Psyllid ID: psy6150

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------15
Protein Sequence
MSTVHTWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERTLELLFCFTQ
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEEEEEccccccccccEEEEEEccccEEEEEEEEcccccccccccccccccEEEccEEccccccccccccEEEEcccccccccccEEEEEccccccccccccEEEEEEcccccEEEcccccEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccEEcccccccccEEEEccccEEEEEcccccccEEEEEEccccEHHHHHHHHHHccccccHHHHHcHHHHHHHHHccccccccccEEHHccccccccEEEEEEEccccccccccccHHHHHHHHcccccEcEccccccEEEEEEEcc
Coil and Loop (DISEMBL)
mstvhtwstpsldevnlccrgsvrfqstsidgvDHVWTQLTKKNAVYSRVARVcksdkggphhfgdrWTTFLKSrlncsvpgdypfyfdeirlpedcvnlqdpycawdlkLRKDcvnlqdpycawdlklrkcvpyqERTLELLFCFTQ
Flexible Loop (DISEMBL)
mstvhtwstpsldeVNLCCRGSVRFqstsidgvdHVWTQltkknavySRVARVCksdkggphhfgdRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERTLELLFCFTQ
Low Complexity Region (SEG)
MSTVHTWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERTLELLFCFTQ
Disordered region (IsUnstruct)
*********PSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERTLELLFCF**
Disordered Region (DISOPRED)
*STVHTWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERTLELLFCFTQ
Disordered Region (DISEMBL)
*********PSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERTLELLFCFTQ
Disordered Region (DISPRO)
******WSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERTLELLFCFTQ
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSTVHTWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERTLELLFCFTQ
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	148	2.2.26 [Sep-21-2011]
Q26473	730	Semaphorin-1A OS=Schistoc	N/A	N/A	0.364	0.073	0.796	2e-21
Q24322	850	Semaphorin-1A OS=Drosophi	yes	N/A	0.439	0.076	0.656	2e-19
Q26972	712	Semaphorin-1A OS=Triboliu	N/A	N/A	0.317	0.066	0.722	1e-18
Q9XZC8	697	Semaphorin-2A OS=Schistoc	N/A	N/A	0.324	0.068	0.645	2e-13
Q17330	712	Semaphorin-1A OS=Caenorha	yes	N/A	0.364	0.075	0.545	5e-13
Q24323	724	Semaphorin-2A OS=Drosophi	no	N/A	0.351	0.071	0.571	1e-12
Q9P283	1151	Semaphorin-5B OS=Homo sap	yes	N/A	0.344	0.044	0.6	9e-12
Q60519	1093	Semaphorin-5B OS=Mus musc	yes	N/A	0.344	0.046	0.6	9e-12
Q8NFY4	1073	Semaphorin-6D OS=Homo sap	no	N/A	0.385	0.053	0.551	2e-11
Q5R7F5	1017	Semaphorin-6D OS=Pongo ab	no	N/A	0.385	0.056	0.551	2e-11

>sp|Q26473|SEM1A_SCHAM Semaphorin-1A OS=Schistocerca americana GN=SEMA-1A PE=1 SV=1

 Score =  101 bits (251), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 43/54 (79%), Positives = 48/54 (88%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCV 98
           A+YSRVARVCK DKGGPH FGDRWT+FLKSRLNCSVPGDYPFYF+EI+   D +
Sbjct: 235 AIYSRVARVCKHDKGGPHQFGDRWTSFLKSRLNCSVPGDYPFYFNEIQSTSDII 288

Plays a role in growth cones guidance.
Schistocerca americana (taxid: 7009)

>sp|Q24322|SEM1A_DROME Semaphorin-1A OS=Drosophila melanogaster GN=Sema-1a PE=2 SV=2

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/67 (65%), Positives = 52/67 (77%), Gaps = 2/67 (2%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPY 104
           A+YSRVARVCK DKGGPH F +RWT+FLKSRLNCS+PGDYPFYF+EI+   + V  Q  Y
Sbjct: 230 AIYSRVARVCKWDKGGPHRFRNRWTSFLKSRLNCSIPGDYPFYFNEIQSASNLVEGQ--Y 287

Query: 105 CAWDLKL 111
            +   KL
Sbjct: 288 GSMSSKL 294

Plays a role in growth cones guidance.

