Psyllid ID: psy5308

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
MCLTEGMVTSMAQTNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNNGVKK
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHcccccccccccccccccccccccccccccccccEEEEEEccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEccccccccccccEEEEEccccEEEEEcccEEEEEEEcccccccccc
Coil and Loop (DISEMBL)
MCLTEGMVTSMAQTnadiipdlshltlEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHIclktkfadgvghmcnycnirccarcggkvtlrsnKVSVEVTtrghnnngvkk
Flexible Loop (DISEMBL)
MCLTEGMVTSMAQTNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKvtlrsnkvsvevttrghnnngvkk
Low Complexity Region (SEG)
MCLTEGMVTSMAQTNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNNGVKK
Disordered region (IsUnstruct)
*****************IIPDLSHLTL*************************************************VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV****************
Disordered Region (DISOPRED)
**********************SHLTLEERQIIESVM*********************************************CHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVT***********
Disordered Region (DISEMBL)
MCLTEGMVTSMAQTNADIIPDLSHLTLEERQIIESVM*********ELEIMRRKQDEVHLLEQSI************ELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNNGVKK
Disordered Region (DISPRO)
*********************LSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTR*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCLTEGMVTSMAQTNADIIPDLSHLTLEERQIIxxxxxxxxxxxxxxxxxxxxxQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNNNGVKK
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	137	2.2.26 [Sep-21-2011]
Q22366	1563	Rab-3-interacting molecul	yes	N/A	0.781	0.068	0.481	3e-25
Q9JIS1	1555	Regulating synaptic membr	yes	N/A	0.700	0.061	0.535	3e-23
Q9EQZ7	1530	Regulating synaptic membr	no	N/A	0.751	0.067	0.420	3e-19
Q9UQ26	1411	Regulating synaptic membr	no	N/A	0.751	0.072	0.441	2e-18
Q86UR5	1692	Regulating synaptic membr	no	N/A	0.737	0.059	0.450	9e-17
Q99NE5	1463	Regulating synaptic membr	no	N/A	0.737	0.069	0.383	3e-14
Q9JIR4	1615	Regulating synaptic membr	no	N/A	0.737	0.062	0.383	7e-14

>sp|Q22366|RIM_CAEEL Rab-3-interacting molecule unc-10 OS=Caenorhabditis elegans GN=unc-10 PE=1 SV=2

 Score =  113 bits (283), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 52/108 (48%), Positives = 74/108 (68%), Gaps = 1/108 (0%)

Query: 15  NADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKK 74
           +  ++PDLSHL+ EER+IIE+V  RQK EE +E +I ++  +E+  L++ I +R E  KK
Sbjct: 3   DPSMMPDLSHLSAEEREIIENVFKRQKDEEAKETQISQKASEELSELDKQITERKETSKK 62

Query: 75  -AGVELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             G + DA C IC KTKFADG+GH C YC +R CARCGG+   ++  +
Sbjct: 63  LVGTQDDAICQICQKTKFADGIGHKCFYCQLRSCARCGGRAQSKNKAI 110

Regulates the efficiency of a post-docking step of the release pathway. Acts after vesicle docking likely via regulating priming. May regulate the conformational changes in syntaxin. Binding of vesicles via rab-3[GTP] to Rim may signal the presence of a docked synaptic vesicle. Rim may then signal to unc-13 to change the conformation of syntaxin from the closed to the open state. Syntaxin could then engage synaptobrevin on the docked vesicle to form SNARE complexes and to prime the vesicle for release. Not required for the development or the structural organization of synapses.
Caenorhabditis elegans (taxid: 6239)

>sp|Q9JIS1|RIMS2_RAT Regulating synaptic membrane exocytosis protein 2 OS=Rattus norvegicus GN=Rims2 PE=1 SV=1

 Score =  107 bits (266), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 60/112 (53%), Positives = 74/112 (66%), Gaps = 16/112 (14%)

Query: 19  IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVE 78
           +PDLSHLT EER+II++VM RQK+EEE+E  ++++       L Q      EQ KK G E
Sbjct: 26  MPDLSHLTEEERKIIQAVMDRQKKEEEKEQSVLKK-------LHQQFEMYKEQVKKMGEE 78

Query: 79  L--------DA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
                    DA TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct: 79  SQQQQEQKGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 130

Rab effector involved in exocytosis. May act as scaffold protein.

Rattus norvegicus (taxid: 10116)

>sp|Q9EQZ7|RIMS2_MOUSE Regulating synaptic membrane exocytosis protein 2 OS=Mus musculus GN=Rims2 PE=1 SV=1

 Score = 94.0 bits (232), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 61/145 (42%), Positives = 75/145 (51%), Gaps = 42/145 (28%)

Query: 19  IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHL------------------ 60
           +PDLSHLT EER+II +VM RQK+EEE+E  +++ K++                      
Sbjct: 26  MPDLSHLTEEERKIILAVMDRQKKEEEKEQSVLKIKEEHKAQPTQWFPFSGITELVNNVL 85

Query: 61  ---------------LEQSIRQRSEQQKKAGVEL--------DA-TCHICLKTKFADGVG 96
                          L Q      EQ KK G E         DA TC IC KTKFADG G
Sbjct: 86  QPQQKQPNEKEPQTKLHQQFEMYKEQVKKMGEESQQQQEQKGDAPTCGICHKTKFADGCG 145

Query: 97  HMCNYCNIRCCARCGGKVTLRSNKV 121
           H C+YC  + CARCGG+V+LRSNKV
Sbjct: 146 HNCSYCQTKFCARCGGRVSLRSNKV 170

Rab effector involved in exocytosis. May act as scaffold protein.

Mus musculus (taxid: 10090)

>sp|Q9UQ26|RIMS2_HUMAN Regulating synaptic membrane exocytosis protein 2 OS=Homo sapiens GN=RIMS2 PE=1 SV=2

 Score = 90.9 bits (224), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 60/136 (44%), Positives = 75/136 (55%), Gaps = 33/136 (24%)

Query: 19  IPDLSHLTLEERQIIESVMMRQKQEEERE---------------------LEIMRRKQDE 57
           +PDLSHLT EER+II +VM RQK++ + E                     L+  +++Q+E
Sbjct: 26  MPDLSHLTEEERKIILAVMDRQKKKVKEEHKPQLTQWFPFSGITELVNNVLQPQQKQQNE 85

Query: 58  VH---LLEQSIRQRSEQQKKAGVEL--------DA-TCHICLKTKFADGVGHMCNYCNIR 105
                 L Q      EQ KK G E         DA TC IC KTKFADG GH C+YC  +
Sbjct: 86  KEPQTKLHQQFEMYKEQVKKMGEESQQQQEQKGDAPTCGICHKTKFADGCGHNCSYCQTK 145

Query: 106 CCARCGGKVTLRSNKV 121
            CARCGG+V+LRSNKV
Sbjct: 146 FCARCGGRVSLRSNKV 161

Rab effector involved in exocytosis. May act as scaffold protein.

Homo sapiens (taxid: 9606)

>sp|Q86UR5|RIMS1_HUMAN Regulating synaptic membrane exocytosis protein 1 OS=Homo sapiens GN=RIMS1 PE=1 SV=1

 Score = 85.5 bits (210), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 59/131 (45%), Positives = 74/131 (56%), Gaps = 30/131 (22%)

Query: 19  IPDLSHLTLEERQIIESVMMRQKQEEERELEIM----------------RRKQDEVHL-- 60
           +PDLSHLT EER II +VM RQK+EEE+E  ++                R  +++ H   
Sbjct: 22  LPDLSHLTEEERNIIMAVMDRQKEEEEKEEAMLKCVVRDMAKPAACKTPRNAENQPHQPS 81

Query: 61  --LEQSIRQRSEQQKKAGVEL---------DA-TCHICLKTKFADGVGHMCNYCNIRCCA 108
             L Q      EQ +K G E          DA TC IC KTKFADG GH+C+YC  + CA
Sbjct: 82  PRLHQQFESYKEQVRKIGEEARRYQGEHKDDAPTCGICHKTKFADGCGHLCSYCRTKFCA 141

Query: 109 RCGGKVTLRSN 119
           RCGG+V+LRSN
Sbjct: 142 RCGGRVSLRSN 152

Rab effector involved in exocytosis. May act as scaffold protein that regulates neurotransmitter release at the active zone. Essential for maintaining normal probability of neurotransmitter release and for regulating release during short-term synaptic plasticity.

Homo sapiens (taxid: 9606)

>sp|Q99NE5|RIMS1_MOUSE Regulating synaptic membrane exocytosis protein 1 OS=Mus musculus GN=Rims1 PE=1 SV=2

 Score = 77.0 bits (188), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 59/154 (38%), Positives = 68/154 (44%), Gaps = 53/154 (34%)

Query: 19  IPDLSHLTLEERQIIESVMMRQ-------------------------------KQEEERE 47
           +PDLSHLT EER II +VM RQ                                Q  +  
Sbjct: 22  LPDLSHLTEEERNIIMAVMDRQKEEEEKEEAMLKCVVRDMAKPAACKTPRNAESQPHQPP 81

Query: 48  LEIMR-----RKQ-------DEVHLLEQSIRQRSEQQKKAGVEL---------DA-TCHI 85
           L I R     RK        D    L Q      EQ +K G E          DA TC I
Sbjct: 82  LNIFRCVCVPRKPSSEEGGPDRNWRLHQQFESYKEQVRKIGEEARRYQGEHKDDAPTCGI 141

Query: 86  CLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSN 119
           C KTKFADG GH+C+YC  + CARCGG+V+LRSN
Sbjct: 142 CHKTKFADGCGHLCSYCRTKFCARCGGRVSLRSN 175

Rab effector involved in exocytosis. May act as scaffold protein that regulates neurotransmitter release at the active zone. Essential for maintaining normal probability of neurotransmitter release and for regulating release during short-term synaptic plasticity.

