYLPKYK----GELCAVCTV   81 (122)
Q Consensus        59 ~CP~CgA~Y~p~~k----G~lC~VC~l   81 (122)
                      .||-||+.|+-.|+    ..+|.+|+=
T Consensus         4 ~C~~CG~~Yh~~~~pPk~~g~CD~cg~   30 (35)
T d1s3ga2           4 ICKVCGTSYHLLFNPPQVEGKCDKDGG   30 (35)
T ss_dssp             EETTTCCEEETTTBCCSBTTBCTTTCC
T ss_pred             CCcCcCchhccccCCCCCCCccCCCCC
Confidence            69999999985554    567888863

>d1zina2 g.41.2.1 (A:126-160) Microbial and mitochondrial ADK, insert "zinc finger" domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain
family: Microbial and mitochondrial ADK, insert "zinc finger" domain
domain: Microbial and mitochondrial ADK, insert "zinc finger" domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=82.02  E-value=0.4  Score=26.54  Aligned_cols=24  Identities=33%  Similarity=0.771  Sum_probs=18.1

Q ss_pred             eecCCCCceecCCC----CCcccCcccc
Q psy2693          58 EACVYCGASYLPKY----KGELCAVCTV   81 (122)
Q Consensus        58 v~CP~CgA~Y~p~~----kG~lC~VC~l   81 (122)
                      -.||-||+.|+-.|    +..+|.+|+=
T Consensus         3 r~C~~CG~~Yh~~~~pPk~~g~CD~cG~   30 (35)
T d1zina2           3 RICRNCGATYHLIFHPPAKPGVCDKCGG   30 (35)
T ss_dssp             EEETTTCCEEETTTBCCSSTTBCTTTCC
T ss_pred             cCCcCcCchhccccCCCCCCCcCCCCCC
Confidence            36999999998554    4568888873

>d2dsxa1 g.41.5.1 (A:1-52) Rubredoxin {Desulfovibrio gigas [TaxId: 879]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubredoxin
species: Desulfovibrio gigas [TaxId: 879]

Probab=81.82  E-value=0.42  Score=28.61  Aligned_cols=26  Identities=35%  Similarity=0.694  Sum_probs=18.3

Q ss_pred             eecCCCCceecCCC-----------------CCcccCccccee
Q psy2693          58 EACVYCGASYLPKY-----------------KGELCAVCTVSV   83 (122)
Q Consensus        58 v~CP~CgA~Y~p~~-----------------kG~lC~VC~ls~   83 (122)
                      .+|+.||-.|.|+.                 ..=.|++|+.++
T Consensus         4 y~C~~CgyiYdp~~Gd~~~gi~pGT~F~~LP~~w~CP~C~a~K   46 (52)
T d2dsxa1           4 YVCTVCGYEYDPAKGDPDSGIKPGTKFEDLPDDWACPVCGASK   46 (52)
T ss_dssp             EEETTTCCEECTTTCBGGGTBCTTCCGGGSCTTCBCTTTCCBG
T ss_pred             EEeCCCCeEECcccCCcccCCCCCCCHHHCCCCCCCcCCCCcH
Confidence            47888888887775                 233788887654

>d1nnqa2 g.41.5.1 (A:135-171) Rubrerythrin, C-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Rubredoxin-like
family: Rubredoxin
domain: Rubrerythrin, C-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=80.36  E-value=0.63  Score=26.05  Aligned_cols=25  Identities=28%  Similarity=0.663  Sum_probs=15.3

Q ss_pred             ceecCCCCceecCCCCCcccCcccce
Q psy2693          57 SEACVYCGASYLPKYKGELCAVCTVS   82 (122)
Q Consensus        57 ~v~CP~CgA~Y~p~~kG~lC~VC~ls   82 (122)
                      .-.|+-||-.+.-+ .-..|+||+..
T Consensus         5 ~~~C~vCG~i~~g~-~P~~CPvCg~~   29 (37)
T d1nnqa2           5 VYICPICGYTAVDE-APEYCPVCGAP   29 (37)
T ss_dssp             EEECTTTCCEEESC-CCSBCTTTCCB
T ss_pred             EEECCCCCCEecCC-CCCcCCCCCCc
Confidence            34677777776643 44567777643