Drosophila melanogaster (taxid: 7227)

>sp|Q26972|SEM1A_TRICF Semaphorin-1A OS=Tribolium confusum GN=SEMA-1A PE=2 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 39/54 (72%), Positives = 45/54 (83%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCV 98
            +YSRVARVCK DKGGPH   DRWT+FLK+RLNCS+PG+YPFYFDEI+   D V
Sbjct: 233 VIYSRVARVCKDDKGGPHQSRDRWTSFLKARLNCSIPGEYPFYFDEIQSTSDIV 286

Plays a role in growth cones guidance.

Tribolium confusum (taxid: 7071)

>sp|Q9XZC8|SEM2A_SCHGR Semaphorin-2A OS=Schistocerca gregaria GN=SEMA-2A PE=2 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 31/48 (64%), Positives = 39/48 (81%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
           +VYSRVARVCK D GG +     W TFLK+RLNCS+PG++PFYF+EI+
Sbjct: 251 SVYSRVARVCKKDVGGKNILSQNWATFLKARLNCSIPGEFPFYFNEIQ 298

Acts as chemorepulsive guidance molecule critical for axon fasciculation and for determining both the initial direction and subsequent pathfinding events of the Ti axon projection.

Schistocerca gregaria (taxid: 7010)

>sp|Q17330|SEM1A_CAEEL Semaphorin-1A OS=Caenorhabditis elegans GN=smp-1 PE=2 SV=2

 Score = 73.2 bits (178), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 30/55 (54%), Positives = 43/55 (78%), Gaps = 1/55 (1%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVP-GDYPFYFDEIRLPEDCVN 99
           +Y+RVARVCK+DKGG     +RWT++LK+RLNCS+P G  PFYF+E++   D ++
Sbjct: 254 IYARVARVCKNDKGGARPANERWTSYLKARLNCSLPSGSSPFYFNELKAVSDPID 308

May function in growth cone guidance.

Caenorhabditis elegans (taxid: 6239)

>sp|Q24323|SEM2A_DROME Semaphorin-2A OS=Drosophila melanogaster GN=Sema-2a PE=1 SV=2

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/56 (57%), Positives = 41/56 (73%), Gaps = 4/56 (7%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEI----RLPED 96
           AVYSR+ARVCK D GG +     W T+LK+RLNCS+ G++PFYF+EI    +LP D
Sbjct: 282 AVYSRIARVCKKDVGGKNLLAHNWATYLKARLNCSISGEFPFYFNEIQSVYQLPSD 337

Plays a role in growth cones guidance. Required for both proper adult behavior and survival. Can function in vivo as a selective target-derived signal that inhibits the formation of specific synaptic terminal arbors.

Drosophila melanogaster (taxid: 7227)

>sp|Q9P283|SEM5B_HUMAN Semaphorin-5B OS=Homo sapiens GN=SEMA5B PE=2 SV=4

 Score = 69.3 bits (168), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 41/55 (74%), Gaps = 4/55 (7%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR----LPED 96
           VYSRVARVCK+D GG     D WTTF+K+RLNCS PG+ PFY++E++    LPE 
Sbjct: 314 VYSRVARVCKNDVGGRFLLEDTWTTFMKARLNCSRPGEVPFYYNELQSAFHLPEQ 368

May act as positive axonal guidance cues.

Homo sapiens (taxid: 9606)

>sp|Q60519|SEM5B_MOUSE Semaphorin-5B OS=Mus musculus GN=Sema5b PE=2 SV=2

 Score = 68.9 bits (167), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 41/55 (74%), Gaps = 4/55 (7%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR----LPED 96
           VYSRVARVCK+D GG     D WTTF+K+RLNCS PG+ PFY++E++    LPE 
Sbjct: 256 VYSRVARVCKNDVGGRFLLEDTWTTFMKARLNCSRPGEVPFYYNELQSAFHLPEQ 310

May act as positive axonal guidance cues.

Mus musculus (taxid: 10090)

>sp|Q8NFY4|SEM6D_HUMAN Semaphorin-6D OS=Homo sapiens GN=SEMA6D PE=2 SV=1

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 42/58 (72%), Gaps = 1/58 (1%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDR-WTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQ 101
           AVYSRVAR+CK+D GG     ++ WT+FLK+RLNCSVPGD  FYFD ++   D + + 
Sbjct: 250 AVYSRVARICKNDMGGSQRVLEKHWTSFLKARLNCSVPGDSFFYFDVLQSITDIIQIN 307

Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections.