Mus musculus (taxid: 10090)

>sp|Q9JIR4|RIMS1_RAT Regulating synaptic membrane exocytosis protein 1 OS=Rattus norvegicus GN=Rims1 PE=1 SV=1

 Score = 75.9 bits (185), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 59/154 (38%), Positives = 73/154 (47%), Gaps = 53/154 (34%)

Query: 19  IPDLSHLTLEERQIIESVMMRQKQEEERELEIM----------------RRKQDEVHL-- 60
           +PDLSHLT EER II +VM RQK+EEE+E  ++                R  + + H   
Sbjct: 22  LPDLSHLTEEERNIIMAVMDRQKEEEEKEEAMLKCVVRDMAKPAACKTPRNAESQPHQPP 81

Query: 61  -------------------------LEQSIRQRSEQQKKAGVEL---------DA-TCHI 85
                                    L Q      EQ +K G E          DA TC I
Sbjct: 82  LNIFRCVCVPRKPSSEEGGPERDWRLHQQFESYKEQVRKIGEEARRYQGEHKDDAPTCGI 141

Query: 86  CLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSN 119
           C KTKFADG GH+C+YC  + CARCGG+V+LRSN
Sbjct: 142 CHKTKFADGCGHLCSYCRTKFCARCGGRVSLRSN 175

Rab effector involved in exocytosis. May act as scaffold protein that regulates neurotransmitter release at the active zone. Essential for maintaining normal probability of neurotransmitter release and for regulating release during short-term synaptic plasticity.

Rattus norvegicus (taxid: 10116)

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	137
242020225	356	rab3 interacting molecule, putative [Ped	0.744	0.286	0.901	2e-48
195570025	2270	GD20205 [Drosophila simulans] gi|1941989	0.766	0.046	0.838	5e-47
195348985	2819	GM15331 [Drosophila sechellia] gi|194122	0.766	0.037	0.838	5e-47
386765989	2792	Rim, isoform P [Drosophila melanogaster]	0.766	0.037	0.838	7e-47
386765995	2798	Rim, isoform F [Drosophila melanogaster]	0.766	0.037	0.838	7e-47
194900320	2881	GG16745 [Drosophila erecta] gi|190651408	0.766	0.036	0.838	1e-46
195497494	2337	GE25240 [Drosophila yakuba] gi|194182225	0.766	0.044	0.838	2e-46
195107389	2883	GI23883 [Drosophila mojavensis] gi|19391	0.766	0.036	0.838	2e-46
195389859	2919	GJ23976 [Drosophila virilis] gi|19415167	0.766	0.035	0.838	3e-46
442619701	2595	Rim, isoform W [Drosophila melanogaster]	0.766	0.040	0.838	3e-46

>gi|242020225|ref|XP_002430556.1| rab3 interacting molecule, putative [Pediculus humanus corporis] gi|212515720|gb|EEB17818.1| rab3 interacting molecule, putative [Pediculus humanus corporis]

 Score =  196 bits (499), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 92/102 (90%), Positives = 98/102 (96%)

Query: 20  PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVEL 79
           PDLSHLT EERQIIE VMMRQKQEEERE EIMRRKQDEV +LE++IRQRSEQQKKAG+EL
Sbjct: 5   PDLSHLTEEERQIIEKVMMRQKQEEERENEIMRRKQDEVQVLEETIRQRSEQQKKAGIEL 64

Query: 80  DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           DATCHICLKTKFADGVGH+CNYC+IRCCARCGGKVTLRSNKV
Sbjct: 65  DATCHICLKTKFADGVGHICNYCSIRCCARCGGKVTLRSNKV 106

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195570025|ref|XP_002103009.1| GD20205 [Drosophila simulans] gi|194198936|gb|EDX12512.1| GD20205 [Drosophila simulans]

 Score =  192 bits (487), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195348985|ref|XP_002041027.1| GM15331 [Drosophila sechellia] gi|194122632|gb|EDW44675.1| GM15331 [Drosophila sechellia]

 Score =  192 bits (487), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|386765989|ref|NP_001247160.1| Rim, isoform P [Drosophila melanogaster] gi|383292776|gb|AFH06478.1| Rim, isoform P [Drosophila melanogaster]

 Score =  191 bits (486), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|386765995|ref|NP_001247163.1| Rim, isoform F [Drosophila melanogaster] gi|386766005|ref|NP_001247168.1| Rim, isoform K [Drosophila melanogaster] gi|383292779|gb|AFH06481.1| Rim, isoform F [Drosophila melanogaster] gi|383292784|gb|AFH06486.1| Rim, isoform K [Drosophila melanogaster]

 Score =  191 bits (486), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194900320|ref|XP_001979705.1| GG16745 [Drosophila erecta] gi|190651408|gb|EDV48663.1| GG16745 [Drosophila erecta]

 Score =  191 bits (484), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195497494|ref|XP_002096124.1| GE25240 [Drosophila yakuba] gi|194182225|gb|EDW95836.1| GE25240 [Drosophila yakuba]

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195107389|ref|XP_001998296.1| GI23883 [Drosophila mojavensis] gi|193914890|gb|EDW13757.1| GI23883 [Drosophila mojavensis]

 Score =  189 bits (481), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195389859|ref|XP_002053591.1| GJ23976 [Drosophila virilis] gi|194151677|gb|EDW67111.1| GJ23976 [Drosophila virilis]

 Score =  189 bits (481), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442619701|ref|NP_001247169.2| Rim, isoform W [Drosophila melanogaster] gi|440217565|gb|AFH06487.2| Rim, isoform W [Drosophila melanogaster]

 Score =  189 bits (480), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query: 17  DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
           D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct: 2   DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query: 77  VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
           VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct: 62  VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	137
FB|FBgn0053547	2908	Rim "Rab3 interacting molecule	0.766	0.036	0.838	3.4e-42
UNIPROTKB|D4ABU5	1292	Rims2 "Regulating synaptic mem	0.751	0.079	0.514	4.7e-24
RGD|620001	1555	Rims2 "regulating synaptic mem	0.751	0.066	0.514	6.1e-24
UNIPROTKB|F1LNC5	1555	Rims2 "Regulating synaptic mem	0.751	0.066	0.514	6.1e-24
UNIPROTKB|Q9JIS1	1555	Rims2 "Regulating synaptic mem	0.751	0.066	0.514	6.1e-24
UNIPROTKB|D4AEJ9	1557	Rims2 "Regulating synaptic mem	0.751	0.066	0.514	6.1e-24
WB|WBGene00006750	1563	unc-10 [Caenorhabditis elegans	0.759	0.066	0.495	6.1e-24
UNIPROTKB|E9PFB6	1111	RIMS2 "Regulating synaptic mem	0.751	0.092	0.514	1.3e-23
UNIPROTKB|J9NYS3	1611	RIMS2 "Uncharacterized protein	0.751	0.063	0.514	2.2e-23
ZFIN|ZDB-GENE-040426-1656	1473	rims2a "regulating synaptic me	0.744	0.069	0.518	5.2e-23

FB|FBgn0053547 Rim "Rab3 interacting molecule" [Drosophila melanogaster (taxid:7227)]

 Score = 464 (168.4 bits), Expect = 3.4e-42, P = 3.4e-42
 Identities = 88/105 (83%), Positives = 95/105 (90%)

Query:    17 DIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAG 76
             D +PDLSHLT  ER  IE+V+MRQKQEEE++ EIMRRKQDEV  LE  IRQRSEQQKKAG
Sbjct:     2 DEMPDLSHLTPHERMQIENVLMRQKQEEEKQNEIMRRKQDEVVTLEMQIRQRSEQQKKAG 61

Query:    77 VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             VELDATCHICLKTKFADGVGH+C+YCNIRCCARCGGKVTLRSNKV
Sbjct:    62 VELDATCHICLKTKFADGVGHICHYCNIRCCARCGGKVTLRSNKV 106

GO:0008021 "synaptic vesicle" evidence=NAS

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

GO:0007269 "neurotransmitter secretion" evidence=NAS

GO:0016079 "synaptic vesicle exocytosis" evidence=ISS

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0017137 "Rab GTPase binding" evidence=IEA

GO:0005083 "small GTPase regulator activity" evidence=ISS

GO:0017157 "regulation of exocytosis" evidence=ISS

GO:0070073 "clustering of voltage-gated calcium channels" evidence=IMP

GO:0007274 "neuromuscular synaptic transmission" evidence=IMP

GO:0048786 "presynaptic active zone" evidence=IDA

UNIPROTKB|D4ABU5 Rims2 "Regulating synaptic membrane exocytosis protein 2" [Rattus norvegicus (taxid:10116)]

 Score = 289 (106.8 bits), Expect = 4.7e-24, P = 4.7e-24
 Identities = 54/105 (51%), Positives = 79/105 (75%)

Query:    19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ-QKKAGV 77
             +PDLSHLT EER+II++VM RQK+EEE+E  ++++   +  + ++ +++  E+ Q++   
Sbjct:    26 MPDLSHLTEEERKIIQAVMDRQKKEEEKEQSVLKKLHQQFEMYKEQVKKMGEESQQQQEQ 85

Query:    78 ELDA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             + DA TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct:    86 KGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 130

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0017137 "Rab GTPase binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

RGD|620001 Rims2 "regulating synaptic membrane exocytosis 2" [Rattus norvegicus (taxid:10116)]

 Score = 289 (106.8 bits), Expect = 6.1e-24, P = 6.1e-24
 Identities = 54/105 (51%), Positives = 79/105 (75%)

Query:    19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ-QKKAGV 77
             +PDLSHLT EER+II++VM RQK+EEE+E  ++++   +  + ++ +++  E+ Q++   
Sbjct:    26 MPDLSHLTEEERKIIQAVMDRQKKEEEKEQSVLKKLHQQFEMYKEQVKKMGEESQQQQEQ 85

Query:    78 ELDA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             + DA TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct:    86 KGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 130

GO:0005515 "protein binding" evidence=IPI

GO:0006887 "exocytosis" evidence=TAS

GO:0017156 "calcium ion-dependent exocytosis" evidence=ISO

GO:0017157 "regulation of exocytosis" evidence=ISO

GO:0019904 "protein domain specific binding" evidence=IDA

GO:0019933 "cAMP-mediated signaling" evidence=ISO

GO:0030073 "insulin secretion" evidence=ISO

GO:0042391 "regulation of membrane potential" evidence=ISO

GO:0043234 "protein complex" evidence=IDA

GO:0044325 "ion channel binding" evidence=ISO

GO:0045202 "synapse" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IDA

GO:0048791 "calcium ion-dependent exocytosis of neurotransmitter" evidence=ISO

GO:2000300 "regulation of synaptic vesicle exocytosis" evidence=IMP

UNIPROTKB|F1LNC5 Rims2 "Regulating synaptic membrane exocytosis protein 2" [Rattus norvegicus (taxid:10116)]

 Score = 289 (106.8 bits), Expect = 6.1e-24, P = 6.1e-24
 Identities = 54/105 (51%), Positives = 79/105 (75%)

Query:    19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ-QKKAGV 77
             +PDLSHLT EER+II++VM RQK+EEE+E  ++++   +  + ++ +++  E+ Q++   
Sbjct:    26 MPDLSHLTEEERKIIQAVMDRQKKEEEKEQSVLKKLHQQFEMYKEQVKKMGEESQQQQEQ 85

Query:    78 ELDA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             + DA TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct:    86 KGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 130

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0017137 "Rab GTPase binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q9JIS1 Rims2 "Regulating synaptic membrane exocytosis protein 2" [Rattus norvegicus (taxid:10116)]

 Score = 289 (106.8 bits), Expect = 6.1e-24, P = 6.1e-24
 Identities = 54/105 (51%), Positives = 79/105 (75%)

Query:    19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ-QKKAGV 77
             +PDLSHLT EER+II++VM RQK+EEE+E  ++++   +  + ++ +++  E+ Q++   
Sbjct:    26 MPDLSHLTEEERKIIQAVMDRQKKEEEKEQSVLKKLHQQFEMYKEQVKKMGEESQQQQEQ 85

Query:    78 ELDA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             + DA TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct:    86 KGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 130

GO:0005886 "plasma membrane" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0017137 "Rab GTPase binding" evidence=IEA

GO:0017156 "calcium ion-dependent exocytosis" evidence=IEA

GO:0019933 "cAMP-mediated signaling" evidence=IEA

GO:0030054 "cell junction" evidence=IEA

GO:0030073 "insulin secretion" evidence=IEA

GO:0042391 "regulation of membrane potential" evidence=IEA

GO:0042734 "presynaptic membrane" evidence=IEA

GO:0044325 "ion channel binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0048791 "calcium ion-dependent exocytosis of neurotransmitter" evidence=IEA

UNIPROTKB|D4AEJ9 Rims2 "Regulating synaptic membrane exocytosis protein 2" [Rattus norvegicus (taxid:10116)]

 Score = 289 (106.8 bits), Expect = 6.1e-24, P = 6.1e-24
 Identities = 54/105 (51%), Positives = 79/105 (75%)

Query:    19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ-QKKAGV 77
             +PDLSHLT EER+II++VM RQK+EEE+E  ++++   +  + ++ +++  E+ Q++   
Sbjct:    26 MPDLSHLTEEERKIIQAVMDRQKKEEEKEQSVLKKLHQQFEMYKEQVKKMGEESQQQQEQ 85

Query:    78 ELDA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             + DA TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct:    86 KGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 130

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0017137 "Rab GTPase binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

WB|WBGene00006750 unc-10 [Caenorhabditis elegans (taxid:6239)]

 Score = 289 (106.8 bits), Expect = 6.1e-24, P = 6.1e-24
 Identities = 52/105 (49%), Positives = 73/105 (69%)

Query:    18 IIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKK-AG 76
             ++PDLSHL+ EER+IIE+V  RQK EE +E +I ++  +E+  L++ I +R E  KK  G
Sbjct:     6 MMPDLSHLSAEEREIIENVFKRQKDEEAKETQISQKASEELSELDKQITERKETSKKLVG 65

Query:    77 VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
              + DA C IC KTKFADG+GH C YC +R CARCGG+   ++  +
Sbjct:    66 TQDDAICQICQKTKFADGIGHKCFYCQLRSCARCGGRAQSKNKAI 110

GO:0040011 "locomotion" evidence=IMP

GO:0007626 "locomotory behavior" evidence=IMP

GO:0043051 "regulation of pharyngeal pumping" evidence=IMP

GO:0040018 "positive regulation of multicellular organism growth" evidence=IMP

GO:0030421 "defecation" evidence=IMP

GO:0007617 "mating behavior" evidence=IMP

GO:0050806 "positive regulation of synaptic transmission" evidence=IDA

GO:0016082 "synaptic vesicle priming" evidence=IDA

GO:0032224 "positive regulation of synaptic transmission, cholinergic" evidence=IMP

GO:0008104 "protein localization" evidence=IMP

GO:0030424 "axon" evidence=IDA

GO:0048786 "presynaptic active zone" evidence=IDA

GO:0017137 "Rab GTPase binding" evidence=IGI

GO:0005509 "calcium ion binding" evidence=ISS

GO:0030742 "GTP-dependent protein binding" evidence=ISS

GO:0008022 "protein C-terminus binding" evidence=IPI

GO:0007271 "synaptic transmission, cholinergic" evidence=IMP

UNIPROTKB|E9PFB6 RIMS2 "Regulating synaptic membrane exocytosis protein 2" [Homo sapiens (taxid:9606)]

 Score = 284 (105.0 bits), Expect = 1.3e-23, P = 1.3e-23
 Identities = 54/105 (51%), Positives = 78/105 (74%)

Query:    19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ-QKKAGV 77
             +PDLSHLT EER+II +VM RQK+EEE+E  ++++   +  + ++ +++  E+ Q++   
Sbjct:    26 MPDLSHLTEEERKIILAVMDRQKKEEEKEQSVLKKLHQQFEMYKEQVKKMGEESQQQQEQ 85

Query:    78 ELDA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             + DA TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct:    86 KGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 130

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0017137 "Rab GTPase binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0017156 "calcium ion-dependent exocytosis" evidence=IEA

GO:0019933 "cAMP-mediated signaling" evidence=IEA

GO:0030073 "insulin secretion" evidence=IEA

GO:0042391 "regulation of membrane potential" evidence=IEA

GO:0044325 "ion channel binding" evidence=IEA

GO:0048791 "calcium ion-dependent exocytosis of neurotransmitter" evidence=IEA

UNIPROTKB|J9NYS3 RIMS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 284 (105.0 bits), Expect = 2.2e-23, P = 2.2e-23
 Identities = 54/105 (51%), Positives = 78/105 (74%)

Query:    19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQ-QKKAGV 77
             +PDLSHLT EER+II +VM RQK+EEE+E  ++++   +  + ++ +++  E+ Q++   
Sbjct:    26 MPDLSHLTEEERKIILAVMDRQKKEEEKEQSVLKKLHQQFEMYKEQVKKMGEESQQQQEQ 85

Query:    78 ELDA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             + DA TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct:    86 KGDAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 130

GO:0046872 "metal ion binding" evidence=IEA

GO:0017137 "Rab GTPase binding" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

ZFIN|ZDB-GENE-040426-1656 rims2a "regulating synaptic membrane exocytosis 2a" [Danio rerio (taxid:7955)]

 Score = 280 (103.6 bits), Expect = 5.2e-23, P = 5.2e-23
 Identities = 55/106 (51%), Positives = 77/106 (72%)

Query:    19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVE 78
             +PDLSHLT EER+II  VM RQK+EEE+E  ++++   +  + +  +++  E+ + +G E
Sbjct:    16 MPDLSHLTEEERKIILGVMDRQKKEEEKEQSMLKKLHQQFEMYKDQVQKMGEEAQ-SGPE 74

Query:    79 L--DA-TCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
                DA TC IC KTKFADG GH+C+YC  + CARCGG+V+LRSNKV
Sbjct:    75 QKSDAPTCGICHKTKFADGCGHLCSYCQTKFCARCGGRVSLRSNKV 120

GO:0017137 "Rab GTPase binding" evidence=IEA

GO:0006886 "intracellular protein transport" evidence=IEA

GO:0046872 "metal ion binding" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9JIS1	RIMS2_RAT	No assigned EC number	0.5357	0.7007	0.0617	yes	N/A

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

No hit with e-value below 0.005

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
KOG3799|consensus	169		100.0
PF02318	118	FYVE_2: FYVE-type zinc finger; InterPro: IPR003315	99.96
cd00065	57	FYVE FYVE domain; Zinc-binding domain; targets pro	94.65
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	93.48
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	92.36
smart00064	68	FYVE Protein present in Fab1, YOTB, Vac1, and EEA1	90.93
PF05715	61	zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899	90.78
PF04810	40	zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro:	90.72
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	87.33
PRK12495	226	hypothetical protein; Provisional	86.05
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	85.07
KOG1013|consensus	362		84.37
smart00661	52	RPOL9 RNA polymerase subunit 9.	83.16
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	81.98
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	81.19

>KOG3799|consensus

Probab=100.00  E-value=1.8e-35  Score=226.64  Aligned_cols=114  Identities=56%  Similarity=0.875  Sum_probs=110.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCccccccccccccccccCCC
Q psy5308          16 ADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGV   95 (137)
Q Consensus        16 ~~~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktkf~~g~   95 (137)
                      |.++|||||||+.||=.|..|+.|++.++.++-+..++..+++-+|.++|..++++.+++|.+++++|+||+|||||||+
T Consensus         1 ~~~~~d~sh~T~he~~qik~vf~rqk~ee~kq~ei~~~~~~e~~el~~Qi~erkEqqKKaGv~ddatC~IC~KTKFADG~   80 (169)
T KOG3799|consen    1 MDEMPDLSHLTPHERMQIKEVFIRQKIEEHKQFEIYKEQVKEMGELSQQIQERKEQQKKAGVGDDATCGICHKTKFADGC   80 (169)
T ss_pred             CccccchhhcCccchHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCcCcchhhhhhccccccc
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccccccccccCCceeecCCCCcceEEeeec
Q psy5308          96 GHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRG  129 (137)
Q Consensus        96 G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~  129 (137)
                      ||.|.||+.|+|+|||++|++++|+++|+|..|-
T Consensus        81 GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~  114 (169)
T KOG3799|consen   81 GHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCR  114 (169)
T ss_pred             CcccchhhhhHHHhcCCeeeeccCceEEeccCCc
Confidence            9999999999999999999999999999999974