Homo sapiens (taxid: 9606)

>sp|Q5R7F5|SEM6D_PONAB Semaphorin-6D OS=Pongo abelii GN=SEMA6D PE=2 SV=1

 Score = 68.2 bits (165), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 42/58 (72%), Gaps = 1/58 (1%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDR-WTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQ 101
           AVYSRVAR+CK+D GG     ++ WT+FLK+RLNCSVPGD  FYFD ++   D + + 
Sbjct: 250 AVYSRVARICKNDMGGSQRVLEKHWTSFLKARLNCSVPGDSFFYFDVLQSITDIIQIN 307

Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections.

Pongo abelii (taxid: 9601)

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	148
8134678	730	RecName: Full=Semaphorin-1A; AltName: Fu	0.364	0.073	0.796	1e-19
242005253	635	Semaphorin-1A precursor, putative [Pedic	0.344	0.080	0.830	3e-19
345482246	953	PREDICTED: semaphorin-1A-like [Nasonia v	0.364	0.056	0.796	4e-19
357622029	602	Semaphorin-1A [Danaus plexippus]	0.317	0.078	0.709	1e-18
380014169	775	PREDICTED: semaphorin-1A-like, partial [	0.351	0.067	0.75	3e-18
157133916	776	semaphorin [Aedes aegypti] gi|108881440|	0.371	0.070	0.690	4e-18
302393611	546	MIP14656p [Drosophila melanogaster]	0.385	0.104	0.719	4e-18
194760726	917	GF15536 [Drosophila ananassae] gi|190616	0.439	0.070	0.656	7e-18
312370919	899	hypothetical protein AND_22880 [Anophele	0.371	0.061	0.672	8e-18
442626901	1131	Sema-1a, isoform G [Drosophila melanogas	0.439	0.057	0.656	1e-17

>gi|8134678|sp|Q26473.1|SEM1A_SCHAM RecName: Full=Semaphorin-1A; AltName: Full=Fasciclin IV; AltName: Full=Fasciclin-4; AltName: Full=Semaphorin-I; Short=Sema I; Flags: Precursor gi|160845|gb|AAA29808.1| fasciclin IV [Schistocerca americana]

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/54 (79%), Positives = 48/54 (88%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCV 98
           A+YSRVARVCK DKGGPH FGDRWT+FLKSRLNCSVPGDYPFYF+EI+   D +
Sbjct: 235 AIYSRVARVCKHDKGGPHQFGDRWTSFLKSRLNCSVPGDYPFYFNEIQSTSDII 288

Source: Schistocerca americana

Species: Schistocerca americana

Genus: Schistocerca

Family: Acrididae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242005253|ref|XP_002423485.1| Semaphorin-1A precursor, putative [Pediculus humanus corporis] gi|212506580|gb|EEB10747.1| Semaphorin-1A precursor, putative [Pediculus humanus corporis]

 Score = 99.8 bits (247), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 44/53 (83%), Positives = 47/53 (88%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCV 98
           VYSRVARVCK DKGGPH FGDRWT+FLKSRLNCSVPGDYPFYFDEI+   + V
Sbjct: 164 VYSRVARVCKHDKGGPHQFGDRWTSFLKSRLNCSVPGDYPFYFDEIQSMSEMV 216

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345482246|ref|XP_001607258.2| PREDICTED: semaphorin-1A-like [Nasonia vitripennis]

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 43/54 (79%), Positives = 47/54 (87%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCV 98
           AVYSRVARVCK DKGGPH FGDRWT+FLK+RLNCSVPGDYPFYF+EI+   D  
Sbjct: 217 AVYSRVARVCKHDKGGPHAFGDRWTSFLKARLNCSVPGDYPFYFNEIQSTSDVT 270

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357622029|gb|EHJ73649.1| Semaphorin-1A [Danaus plexippus]

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 39/55 (70%), Positives = 48/55 (87%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVN 99
           +VYSRVARVC +DKGGPH F DRWT+FLK+RLNCS+PG+YPFYFDEI+   + +N
Sbjct: 84  SVYSRVARVCLNDKGGPHPFNDRWTSFLKARLNCSIPGEYPFYFDEIQATTEIIN 138

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380014169|ref|XP_003691112.1| PREDICTED: semaphorin-1A-like, partial [Apis florea]