>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A

Probab=99.96  E-value=3.2e-30  Score=189.58  Aligned_cols=99  Identities=26%  Similarity=0.404  Sum_probs=79.8

Q ss_pred             CCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH--HHHHHHHHhHHHHhhhCcccccccccccccc-ccCCCCCCC
Q psy5308          23 SHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVH--LLEQSIRQRSEQQKKAGVELDATCHICLKTK-FADGVGHMC   99 (137)
Q Consensus        23 S~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~--~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk-f~~g~G~~C   99 (137)
                      ||||++||++|++||+||++++++|++||++|+++|+  .+++.+.      ...+.+++++|++|++++ |++++|++|
T Consensus         1 s~Lt~eE~~~I~~Vl~R~~~l~~~E~~Ri~kLk~~L~~e~~r~~~~------~~~~~~~~~~C~~C~~~fg~l~~~~~~C   74 (118)
T PF02318_consen    1 SHLTEEEREIILQVLQRDEELRKKEEERIRKLKQELQKEKMRREAL------GNSQKYGERHCARCGKPFGFLFNRGRVC   74 (118)
T ss_dssp             TTS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC------SCSTTHCCSB-TTTS-BCSCTSTTCEEE
T ss_pred             CCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcc------ccccccCCcchhhhCCcccccCCCCCcC
Confidence            8999999999999999999999999999999999994  3443321      112233479999999865 999999999


Q ss_pred             ccccccccccCCceeecCCCCcceEEeeecc
Q psy5308         100 NYCNIRCCARCGGKVTLRSNKVSVEVTTRGH  130 (137)
Q Consensus       100 ~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~  130 (137)
                      .+|+++||++||++   .++...|+|+||..
T Consensus        75 ~~C~~~VC~~C~~~---~~~~~~WlC~vC~k  102 (118)
T PF02318_consen   75 VDCKHRVCKKCGVY---SKKEPIWLCKVCQK  102 (118)
T ss_dssp             TTTTEEEETTSEEE---TSSSCCEEEHHHHH
T ss_pred             CcCCccccCccCCc---CCCCCCEEChhhHH
Confidence            99999999999987   33467999999764

The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.

>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;

Probab=94.65  E-value=0.021  Score=36.01  Aligned_cols=50  Identities=18%  Similarity=0.288  Sum_probs=38.4

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCceeecC----CCCcceEEeeec
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLR----SNKVSVEVTTRG  129 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr----~n~~~W~Ctvc~  129 (137)
                      ...|..|.+.+....+.|.|..|...||..|-.+....    .+.++.+|..|.
T Consensus         2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C~   55 (57)
T cd00065           2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCY   55 (57)
T ss_pred             cCcCcccCccccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHHh
Confidence            36799999776556799999999999999998765432    234678888764

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=93.48  E-value=0.043  Score=31.68  Aligned_cols=29  Identities=28%  Similarity=0.540  Sum_probs=15.7

Q ss_pred             cccccccCCceeecCCCCcceEEeeeccC
Q psy5308         103 NIRCCARCGGKVTLRSNKVSVEVTTRGHN  131 (137)
Q Consensus       103 ~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~  131 (137)
                      ++++|++||..+.....+..=+|.-|++.
T Consensus         2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    2 NHRFCGRCGAPTKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             TTSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred             CCcccCcCCccccCCCCcCEeECCCCcCE
Confidence            46788888888766655555567777654

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=92.36  E-value=0.047  Score=35.79  Aligned_cols=50  Identities=18%  Similarity=0.284  Sum_probs=27.8

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCceeecCC------CCcceEEeeec
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRS------NKVSVEVTTRG  129 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~------n~~~W~Ctvc~  129 (137)
                      ...|.+|.+.+.++.+-|.|..|-..||+.|-......+      ..+.-+|..|.
T Consensus         9 ~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~   64 (69)
T PF01363_consen    9 ASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCY   64 (69)
T ss_dssp             -SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHH
T ss_pred             CCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHH
Confidence            588999998865557999999999999999987654221      22456666653

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. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....

>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1

Probab=90.93  E-value=0.15  Score=33.27  Aligned_cols=50  Identities=18%  Similarity=0.253  Sum_probs=36.8

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCceeec-CCC---CcceEEeeec
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTL-RSN---KVSVEVTTRG  129 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~l-r~n---~~~W~Ctvc~  129 (137)
                      ...|..|++.+..+.+.|.|..|...||..|-..... ...   .+..+|..|-
T Consensus        10 ~~~C~~C~~~F~~~~rk~hCr~CG~i~C~~C~~~~~~~~~~~~~~p~rvC~~C~   63 (68)
T smart00064       10 VSNCMGCGKEFNLTKRRHHCRNCGRIFCSKCSSKKAPLPKLGIERPVRVCDDCY   63 (68)
T ss_pred             CCcCcccCccccCcccccccccCCCCcChHHcCCeeecCccCCCCCcEECHHHH
Confidence            4689999987655679999999999999999765422 211   2567777754

The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the

>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=90.78  E-value=0.16  Score=34.26  Aligned_cols=46  Identities=17%  Similarity=0.322  Sum_probs=32.0

Q ss_pred             ccccccccccccC----CCCCCCccccccccccCCceeecCCC---CcceEEeee
Q psy5308          81 ATCHICLKTKFAD----GVGHMCNYCNIRCCARCGGKVTLRSN---KVSVEVTTR  128 (137)
Q Consensus        81 ~~C~~C~ktkf~~----g~G~~C~~C~~rvC~rCg~~v~lr~n---~~~W~Ctvc  128 (137)
                      ..|.+|..++...    .--+.|..|+..||+-||.-  -.+|   ..-|+|--|
T Consensus         3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFN--P~Phl~E~~eWLCLnC   55 (61)
T PF05715_consen    3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFN--PTPHLTEVKEWLCLNC   55 (61)
T ss_pred             ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCC--CCccccccceeeeecc
Confidence            6799998665332    13468999999999999943  2222   257999765

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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse

>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=90.72  E-value=0.08  Score=32.17  Aligned_cols=13  Identities=15%  Similarity=0.013  Sum_probs=8.8

Q ss_pred             CcceEEeeeccCC
Q psy5308         120 KVSVEVTTRGHNN  132 (137)
Q Consensus       120 ~~~W~Ctvc~~~~  132 (137)
                      +..|+|.+|.+.|
T Consensus        22 ~~~w~C~~C~~~N   34 (40)
T PF04810_consen   22 GKTWICNFCGTKN   34 (40)
T ss_dssp             TTEEEETTT--EE
T ss_pred             CCEEECcCCCCcC
Confidence            3589999998865

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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=87.33  E-value=0.27  Score=29.01  Aligned_cols=24  Identities=29%  Similarity=0.787  Sum_probs=15.9

Q ss_pred             ccccCCceeecCCCCcceEEeeecc
Q psy5308         106 CCARCGGKVTLRSNKVSVEVTTRGH  130 (137)
Q Consensus       106 vC~rCg~~v~lr~n~~~W~Ctvc~~  130 (137)
                      +|.+||..+.+.++. .-.|.-|+|
T Consensus         2 ~C~~Cg~~~~~~~~~-~irC~~CG~   25 (32)
T PF03604_consen    2 ICGECGAEVELKPGD-PIRCPECGH   25 (32)
T ss_dssp             BESSSSSSE-BSTSS-TSSBSSSS-
T ss_pred             CCCcCCCeeEcCCCC-cEECCcCCC
Confidence            678888888777655 457877776

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>PRK12495 hypothetical protein; Provisional

Probab=86.05  E-value=2  Score=35.71  Aligned_cols=65  Identities=17%  Similarity=0.276  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCccccccccccccccccCCCCCCCcccc
Q psy5308          24 HLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTKFADGVGHMCNYCN  103 (137)
Q Consensus        24 ~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktkf~~g~G~~C~~C~  103 (137)
                      |=.|.||+.+-+-..+|++-++.-    +++-+.|.         ++     ..-+...|..|+.++|...--..|..|+
T Consensus         4 FDkEaEREkLREKye~d~~~R~~~----~~ma~lL~---------~g-----atmsa~hC~~CG~PIpa~pG~~~Cp~CQ   65 (226)
T PRK12495          4 FDKEAEREKLREKYEQDEQKREAT----ERMSELLL---------QG-----ATMTNAHCDECGDPIFRHDGQEFCPTCQ   65 (226)
T ss_pred             hhHHHHHHHHHHHHhhhHHHHHHH----HHHHHHHH---------hh-----cccchhhcccccCcccCCCCeeECCCCC
Confidence            445778888776555555433222    22222121         11     1223688999999999753333466666


Q ss_pred             ccc
Q psy5308         104 IRC  106 (137)
Q Consensus       104 ~rv  106 (137)
                      ..|
T Consensus        66 ~~~   68 (226)
T PRK12495         66 QPV   68 (226)
T ss_pred             Ccc
Confidence            443

>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production

Probab=85.07  E-value=0.57  Score=33.75  Aligned_cols=34  Identities=35%  Similarity=0.813  Sum_probs=27.2

Q ss_pred             cccccccccccccCCCCCCCccc--cccccccCCcee
Q psy5308          80 DATCHICLKTKFADGVGHMCNYC--NIRCCARCGGKV  114 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C--~~rvC~rCg~~v  114 (137)
                      ...|.+|. ++....-++.|+.|  ++-+|+-||..+
T Consensus        44 ~~~C~~CK-~~v~q~g~~YCq~CAYkkGiCamCGKki   79 (90)
T PF10235_consen   44 SSKCKICK-TKVHQPGAKYCQTCAYKKGICAMCGKKI   79 (90)
T ss_pred             Cccccccc-cccccCCCccChhhhcccCcccccCCee
Confidence            36899995 66555466899999  578999999887

This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].