 Score = 96.3 bits (238), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 39/52 (75%), Positives = 45/52 (86%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPED 96
           AVYSRV RVC+ DKGGPH F DRWT+FLK+RLNCSVPG+YPFYF+EI+   D
Sbjct: 65  AVYSRVGRVCQHDKGGPHAFNDRWTSFLKARLNCSVPGEYPFYFNEIQSTSD 116

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157133916|ref|XP_001663071.1| semaphorin [Aedes aegypti] gi|108881440|gb|EAT45665.1| AAEL003063-PA [Aedes aegypti]

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 38/55 (69%), Positives = 47/55 (85%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVN 99
           A+YSRV+RVCK+DKGGPH   DRWT+FLK+RLNCS+PG+YPFYFDEI+     +N
Sbjct: 235 AIYSRVSRVCKNDKGGPHPLNDRWTSFLKARLNCSIPGEYPFYFDEIQSTTKTIN 289

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|302393611|gb|ADL32751.1| MIP14656p [Drosophila melanogaster]

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 41/57 (71%), Positives = 48/57 (84%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQ 101
           A+YSRVARVCK DKGGPH F +RWT+FLKSRLNCS+PGDYPFYF+EI+   + V  Q
Sbjct: 140 AIYSRVARVCKWDKGGPHRFRNRWTSFLKSRLNCSIPGDYPFYFNEIQSASNLVEGQ 196

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194760726|ref|XP_001962588.1| GF15536 [Drosophila ananassae] gi|190616285|gb|EDV31809.1| GF15536 [Drosophila ananassae]

 Score = 95.5 bits (236), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 44/67 (65%), Positives = 54/67 (80%), Gaps = 2/67 (2%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPY 104
           A+YSRVARVCK DKGGPH F +RWT+FLKSRLNCS+PGDYPFYF+EI+   + V+ Q  Y
Sbjct: 296 AIYSRVARVCKWDKGGPHRFRNRWTSFLKSRLNCSIPGDYPFYFNEIQSASNLVDGQ--Y 353

Query: 105 CAWDLKL 111
            + + KL
Sbjct: 354 GSMNSKL 360

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312370919|gb|EFR19219.1| hypothetical protein AND_22880 [Anopheles darlingi]

 Score = 95.1 bits (235), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 37/55 (67%), Positives = 48/55 (87%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVN 99
           A+YSRVARVCK+DKGGP+ F DRWT++LK+RLNCS+PG+YPFYFDE++     +N
Sbjct: 352 AIYSRVARVCKNDKGGPYPFQDRWTSYLKARLNCSIPGEYPFYFDELQATTKTIN 406

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442626901|ref|NP_001260265.1| Sema-1a, isoform G [Drosophila melanogaster] gi|440213576|gb|AGB92801.1| Sema-1a, isoform G [Drosophila melanogaster]

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/67 (65%), Positives = 52/67 (77%), Gaps = 2/67 (2%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPY 104
           A+YSRVARVCK DKGGPH F +RWT+FLKSRLNCS+PGDYPFYF+EI+   + V  Q  Y
Sbjct: 279 AIYSRVARVCKWDKGGPHRFRNRWTSFLKSRLNCSIPGDYPFYFNEIQSASNLVEGQ--Y 336

Query: 105 CAWDLKL 111
            +   KL
Sbjct: 337 GSMSSKL 343

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	148
FB|FBgn0011259	850	Sema-1a "Sema-1a" [Drosophila	0.385	0.067	0.719	1.2e-23
FB|FBgn0016059	770	Sema-1b "Sema-1b" [Drosophila	0.324	0.062	0.75	1.5e-21
WB|WBGene00004889	712	smp-1 [Caenorhabditis elegans	0.364	0.075	0.545	1.6e-18
UNIPROTKB|Q13591	1074	SEMA5A "Semaphorin-5A" [Homo s	0.337	0.046	0.574	1.3e-17
FB|FBgn0250876	1093	Sema-5c "Semaphorin-5c" [Droso	0.317	0.043	0.666	1.6e-17
UNIPROTKB|F1PBV7	1073	SEMA5A "Uncharacterized protei	0.317	0.043	0.595	1.6e-17
UNIPROTKB|F1ML13	977	SEMA5A "Uncharacterized protei	0.337	0.051	0.574	2.1e-17
FB|FBgn0264273	785	Sema-2b "Semaphorin-2b" [Droso	0.398	0.075	0.491	3.7e-17
UNIPROTKB|F1NJN3	983	SEMA5A "Uncharacterized protei	0.337	0.050	0.574	4.4e-17
RGD|1308650	1074	Sema5a "sema domain, seven thr	0.337	0.046	0.574	5.5e-17

FB|FBgn0011259 Sema-1a "Sema-1a" [Drosophila melanogaster (taxid:7227)]

 Score = 231 (86.4 bits), Expect = 1.2e-23, Sum P(2) = 1.2e-23
 Identities = 41/57 (71%), Positives = 48/57 (84%)

Query:    45 AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQ 101
             A+YSRVARVCK DKGGPH F +RWT+FLKSRLNCS+PGDYPFYF+EI+   + V  Q
Sbjct:   230 AIYSRVARVCKWDKGGPHRFRNRWTSFLKSRLNCSIPGDYPFYFNEIQSASNLVEGQ 286

GO:0016021 "integral to membrane" evidence=ISS;NAS

GO:0007411 "axon guidance" evidence=ISS;IDA;IMP;NAS

GO:0005886 "plasma membrane" evidence=ISS;IDA

GO:0007416 "synapse assembly" evidence=IMP

GO:0030215 "semaphorin receptor binding" evidence=TAS

GO:0004872 "receptor activity" evidence=IEA

GO:0016199 "axon midline choice point recognition" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0008039 "synaptic target recognition" evidence=IMP

GO:0048813 "dendrite morphogenesis" evidence=IMP

GO:0031987 "locomotion involved in locomotory behavior" evidence=IMP

GO:0001964 "startle response" evidence=IMP

GO:0048854 "brain morphogenesis" evidence=IMP

GO:2000305 "semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance" evidence=IGI

GO:0045792 "negative regulation of cell size" evidence=IMP

FB|FBgn0016059 Sema-1b "Sema-1b" [Drosophila melanogaster (taxid:7227)]

 Score = 212 (79.7 bits), Expect = 1.5e-21, Sum P(2) = 1.5e-21
 Identities = 36/48 (75%), Positives = 44/48 (91%)

Query:    45 AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
             AVYSRVARVCK+D+GGP+  G  WT+FLK+RLNCSVPG++PFYFDEI+
Sbjct:   257 AVYSRVARVCKNDRGGPYSHGKSWTSFLKARLNCSVPGEFPFYFDEIQ 304

GO:0005886 "plasma membrane" evidence=ISS;NAS

GO:0007411 "axon guidance" evidence=ISS

GO:0001700 "embryonic development via the syncytial blastoderm" evidence=IEP

GO:0004872 "receptor activity" evidence=IEA

WB|WBGene00004889 smp-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 174 (66.3 bits), Expect = 1.6e-18, Sum P(2) = 1.6e-18
 Identities = 30/55 (54%), Positives = 43/55 (78%)

Query:    46 VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVP-GDYPFYFDEIRLPEDCVN 99
             +Y+RVARVCK+DKGG     +RWT++LK+RLNCS+P G  PFYF+E++   D ++
Sbjct:   254 IYARVARVCKNDKGGARPANERWTSYLKARLNCSLPSGSSPFYFNELKAVSDPID 308

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|Q13591 SEMA5A "Semaphorin-5A" [Homo sapiens (taxid:9606)]

 Score = 163 (62.4 bits), Expect = 1.3e-17, Sum P(2) = 1.3e-17
 Identities = 31/54 (57%), Positives = 40/54 (74%)

Query:    46 VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR----LPE 95
             V+SR ARVCK+D GG     D WTTF+K+RLNCS PG+ PFY++E++    LPE
Sbjct:   246 VFSRAARVCKNDIGGRFLLEDTWTTFMKARLNCSRPGEVPFYYNELQSTFFLPE 299

GO:0001569 "patterning of blood vessels" evidence=IEA

GO:0008046 "axon guidance receptor activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0007155 "cell adhesion" evidence=TAS

GO:0007267 "cell-cell signaling" evidence=TAS

GO:0007399 "nervous system development" evidence=TAS

GO:0005886 "plasma membrane" evidence=TAS

GO:0007411 "axon guidance" evidence=TAS

FB|FBgn0250876 Sema-5c "Semaphorin-5c" [Drosophila melanogaster (taxid:7227)]

 Score = 181 (68.8 bits), Expect = 1.6e-17, Sum P(2) = 1.6e-17
 Identities = 32/48 (66%), Positives = 40/48 (83%)