>KOG1013|consensus

Probab=84.37  E-value=0.64  Score=40.78  Aligned_cols=100  Identities=5%  Similarity=-0.177  Sum_probs=72.1

Q ss_pred             CCCCCCCHHHHHH---------HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCcccccccccccccc
Q psy5308          20 PDLSHLTLEERQI---------IESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTK   90 (137)
Q Consensus        20 ~dLS~LteeEr~~---------Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk   90 (137)
                      ++|++|-..|...         -|.||++.......+..++..+..++..|+...         ++. ..+.|-.|-.+.
T Consensus        82 ~~~~~~y~~~~~~~~~tl~~a~~lk~~~~~~~~d~~~~~~llpga~kl~slr~~t---------~~n-~lN~~w~etev~  151 (362)
T KOG1013|consen   82 LEFELLYDSESRMLDTTLDRAKGLKPMDINGLADPYVKLHLLPGAGKLNSLRTKT---------TRN-TLNPEWNETEVY  151 (362)
T ss_pred             hhhhhhhhhhhhhcceeechhcccchhhhhhhcchHHhhhcccchhhhhhhhHHh---------hcc-CcCcceecccee
Confidence            4455555555443         367788888888888888888888888887532         121 157789998885


Q ss_pred             -ccCCCCCCCccccccccccCCce--eecCCCCcceEEeeecc
Q psy5308          91 -FADGVGHMCNYCNIRCCARCGGK--VTLRSNKVSVEVTTRGH  130 (137)
Q Consensus        91 -f~~g~G~~C~~C~~rvC~rCg~~--v~lr~n~~~W~Ctvc~~  130 (137)
                       |+......|..|.+.||..|+..  .+... ...|+|++|..
T Consensus       152 ~~i~~~~~~~K~~Rk~vcdn~~~~~~~sqGq-~r~~lkKl~p~  193 (362)
T KOG1013|consen  152 EGITDDDTHLKVLRKVVCDNDKKTHNESQGQ-SRVSLKKLKPL  193 (362)
T ss_pred             cccccchhhhhhhheeeccCcccccccCccc-chhhhhccChh
Confidence             88788999999999999999977  33332 23699999754

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=83.16  E-value=0.68  Score=28.53  Aligned_cols=9  Identities=11%  Similarity=0.006  Sum_probs=4.3

Q ss_pred             ceEEeeecc
Q psy5308         122 SVEVTTRGH  130 (137)
Q Consensus       122 ~W~Ctvc~~  130 (137)
                      .|+|..|++
T Consensus        20 ~~vC~~Cg~   28 (52)
T smart00661       20 RFVCRKCGY   28 (52)
T ss_pred             EEECCcCCC
Confidence            344544444

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=81.98  E-value=4  Score=24.82  Aligned_cols=26  Identities=27%  Similarity=0.284  Sum_probs=19.5

Q ss_pred             CCCCCHHHHHHHHHHHHhhHHHHHHH
Q psy5308          22 LSHLTLEERQIIESVMMRQKQEEERE   47 (137)
Q Consensus        22 LS~LteeEr~~Il~VL~R~~~le~~E   47 (137)
                      |+.|+++||++|.-....+.-++++-
T Consensus         2 l~~L~~~er~vi~~~y~~~~t~~eIa   27 (50)
T PF04545_consen    2 LDQLPPREREVIRLRYFEGLTLEEIA   27 (50)
T ss_dssp             HCTS-HHHHHHHHHHHTST-SHHHHH
T ss_pred             hhhCCHHHHHHHHHHhcCCCCHHHHH
Confidence            57899999999999887776666663

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=81.19  E-value=0.54  Score=28.03  Aligned_cols=27  Identities=22%  Similarity=0.604  Sum_probs=14.2

Q ss_pred             cccccCCceeecC----CCCcceEEeeeccC
Q psy5308         105 RCCARCGGKVTLR----SNKVSVEVTTRGHN  131 (137)
Q Consensus       105 rvC~rCg~~v~lr----~n~~~W~Ctvc~~~  131 (137)
                      ++|..||..+..+    -+..-|+|+-|++-
T Consensus         1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I   31 (34)
T PF14803_consen    1 KFCPQCGGPLERRIPEGDDRERLVCPACGFI   31 (34)
T ss_dssp             -B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred             CccccccChhhhhcCCCCCccceECCCCCCE
Confidence            5889999887543    22357889888764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	137
2a20_A	62	Solution Structure Of Rim2 Zinc Finger Domain Lengt		2e-11

>pdb|2A20|A Chain A, Solution Structure Of Rim2 Zinc Finger Domain Length = 62

Iteration: 1
 Score = 64.7 bits (156), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/41 (70%), Positives = 33/41 (80%)
Query: 81  ATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
            TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct: 10  PTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 50

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	137
2a20_A	62	Regulating synaptic membrane exocytosis protein 2;	2e-17
1zbd_B	134	Rabphilin-3A; G protein, effector, RABCDR, synapti	2e-16
2zet_C	153	Melanophilin; complex, GTP-binding protein, GTPase	1e-12

>2a20_A Regulating synaptic membrane exocytosis protein 2; zinc-finger domain, metal binding protein; NMR {Rattus norvegicus} PDB: 2cjs_C Length = 62

 Score = 70.2 bits (171), Expect = 2e-17
 Identities = 29/42 (69%), Positives = 33/42 (78%)

Query: 80  DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
             TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct: 9   APTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 50

>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: g.50.1.1 Length = 134

 Score = 69.6 bits (169), Expect = 2e-16
 Identities = 21/103 (20%), Positives = 39/103 (37%), Gaps = 11/103 (10%)

Query: 20  PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVEL 79
                LT EE++II  V+ R ++ E  E E + R  D +  + +++      +       
Sbjct: 5   RKQEELTDEEKEIINRVIARAEKMETMEQERIGRLVDRLETMRKNVAGDGVNR------- 57

Query: 80  DATCHICLKTKFADGV-GHMCNYCNIRCCARCGGKVTLRSNKV 121
              C +C +     G    +C  C    C +CG + +      
Sbjct: 58  ---CILCGEQLGMLGSASVVCEDCKKNVCTKCGVETSNNRPHP 97

>2zet_C Melanophilin; complex, GTP-binding protein, GTPase, G-protein, RAB, RAB27B, effector, SLP homology domain, acetylation, lipoprotein, membrane; HET: GTP; 3.00A {Mus musculus} Length = 153

 Score = 60.0 bits (144), Expect = 1e-12
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 5/93 (5%)

Query: 20  PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVEL 79
            DLS LT EE + + +V+ R      RE E ++  + ++    Q    + E         
Sbjct: 12  LDLSTLTDEEAEHVWAVVQRDFDLRRREEERLQGLKGKI----QKESSKRELLSDTAHLN 67

Query: 80  DATCHICLKT-KFADGVGHMCNYCNIRCCARCG 111
           +  C  CL+  +        C  C++  C  C 
Sbjct: 68  ETHCARCLQPYRLLLNSRRQCLECSLFVCKSCS 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
2zet_C	153	Melanophilin; complex, GTP-binding protein, GTPase	100.0
1zbd_B	134	Rabphilin-3A; G protein, effector, RABCDR, synapti	100.0
2a20_A	62	Regulating synaptic membrane exocytosis protein 2;	99.84
2csz_A	76	Synaptotagmin-like protein 4; exophilin 2, granuph	99.65
3bc1_B	59	Synaptotagmin-like protein 2; RAB27, GTPase, RAB,	99.1
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	96.87
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	92.68
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	91.23
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	90.11
3zyq_A	226	Hepatocyte growth factor-regulated tyrosine kinas	89.32
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	88.67
1dvp_A	220	HRS, hepatocyte growth factor-regulated tyrosine k	88.17
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	88.16
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	87.8
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	87.49
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	86.8
2vrw_B	406	P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP	86.53
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	85.38
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	83.63
3j21_g	51	50S ribosomal protein L40E; archaea, archaeal, KIN	83.24

>2zet_C Melanophilin; complex, GTP-binding protein, GTPase, G-protein, RAB, RAB27B, effector, SLP homology domain, acetylation, lipoprotein, membrane; HET: GTP; 3.00A {Mus musculus}

Probab=100.00  E-value=2e-34  Score=220.85  Aligned_cols=111  Identities=18%  Similarity=0.213  Sum_probs=89.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCcccccccccccccc-c
Q psy5308          13 QTNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTK-F   91 (137)
Q Consensus        13 ~~~~~~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk-f   91 (137)
                      +.+|+++||||||||+||++|++||+||++++++|++||++|+++|++++..    ++.....+.+.+++|++|++++ |
T Consensus         5 ~~~m~~~~dLs~LteeEr~~Il~VL~Rd~~l~~~EeeRi~kLk~~l~~~~~k----~~~~~~~~~~~~~~C~~C~~~fg~   80 (153)
T 2zet_C            5 SSGMGKRLDLSTLTDEEAEHVWAVVQRDFDLRRREEERLQGLKGKIQKESSK----RELLSDTAHLNETHCARCLQPYRL   80 (153)
T ss_dssp             ------CCCCTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHTTSTTGGGTBCTTTCCBGGG
T ss_pred             CCCCccCCCcccCCHHHHHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHHHHH----hhhhcccccCCCccchhhcCcccc
Confidence            4567799999999999999999999999999999999999999999988531    1111112344589999999995 9


Q ss_pred             cCCCCCCCccccccccccCCceeecCCCCcceEEeeecc
Q psy5308          92 ADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGH  130 (137)
Q Consensus        92 ~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~  130 (137)
                      ++++|++|.||+++||++||++  +++ ..+|+|+||..
T Consensus        81 l~~~g~~C~~C~~~VC~~C~~~--~~~-~~~W~C~vC~k  116 (153)
T 2zet_C           81 LLNSRRQCLECSLFVCKSCSHA--HPE-EQGWLCDPCHL  116 (153)
T ss_dssp             CSSCCEECTTTCCEECGGGEEC--CSS-SSSCEEHHHHH
T ss_pred             ccCCCCcCCCCCchhhcccccc--cCC-CCcEeeHHHHH
Confidence            9999999999999999999965  454 56999999754

>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: g.50.1.1

Probab=100.00  E-value=5.7e-35  Score=219.57  Aligned_cols=103  Identities=21%  Similarity=0.363  Sum_probs=89.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCcccccccccccccc-ccCCCC
Q psy5308          18 IIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTK-FADGVG   96 (137)
Q Consensus        18 ~~~dLS~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk-f~~g~G   96 (137)
                      ..+|||||||+||++|++||+||++++++|++||++|+++|+++++++         .| +.+++|+||++++ |++++|
T Consensus         3 ~~~dls~LteeE~~~Il~Vl~Rd~~l~~~E~~ri~kL~~~l~~~k~~~---------~~-~~~~~C~~C~~~~g~l~~~g   72 (134)
T 1zbd_B            3 HMRKQEELTDEEKEIINRVIARAEKMETMEQERIGRLVDRLETMRKNV---------AG-DGVNRCILCGEQLGMLGSAS   72 (134)
T ss_dssp             -----CCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC---------CS-CSSSBCSSSCCBCSTTSCCE
T ss_pred             CCCCcccCCHHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHHHHHHHh---------cc-CCCccccccCCCcccccCCC
Confidence            469999999999999999999999999999999999999999998642         33 3479999999999 999999


Q ss_pred             CCCccccccccccCCceeecCCCCcceEEeeecc
Q psy5308          97 HMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGH  130 (137)
Q Consensus        97 ~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~  130 (137)
                      ++|.||+++||++||++++.+++.++|+|+||..
T Consensus        73 ~~C~~C~~~VC~~C~~~~~~~~~~~~W~C~vC~k  106 (134)
T 1zbd_B           73 VVCEDCKKNVCTKCGVETSNNRPHPVWLCKICLE  106 (134)
T ss_dssp             EECTTTCCEEETTSEEECCCSSSSCCEEEHHHHH
T ss_pred             CCCCCCCcccccccCCccCCCCCccceechhhHH
Confidence            9999999999999999986666778999999764

>2a20_A Regulating synaptic membrane exocytosis protein 2; zinc-finger domain, metal binding protein; NMR {Rattus norvegicus} PDB: 2cjs_C

Probab=99.84  E-value=2.2e-22  Score=133.31  Aligned_cols=51  Identities=57%  Similarity=1.033  Sum_probs=49.1

Q ss_pred             ccccccccccccccCCCCCCCccccccccccCCceeecCCCCcceEEeeec
Q psy5308          79 LDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRG  129 (137)
Q Consensus        79 ~~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~  129 (137)
                      +.++|.||+||||+||.||.|.||+.++|+|||+++++++|+++|+|++|-
T Consensus         8 d~~~C~iC~KTKFADG~Gh~C~yCk~r~CaRCGg~v~lr~~k~~WvC~lC~   58 (62)
T 2a20_A            8 DAPTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKVMWVCNLCR   58 (62)
T ss_dssp             CCCCCSSSSCSCCCSSCCEEBTTTCCEECTTSEEEEESSTTCEEEEEHHHH
T ss_pred             CcchhhhhccceeccCCCccccccCCeeecccCCEeeecCCeEEEEehhhh
Confidence            469999999999999999999999999999999999999999999999985

>2csz_A Synaptotagmin-like protein 4; exophilin 2, granuphilin, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=1.9e-18  Score=119.34  Aligned_cols=69  Identities=16%  Similarity=0.231  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHHHHhHHHHhhhCcccccccccccccc-ccCCCCCCCccccccccccCCceeecCCCCcceEEeeeccC
Q psy5308          54 KQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTK-FADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHN  131 (137)
Q Consensus        54 L~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk-f~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~  131 (137)
                      +++||++|++     ++..+..+.+.+++|++|++.+ |++++|++|.+|+++||++|+++.   ++ ..|+|+||.+.
T Consensus         4 ~~~eL~elrr-----kgak~~s~~~~~r~CarC~~~LG~l~~~g~~C~~Ck~rVC~~Crv~~---~~-~~W~C~VC~k~   73 (76)
T 2csz_A            4 GSSGLLEIKR-----KGAKRGSQHYSDRTCARCQESLGRLSPKTNTCRGCNHLVCRDCRIQE---SN-GTWRCKVCSGP   73 (76)
T ss_dssp             CCCCCCCCCC-----CCSCSCCTTCCCCBCSSSCCBCSSSCTTTSEETTTTEECCTTSEEEC---ST-TCEEEHHHHSS
T ss_pred             hHHHHHHHHH-----ccccCcCcCCCccchhhhCccccccccCCCcCcccChhhcccccccC---CC-CCEEEeeCchh
Confidence            5678888873     4555445567799999999998 888999999999999999999773   23 48999998765

>3bc1_B Synaptotagmin-like protein 2; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Homo sapiens}

Probab=99.10  E-value=2.4e-11  Score=80.16  Aligned_cols=41  Identities=22%  Similarity=0.250  Sum_probs=38.8

Q ss_pred             CCCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q psy5308          23 SHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQ   63 (137)
Q Consensus        23 S~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~   63 (137)
                      ++|||+|+++||+||+||.++++.|++||++|++.|+++++
T Consensus         1 ~~l~e~E~~~IL~VL~RD~~lr~~ee~RIrkLk~~l~~~~~   41 (59)
T 3bc1_B            1 GSPEFEEQEAIMKVLQRDAALKRAEEERVRHLPEKIKDDQQ   41 (59)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGTCCCHHH
T ss_pred             CCCCHHHHHHHHHHHhhHHHHhhChHHHHHHHHHHhccHHH
Confidence            47899999999999999999999999999999999998875

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A

Probab=96.87  E-value=0.0046  Score=44.97  Aligned_cols=50  Identities=26%  Similarity=0.329  Sum_probs=38.2

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCceeecC--CCCcceEEeeec
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLR--SNKVSVEVTTRG  129 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr--~n~~~W~Ctvc~  129 (137)
                      ...|.+|++.+-.+.+-|.|..|-.-||+.|-.....-  .+++.-+|..|-
T Consensus        69 ~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~~~~~p~~~~p~RVC~~C~  120 (125)
T 1joc_A           69 VQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKNALTPSSKKPVRVCDACF  120 (125)
T ss_dssp             CCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEECCTTCSSCEEECHHHH
T ss_pred             CCCCcCcCCccccccccccCCCCCeEEChHHhCCccccCCCCCCCEeCHHHH
Confidence            56899999775445799999999999999998664222  234678888764

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=92.68  E-value=0.054  Score=36.34  Aligned_cols=51  Identities=20%  Similarity=0.306  Sum_probs=37.8

Q ss_pred             ccccccccccccccCCCCCCCccccccccccCCceee-c-CCCCcceEEeeec
Q psy5308          79 LDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVT-L-RSNKVSVEVTTRG  129 (137)
Q Consensus        79 ~~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~-l-r~n~~~W~Ctvc~  129 (137)
                      ....|..|++.+-++.+-|.|..|-.-||+.|-.... + ..+++.-+|..|-
T Consensus        18 ~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C~   70 (82)
T 2yw8_A           18 EATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELALPSYPKPVRVCDSCH   70 (82)
T ss_dssp             CCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCEEECCTTCSSCEEECHHHH
T ss_pred             cCCcccCcCCcccCccccccCCCCCCEEChHHhCCeeecCCCCCcCEECHHHH
Confidence            3578999997754457999999999999999976531 1 1234677887764

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=91.23  E-value=0.066  Score=36.64  Aligned_cols=53  Identities=13%  Similarity=0.159  Sum_probs=38.1

Q ss_pred             ccccccccccccccccCCCCCCCccccccccccCCcee-ecCC--CCcceEEeeec
Q psy5308          77 VELDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKV-TLRS--NKVSVEVTTRG  129 (137)
Q Consensus        77 ~~~~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v-~lr~--n~~~W~Ctvc~  129 (137)
                      ......|..|++.+-.+.+-|.|..|-.-||+.|-... .+..  +.+.-+|..|-
T Consensus         6 ~~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~   61 (88)
T 1wfk_A            6 SGMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCH   61 (88)
T ss_dssp             CCCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHH
T ss_pred             CCcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHH
Confidence            33467899999765455799999999999999997652 2221  23567777764

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=90.11  E-value=0.17  Score=33.87  Aligned_cols=34  Identities=24%  Similarity=0.424  Sum_probs=28.9

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCce
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGK  113 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~  113 (137)
                      ...|..|++.+-++.+-|.|..|-.-||+.|-..
T Consensus        14 ~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   47 (84)
T 1x4u_A           14 FGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSF   47 (84)
T ss_dssp             CSSCSSSCCCCCSSSCCEECSSSCCEECTTTSCE
T ss_pred             CCcCcCcCCccccchhhhhhcCCCcEEChhhcCC
Confidence            5789999977544579999999999999999764

>3zyq_A Hepatocyte growth factor-regulated tyrosine kinas substrate; signaling; 1.48A {Homo sapiens} PDB: 4avx_A*

Probab=89.32  E-value=0.08  Score=41.50  Aligned_cols=50  Identities=22%  Similarity=0.339  Sum_probs=37.1

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCcee-ecC---CCCcceEEeeec
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKV-TLR---SNKVSVEVTTRG  129 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v-~lr---~n~~~W~Ctvc~  129 (137)
                      +..|..|++.+-.+.+-|.|..|-.-||+.|-... .+.   .+.+.-+|..|-
T Consensus       164 ~~~C~~C~~~F~~~~RrhHCR~CG~v~C~~Cs~~~~~~p~~~~~~~~RVC~~C~  217 (226)
T 3zyq_A          164 AEECHRCRVQFGVMTRKHHCRACGQIFCGKCSSKYSTIPKFGIEKEVRVCEPCY  217 (226)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECTTTCCEEEEEGGGTEEEEEEECHHHH
T ss_pred             CCCCcCcCCCCCccccccccCCCcCEeChhhcCCcccCCCCCCCCCCEeCHHHH
Confidence            46899999765445799999999999999998653 221   124677888764

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=88.67  E-value=0.18  Score=33.90  Aligned_cols=50  Identities=14%  Similarity=0.252  Sum_probs=36.6

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCcee-ecCC---CCcceEEeeec
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKV-TLRS---NKVSVEVTTRG  129 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v-~lr~---n~~~W~Ctvc~  129 (137)
                      ...|..|++.+-.+.+-|.|..|-.-||+.|-... .+..   +++.-+|..|-
T Consensus        21 ~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~lp~~~~~~~~RVC~~C~   74 (84)
T 1z2q_A           21 APACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHRAAIPMRGITEPERVCDACY   74 (84)
T ss_dssp             CCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCEEEETTTTEEEEEECCHHHH
T ss_pred             CCCCcCcCCccccchhcccccCCCcEEChHHhCCeEeccCCCCCCCCEECHHHH
Confidence            57899999876445799999999999999997553 2221   23566777754