Query:    46 VYSRVARVCKSDKGGPHHF-GDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
             +YSRVARVCK+D GG      D WT+FLK+RLNCS+PG+YP+YFDEI+
Sbjct:   263 IYSRVARVCKNDVGGGGQLLRDNWTSFLKARLNCSLPGEYPYYFDEIQ 310

GO:0005886 "plasma membrane" evidence=ISS

GO:0007411 "axon guidance" evidence=ISS

GO:0001700 "embryonic development via the syncytial blastoderm" evidence=IEP

GO:0004872 "receptor activity" evidence=IEA

GO:0042048 "olfactory behavior" evidence=IMP

GO:0048036 "central complex development" evidence=IMP

GO:0048854 "brain morphogenesis" evidence=IMP

GO:0001964 "startle response" evidence=IMP

GO:0031987 "locomotion involved in locomotory behavior" evidence=IMP

UNIPROTKB|F1PBV7 SEMA5A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 162 (62.1 bits), Expect = 1.6e-17, Sum P(2) = 1.6e-17
 Identities = 28/47 (59%), Positives = 37/47 (78%)

Query:    46 VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
             V+SR ARVCK+D GG     D WTTF+K+RLNCS PG+ PFY++E++
Sbjct:   245 VFSRAARVCKNDIGGRFLLEDTWTTFMKARLNCSRPGEVPFYYNELQ 291

GO:0016021 "integral to membrane" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0004872 "receptor activity" evidence=IEA

UNIPROTKB|F1ML13 SEMA5A "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 161 (61.7 bits), Expect = 2.1e-17, Sum P(2) = 2.1e-17
 Identities = 31/54 (57%), Positives = 39/54 (72%)

Query:    46 VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR----LPE 95
             V+SR ARVCK+D GG     D WTTF+K+RLNCS PG+ PFY+ E++    LPE
Sbjct:   136 VFSRAARVCKNDIGGRFLLEDTWTTFMKARLNCSRPGEVPFYYHELQGTFFLPE 189

GO:0016021 "integral to membrane" evidence=IEA

GO:0008046 "axon guidance receptor activity" evidence=IEA

GO:0001569 "patterning of blood vessels" evidence=IEA

FB|FBgn0264273 Sema-2b "Semaphorin-2b" [Drosophila melanogaster (taxid:7227)]

 Score = 176 (67.0 bits), Expect = 3.7e-17, Sum P(2) = 3.7e-17
 Identities = 29/59 (49%), Positives = 42/59 (71%)

Query:    34 DHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
             +H    +    AVYSRVARVCK+D+GG +     W T+LK+R+NCS+  ++PFYF+EI+
Sbjct:   326 EHAVEYINCGKAVYSRVARVCKNDRGGKYMISQNWATYLKARMNCSISSEFPFYFNEIQ 384

GO:0007411 "axon guidance" evidence=ISS;NAS

GO:0005886 "plasma membrane" evidence=ISS

GO:0005576 "extracellular region" evidence=ISS

GO:2001020 "regulation of response to DNA damage stimulus" evidence=IGI

GO:0016200 "synaptic target attraction" evidence=IMP

GO:0070983 "dendrite guidance" evidence=IGI

UNIPROTKB|F1NJN3 SEMA5A "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 164 (62.8 bits), Expect = 4.4e-17, Sum P(2) = 4.4e-17
 Identities = 31/54 (57%), Positives = 40/54 (74%)

Query:    46 VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR----LPE 95
             V+SR ARVCK+D GG     D WTTF+K+RLNCS PG+ PFY++E++    LPE
Sbjct:   155 VFSRAARVCKNDIGGKFVLEDTWTTFMKARLNCSRPGEIPFYYNELQSTFFLPE 208

GO:0001569 "patterning of blood vessels" evidence=IEA

GO:0008046 "axon guidance receptor activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

RGD|1308650 Sema5a "sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A" [Rattus norvegicus (taxid:10116)]

 Score = 163 (62.4 bits), Expect = 5.5e-17, Sum P(2) = 5.5e-17
 Identities = 31/54 (57%), Positives = 40/54 (74%)

Query:    46 VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR----LPE 95
             V+SR ARVCK+D GG     D WTTF+K+RLNCS PG+ PFY++E++    LPE
Sbjct:   246 VFSRAARVCKNDIGGRFLLEDTWTTFMKARLNCSRPGEVPFYYNELQSTFFLPE 299