>1dvp_A HRS, hepatocyte growth factor-regulated tyrosine kinase substrate; VHS, FYVE, zinc finger, superhelix, transferase; HET: CIT; 2.00A {Drosophila melanogaster} SCOP: a.118.9.2 g.50.1.1

Probab=88.17  E-value=0.12  Score=40.05  Aligned_cols=50  Identities=22%  Similarity=0.332  Sum_probs=36.8

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCceee-cC---CCCcceEEeeec
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVT-LR---SNKVSVEVTTRG  129 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~-lr---~n~~~W~Ctvc~  129 (137)
                      ...|..|++.+-.+.+-|.|..|-.-||+.|-.... +.   .+++.-+|..|-
T Consensus       161 ~~~C~~C~~~F~~~~rrhhCr~CG~v~C~~Cs~~~~~~~~~~~~~~~RvC~~C~  214 (220)
T 1dvp_A          161 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQCPLPKYGIEKEVRVCDGCF  214 (220)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEEEEEGGGTEEEEEEECHHHH
T ss_pred             CCccCCCCCccCCcccccccCCcCCEEChHHhCCeeecCcCCCCCCCEeCHHHH
Confidence            478999997654457999999999999999976532 11   123566787763

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=88.16  E-value=0.19  Score=34.32  Aligned_cols=49  Identities=18%  Similarity=0.318  Sum_probs=36.2

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCceee-cC-CCCcceEEeee
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVT-LR-SNKVSVEVTTR  128 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~-lr-~n~~~W~Ctvc  128 (137)
                      ...|.+|++....+.+-|.|..|-.-||..|-.... +. .+++.-+|..|
T Consensus        20 ~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C   70 (90)
T 3t7l_A           20 APNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVC   70 (90)
T ss_dssp             CCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEEEETTTTEEEEECHHH
T ss_pred             CCcCcCCCCcccchhhCccccCCCCEECCcccCCeeecCCCCCCCeECHHH
Confidence            467999997765557999999999999999976642 11 12356677765

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=87.80  E-value=0.43  Score=28.99  Aligned_cols=27  Identities=19%  Similarity=0.312  Sum_probs=16.2

Q ss_pred             cccccccccccccCCCCCCCccccccccccC
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARC  110 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rC  110 (137)
                      ..+|.||... |.+..   =-.|.|.||..|
T Consensus         6 ~~~C~IC~~~-~~~p~---~l~CgH~fC~~C   32 (56)
T 1bor_A            6 FLRCQQCQAE-AKCPK---LLPCLHTLCSGC   32 (56)
T ss_dssp             CSSCSSSCSS-CBCCS---CSTTSCCSBTTT
T ss_pred             CCCceEeCCc-cCCeE---EcCCCCcccHHH
Confidence            5789999854 33321   123566666666

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1

Probab=87.49  E-value=0.19  Score=32.89  Aligned_cols=50  Identities=18%  Similarity=0.234  Sum_probs=36.7

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCcee-ecCC---CCcceEEeeec
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKV-TLRS---NKVSVEVTTRG  129 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v-~lr~---n~~~W~Ctvc~  129 (137)
                      +..|..|++.+-.+.+-|.|..|-.-||+.|-... .+..   ..+.-+|..|-
T Consensus        11 ~~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~~~~lp~~~~~~~~RVC~~C~   64 (73)
T 1vfy_A           11 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNSIPLPDLGIYEPVRVCDSCF   64 (73)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEEEEEGGGTEEEEEEECHHHH
T ss_pred             CCcccCCCCccCCccccccCCCCCEEEcccccCCeEEcccCCCCCCCEECHHHH
Confidence            36899999775455799999999999999997542 2221   23567787764

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=86.80  E-value=0.21  Score=29.51  Aligned_cols=47  Identities=15%  Similarity=0.173  Sum_probs=28.9

Q ss_pred             ccccccccccccccCCCCCCCccccccccccCCceeecCCCCcceEEeeec
Q psy5308          79 LDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRG  129 (137)
Q Consensus        79 ~~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~  129 (137)
                      .+..|.||.......+....-..|.|.||..|-......    ...|.+|-
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~----~~~CP~Cr   50 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKE----GYRCPLCS   50 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHH----TCCCTTSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHc----CCcCCCCC
Confidence            467899999664332333455668999999995443211    14566654

>2vrw_B P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP-binding, metal-binding, phosphoprotein, exchange factor, RAC, GTPase, membrane domain; 1.85A {Mus musculus} PDB: 3bji_A 1f5x_A

Probab=86.53  E-value=0.15  Score=41.99  Aligned_cols=35  Identities=23%  Similarity=0.439  Sum_probs=29.7

Q ss_pred             cccccccccccc-cCCCCCCCccccccccccCCcee
Q psy5308          80 DATCHICLKTKF-ADGVGHMCNYCNIRCCARCGGKV  114 (137)
Q Consensus        80 ~~~C~~C~ktkf-~~g~G~~C~~C~~rvC~rCg~~v  114 (137)
                      ...|..|++... ....|+.|..|...||.+|...|
T Consensus       357 ~t~C~~C~~~~~g~~~qg~~C~~C~~~~h~~C~~~~  392 (406)
T 2vrw_B          357 TTSCKACQMLLRGTFYQGYRCYRCRAPAHKECLGRV  392 (406)
T ss_dssp             CCBCTTTCCBCCSSSSCEEEETTTCCEECGGGGGGS
T ss_pred             CCCCccccchhceeCCCCCCCCCCcCccchhhhhhC
Confidence            578999997763 45699999999999999997664

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=85.38  E-value=0.15  Score=37.08  Aligned_cols=46  Identities=15%  Similarity=0.319  Sum_probs=32.8

Q ss_pred             ccccccccccccccCCCCCCCccccccccccCCceeecCCCCcceEEeee
Q psy5308          79 LDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTR  128 (137)
Q Consensus        79 ~~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc  128 (137)
                      ....|..|+...-.+.+-|.|..|-.-||+.|-..   +. .+.-+|..|
T Consensus        18 ~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~---~~-~~vRVC~~C   63 (120)
T 1y02_A           18 LEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQ---VG-NGPRLCLLC   63 (120)
T ss_dssp             --CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC--------CCEEHHH
T ss_pred             ccCcccCcCCccccccccccCCCCCCeeCHHHhCC---CC-CCceECHHH
Confidence            35789999966433569999999999999999644   22 236788886

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=83.63  E-value=0.23  Score=30.89  Aligned_cols=29  Identities=21%  Similarity=0.367  Sum_probs=18.7

Q ss_pred             cccccccCCceeecCCCCcceEEeeeccC
Q psy5308         103 NIRCCARCGGKVTLRSNKVSVEVTTRGHN  131 (137)
Q Consensus       103 ~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~  131 (137)
                      ..++|.+||..+...++...|.|.-|++.
T Consensus        18 ~~k~CP~CG~~~fm~~~~~R~~C~kCG~t   46 (50)
T 3j20_Y           18 KNKFCPRCGPGVFMADHGDRWACGKCGYT   46 (50)
T ss_dssp             SSEECSSSCSSCEEEECSSEEECSSSCCE
T ss_pred             ecccCCCCCCceEEecCCCeEECCCCCCE
Confidence            45777777764444455567777777654

>3j21_g 50S ribosomal protein L40E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=83.24  E-value=0.29  Score=30.87  Aligned_cols=27  Identities=19%  Similarity=0.320  Sum_probs=20.2

Q ss_pred             ccccccccCCceeecCCCCcceEEeeeccCC
Q psy5308         102 CNIRCCARCGGKVTLRSNKVSVEVTTRGHNN  132 (137)
Q Consensus       102 C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~~  132 (137)
                      .+..+|.+|+.++  . .+ +|.|.-|+|-+
T Consensus        12 ~~k~iCpkC~a~~--~-~g-aw~CrKCG~~~   38 (51)
T 3j21_g           12 FKKYVCLRCGATN--P-WG-AKKCRKCGYKR   38 (51)
T ss_dssp             SSEEECTTTCCEE--C-TT-CSSCSSSSSCC
T ss_pred             hCCccCCCCCCcC--C-CC-ceecCCCCCcc
Confidence            3568899998774  3 23 89999998874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	137
d1zbdb_	124	g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat	7e-14

>d1zbdb_ g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 124

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Effector domain of rabphilin-3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 61.7 bits (149), Expect = 7e-14
 Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 11/97 (11%)

Query: 25  LTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCH 84
           LT EE++II  V+ R ++ E  E E + R  D +  + +++      +          C 
Sbjct: 3   LTDEEKEIINRVIARAEKMETMEQERIGRLVDRLETMRKNVAGDGVNR----------CI 52

Query: 85  ICLKT-KFADGVGHMCNYCNIRCCARCGGKVTLRSNK 120
           +C +          +C  C    C +CG + +     
Sbjct: 53  LCGEQLGMLGSASVVCEDCKKNVCTKCGVETSNNRPH 89

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	137
d1zbdb_	124	Effector domain of rabphilin-3a {Rat (Rattus norve	99.87
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	95.92
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	88.88
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	88.81
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	88.43
d1wfka_	88	Zinc finger FYVE domain containing protein 19 {Mou	87.49
d1pd0a5	85	Sec24 {Baker's yeast (Saccharomyces cerevisiae) [T	87.13
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	86.81
d1twfl_	46	RBP12 subunit of RNA polymerase II {Baker's yeast	81.05
d1nnqa2	37	Rubrerythrin, C-terminal domain {Archaeon Pyrococc	80.47
d1yuza2	36	Nigerythrin, C-terminal domain {Desulfovibrio vulg	80.05

>d1zbdb_ g.50.1.1 (B:) Effector domain of rabphilin-3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Effector domain of rabphilin-3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.87  E-value=4.7e-23  Score=149.67  Aligned_cols=97  Identities=21%  Similarity=0.351  Sum_probs=84.3

Q ss_pred             CCCHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhCcccccccccccccc-ccCCCCCCCccc
Q psy5308          24 HLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTK-FADGVGHMCNYC  102 (137)
Q Consensus        24 ~LteeEr~~Il~VL~R~~~le~~E~~RirkL~~el~~lk~~~~~~~~~~r~~G~~~~~~C~~C~ktk-f~~g~G~~C~~C  102 (137)
                      .||+||+++|++||+||+++++.|.+|+++|+++|.++++.+          ...+...|.+|++++ |+++.+|.|.+|
T Consensus         2 ~LT~eE~~~i~~VL~r~~~l~~~E~~rl~~l~~~l~~~~~~~----------~~~~~~~C~~C~~~f~~~~~~~~~C~~C   71 (124)
T d1zbdb_           2 ELTDEEKEIINRVIARAEKMETMEQERIGRLVDRLETMRKNV----------AGDGVNRCILCGEQLGMLGSASVVCEDC   71 (124)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC----------CSCSSSBCSSSCCBCSTTSCCEEECTTT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----------hccCCCcCcccCCcccCCCCCCCcCccC
Confidence            589999999999999999999999999999999999987532          222368899999886 667899999999


Q ss_pred             cccccccCCceeecCCCCcceEEeeecc
Q psy5308         103 NIRCCARCGGKVTLRSNKVSVEVTTRGH  130 (137)
Q Consensus       103 ~~rvC~rCg~~v~lr~n~~~W~Ctvc~~  130 (137)
                      .+.||++|++..+..+++++|+|.+|..
T Consensus        72 ~~~~C~~C~~~~~~~~~~~~w~C~~C~k   99 (124)
T d1zbdb_          72 KKNVCTKCGVETSNNRPHPVWLCKICLE   99 (124)
T ss_dssp             CCEEETTSEEECCCSSSSCCEEEHHHHH
T ss_pred             CcccccCCCCCccCCCCCCCEECccCcc
Confidence            9999999998876566678999999865

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.92  E-value=0.00054  Score=41.67  Aligned_cols=45  Identities=13%  Similarity=0.269  Sum_probs=33.4

Q ss_pred             ccccccccccccCCCCCCCccccccccccCCceeecCCCCcceEEeeec
Q psy5308          81 ATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRG  129 (137)
Q Consensus        81 ~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~  129 (137)
                      +.|..|.+.+-.+.+-|.|..|-..||+.|...   . ++..|+|.+|-
T Consensus         1 p~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~---~-~~~~RvC~~C~   45 (51)
T d1y02a2           1 PSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQ---V-GNGPRLCLLCQ   45 (51)
T ss_dssp             CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC--------CCEEHHHH
T ss_pred             CCccccCCcccCCccCcccccCCcccCccccCC---C-CCCCeECHhHh
Confidence            469999976544568899999999999999644   3 24579999863

>d1dvpa2 g.50.1.1 (A:149-220) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=88.88  E-value=0.076  Score=33.47  Aligned_cols=34  Identities=26%  Similarity=0.603  Sum_probs=28.6

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCce
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGK  113 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~  113 (137)
                      +..|..|++...++.+-|.|..|-..||+.|-..
T Consensus        13 ~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~   46 (72)
T d1dvpa2          13 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAK   46 (72)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCE
T ss_pred             CCccccCCCcccCccccccccccCCeeChhhhCC
Confidence            4679999977655579999999999999999744

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.81  E-value=0.077  Score=32.60  Aligned_cols=35  Identities=29%  Similarity=0.497  Sum_probs=29.1

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCcee
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKV  114 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v  114 (137)
                      ...|.+|++.+-++.+-|.|..|-.-||+.|...-
T Consensus         8 ~~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~~~   42 (64)
T d1joca1           8 VQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN   42 (64)
T ss_dssp             CCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             CCcCcCcCCcccCCccccchhhhCCeecccccCCc
Confidence            57899999775444688999999999999998754

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: vps27p protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.43  E-value=0.075  Score=32.95  Aligned_cols=34  Identities=24%  Similarity=0.441  Sum_probs=28.2

Q ss_pred             cccccccccccccCCCCCCCccccccccccCCce
Q psy5308          80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGK  113 (137)
Q Consensus        80 ~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~  113 (137)
                      +..|.+|++.+-++.+-|.|..|-..||..|...
T Consensus         5 ~~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~   38 (67)
T d1vfya_           5 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSN   38 (67)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCE
T ss_pred             CcccccCCCcccCcccccccccCCCEecccccCC
Confidence            3579999977545578999999999999999644

>d1wfka_ g.50.1.1 (A:) Zinc finger FYVE domain containing protein 19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Zinc finger FYVE domain containing protein 19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.49  E-value=0.096  Score=34.28  Aligned_cols=50  Identities=14%  Similarity=0.189  Sum_probs=36.4

Q ss_pred             ccccccccccccccCCCCCCCccccccccccCCcee-ecCC--CCcceEEeee
Q psy5308          79 LDATCHICLKTKFADGVGHMCNYCNIRCCARCGGKV-TLRS--NKVSVEVTTR  128 (137)
Q Consensus        79 ~~~~C~~C~ktkf~~g~G~~C~~C~~rvC~rCg~~v-~lr~--n~~~W~Ctvc  128 (137)
                      .+..|.+|++.+-++.+-|.|..|-.-||..|.... .+..  +.++=+|..|
T Consensus         8 ~~s~C~~C~~~Fs~~~rrhhCr~CG~vfC~~Cs~~~~~lp~~~~~~~RVC~~C   60 (88)
T d1wfka_           8 MESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQC   60 (88)
T ss_dssp             CCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHH
T ss_pred             ccCcCcccCchhccccccccccccChhhChHHhCCccccCCCCCCCCeECHHH
Confidence            468899999776556789999999999999997643 2221  2234567665

>d1pd0a5 g.41.10.1 (A:216-300) Sec24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-finger domain of Sec23/24
family: Zn-finger domain of Sec23/24
domain: Sec24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.13  E-value=0.061  Score=34.91  Aligned_cols=13  Identities=8%  Similarity=-0.222  Sum_probs=10.4

Q ss_pred             CcceEEeeeccCC
Q psy5308         120 KVSVEVTTRGHNN  132 (137)
Q Consensus       120 ~~~W~Ctvc~~~~  132 (137)
                      +..|+|.+|.+.|
T Consensus        33 g~~w~C~~C~~~N   45 (85)
T d1pd0a5          33 GRRWRCNFCRLAN   45 (85)
T ss_dssp             TTEEECTTTCCEE
T ss_pred             CCEEECCCCCccc
Confidence            3579999998766

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=86.81  E-value=0.024  Score=34.05  Aligned_cols=52  Identities=15%  Similarity=0.077  Sum_probs=34.2

Q ss_pred             cccccccccccccccCC--CCCCCccccccccccCCceeecCCCCcceEEeeeccCC
Q psy5308          78 ELDATCHICLKTKFADG--VGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRGHNN  132 (137)
Q Consensus        78 ~~~~~C~~C~ktkf~~g--~G~~C~~C~~rvC~rCg~~v~lr~n~~~W~Ctvc~~~~  132 (137)
                      +...+|.||..+. .+.  ..-.|.+|.|.|+..|=......+  ..+.|.+|-...
T Consensus         4 ed~~~C~IC~~~~-~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~--~~~~CP~Cr~~~   57 (60)
T d1vyxa_           4 EDVPVCWICNEEL-GNERFRACGCTGELENVHRSCLSTWLTIS--RNTACQICGVVY   57 (60)
T ss_dssp             CSCCEETTTTEEC-SCCCCCSCCCSSGGGSCCHHHHHHHHHHH--TCSBCTTTCCBC
T ss_pred             CCCCCCccCCccC-CCceeEecccCCCCCEEcHHHHHHHHhhC--CCCCCcccCCee
Confidence            3468999999763 222  333678999999999965542222  236788876544

>d1twfl_ g.41.9.2 (L:) RBP12 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: RNA polymerase subunits
family: RBP12 subunit of RNA polymerase II
domain: RBP12 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.05  E-value=0.2  Score=29.66  Aligned_cols=25  Identities=32%  Similarity=0.670  Sum_probs=19.0

Q ss_pred             cccccCCceeecCCCCcceEEeeecc
Q psy5308         105 RCCARCGGKVTLRSNKVSVEVTTRGH  130 (137)
Q Consensus       105 rvC~rCg~~v~lr~n~~~W~Ctvc~~  130 (137)
                      .+|..||..+++.++. .-.|+-|||
T Consensus         5 YiCgeCg~~~~l~~~d-~irCreCG~   29 (46)
T d1twfl_           5 YICAECSSKLSLSRTD-AVRCKDCGH   29 (46)
T ss_dssp             EECSSSCCEECCCTTS-TTCCSSSCC
T ss_pred             EEcccCCCceEeCCCC-cEEeccCCc
Confidence            5788888888877755 677888776

>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=80.47  E-value=0.15  Score=28.76  Aligned_cols=13  Identities=8%  Similarity=-0.171  Sum_probs=10.9

Q ss_pred             cceEEeeeccCCC
Q psy5308         121 VSVEVTTRGHNNN  133 (137)
Q Consensus       121 ~~W~Ctvc~~~~~  133 (137)
                      ..|+|.||||-+-
T Consensus         4 ~~~~C~vCG~i~~   16 (37)
T d1nnqa2           4 KVYICPICGYTAV   16 (37)
T ss_dssp             CEEECTTTCCEEE
T ss_pred             cEEECCCCCCEec
Confidence            5899999999754

>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=80.05  E-value=0.15  Score=28.69  Aligned_cols=14  Identities=14%  Similarity=-0.040  Sum_probs=10.6

Q ss_pred             cceEEeeeccCCCC
Q psy5308         121 VSVEVTTRGHNNNG  134 (137)
Q Consensus       121 ~~W~Ctvc~~~~~~  134 (137)
                      ..|+|.||||.+.|
T Consensus         4 ~~~vC~vCGyi~~g   17 (36)
T d1yuza2           4 KFHLCPICGYIHKG   17 (36)
T ss_dssp             CEEECSSSCCEEES
T ss_pred             CEEECCCCCCEeeC
Confidence            47999999887543