GO:0001569 "patterning of blood vessels" evidence=IEA;ISO

GO:0007165 "signal transduction" evidence=ISO

GO:0007411 "axon guidance" evidence=ISO

GO:0008046 "axon guidance receptor activity" evidence=IEA;ISO

GO:0016021 "integral to membrane" evidence=IEA;ISO

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=ISO

---

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)
Q24322	SEM1A_DROME	No assigned EC number	0.6567	0.4391	0.0764	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

ID	Length	Definition	E-value
Query	148
cd11237	446	cd11237, Sema_1A, The Sema domain, a protein inter	3e-32
cd11235	437	cd11235, Sema_semaphorin, The Sema domain, a prote	3e-25
cd11265	433	cd11265, Sema_5C, The Sema domain, a protein inter	5e-22
cd11238	452	cd11238, Sema_2A, The Sema domain, a protein inter	7e-21
cd11241	438	cd11241, Sema_5, The Sema domain, a protein intera	1e-20
smart00630	390	smart00630, Sema, semaphorin domain	3e-19
pfam01403	435	pfam01403, Sema, Sema domain	4e-18
cd11242	465	cd11242, Sema_6, The Sema domain, a protein intera	6e-17
cd11264	437	cd11264, Sema_5B, The Sema domain, a protein inter	1e-16
cd11267	466	cd11267, Sema_6B, The Sema domain, a protein inter	6e-16
cd11263	436	cd11263, Sema_5A, The Sema domain, a protein inter	1e-15
cd11269	465	cd11269, Sema_6D, The Sema domain, a protein inter	5e-15
cd11268	465	cd11268, Sema_6C, The Sema domain, a protein inter	5e-14
cd11239	471	cd11239, Sema_3, The Sema domain, a protein intera	7e-14
cd11270	462	cd11270, Sema_6E, The Sema domain, a protein inter	5e-13
cd11266	466	cd11266, Sema_6A, The Sema domain, a protein inter	5e-13
cd11253	471	cd11253, Sema_3E, The Sema domain, a protein inter	4e-12
cd11257	464	cd11257, Sema_4B, The Sema domain, a protein inter	6e-12
cd11252	474	cd11252, Sema_3D, The Sema domain, a protein inter	9e-12
cd11240	456	cd11240, Sema_4, The Sema domain, a protein intera	1e-11
cd11254	470	cd11254, Sema_3F, The Sema domain, a protein inter	2e-11
cd11256	447	cd11256, Sema_4A, The Sema domain, a protein inter	3e-11
cd11262	457	cd11262, Sema_4G, The Sema domain, a protein inter	4e-11
cd11258	458	cd11258, Sema_4C, The Sema domain, a protein inter	2e-10
cd11250	471	cd11250, Sema_3B, The Sema domain, a protein inter	6e-10
cd11260	456	cd11260, Sema_4E, The Sema domain, a protein inter	8e-10
cd11249	493	cd11249, Sema_3A, The Sema domain, a protein inter	2e-09
cd11255	474	cd11255, Sema_3G, The Sema domain, a protein inter	2e-09
cd11259	471	cd11259, Sema_4D, The Sema domain, a protein inter	6e-09
cd11251	470	cd11251, Sema_3C, The Sema domain, a protein inter	6e-09
cd09295	392	cd09295, Sema, The Sema domain, a protein interact	2e-07
cd11243	414	cd11243, Sema_7A, The Sema domain, a protein inter	3e-07
cd11261	460	cd11261, Sema_4F, The Sema domain, a protein inter	6e-07

>gnl|CDD|200498 cd11237, Sema_1A, The Sema domain, a protein interacting module, of semaphorin 1A (Sema1A)

 Score =  118 bits (297), Expect = 3e-32
 Identities = 41/55 (74%), Positives = 48/55 (87%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVN 99
           A+YSRVARVCK+DKGGPH F DRWT+FLK+RLNCSVPG+YPFYF+EI+   D V 
Sbjct: 189 AIYSRVARVCKNDKGGPHPFRDRWTSFLKARLNCSVPGEYPFYFNEIQSTSDIVE 243

Sema1A is a transmembrane protein. It has been shown to mediate the defasciculation of motor axon bundles at specific choice points. Sema1A binds to its receptor plexin A (PlexA), which in turn triggers downstream signaling events involving the receptor tyrosine kinase Otk, the evolutionarily conserved flavoprotein monooxygenase molecule interacting with CasL (MICAL), and the A kinase anchoring protein Nervy, leading to repulsive growth-cone response. Sema1A has also been shown to be involved in synaptic formation. It is a member of the semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 446

>gnl|CDD|200496 cd11235, Sema_semaphorin, The Sema domain, a protein interacting module, of semaphorins

 Score = 99.0 bits (247), Expect = 3e-25
 Identities = 33/48 (68%), Positives = 42/48 (87%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
           AVYSRVARVCK+D+GG      +WTTFLK+RLNCSVPG++PFYF+E++
Sbjct: 191 AVYSRVARVCKNDQGGSRSLEKKWTTFLKARLNCSVPGEFPFYFNELQ 238

Semaphorins are regulator molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. They can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted proteins; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. The semaphorins exert their function through their receptors, the neuropilin and plexin families. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 437

>gnl|CDD|200526 cd11265, Sema_5C, The Sema domain, a protein interacting module, of semaphorin 5C (sema5C)

 Score = 90.2 bits (224), Expect = 5e-22
 Identities = 33/49 (67%), Positives = 40/49 (81%), Gaps = 1/49 (2%)

Query: 45  AVYSRVARVCKSDKGG-PHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
            +YSR+ARVCK+D GG      D WTTFLK+RLNCS+PG+YPFYFDEI+
Sbjct: 199 VIYSRIARVCKNDVGGGTMLLKDNWTTFLKARLNCSLPGEYPFYFDEIQ 247

In Drosophila, Sema5C was identified as an early development gene, which is expressed in stage 2 embryos with a striped pattern emerging at later stages. Sema5c may play a role in odor-guided behavior and in tumorigenesis. Sema5C belongs to class 5 semaphorin family of proteins, which are transmembrane glycoproteins characterized by unique thrombospondin specific repeats in the extracellular region of the protein. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 433

>gnl|CDD|200499 cd11238, Sema_2A, The Sema domain, a protein interacting module, of semaphorin 2A (Sema2A)

 Score = 87.1 bits (216), Expect = 7e-21
 Identities = 31/48 (64%), Positives = 38/48 (79%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
            VYSRVARVCK D GG +     WTTFLK+RLNCS+ G++PFYF+EI+
Sbjct: 214 VVYSRVARVCKKDTGGKNVLRQNWTTFLKARLNCSISGEFPFYFNEIQ 261

Sema2A, a secreted semaphorin, signals through its receptor plexin B (PlexB) to regulate central and peripheral axon pathfinding. In the Drosophila embryo, Sema2A secreted by oenocytes interacts with PlexB to guide sensory axons. Sema2A is a member of the semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 452

>gnl|CDD|200502 cd11241, Sema_5, The Sema domain, a protein interacting module, of semaphorin 5 (Sema5)

 Score = 86.1 bits (213), Expect = 1e-20
 Identities = 33/56 (58%), Positives = 42/56 (75%), Gaps = 4/56 (7%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEI----RLPE 95
             VYSR+ARVCK+D GG     D WTTF+K+RLNCS+PG++PFY++EI     LPE
Sbjct: 196 KTVYSRIARVCKNDIGGRFLLEDTWTTFMKARLNCSLPGEFPFYYNEIQGTFYLPE 251

Class 5 semaphorins are transmembrane glycoproteins characterized by unique thrombospondin specific repeats in the extracellular region of the protein. There are three subfamilies in class 5 semaphorins, namely 5A, 5B and 5C. Sema5A and Sema5B function as guidance cues for optic and corticofugal nerve development, respectively. Sema5A-induced cell migration requires Met signaling. Sema5C is an early development gene and may play a role in odor-guided behavior. Sema5A is also implicated in cancer. In a screening model for metastasis, the Drosophila Sema5A ortholog, Dsema-5C, has been found to be required in tumorigenicity and metastasis. Sema5A is highly expressed in human pancreatic cancer cells and is associated with tumor growth, invasion and metastasis. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 438

>gnl|CDD|214747 smart00630, Sema, semaphorin domain

 Score = 82.0 bits (203), Expect = 3e-19
 Identities = 31/48 (64%), Positives = 40/48 (83%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
           AV+SRVARVCK+D GGP     +WT+FLK+RL CSVPG+ PFYF+E++
Sbjct: 168 AVHSRVARVCKNDVGGPRSLDKKWTSFLKARLECSVPGEDPFYFNELQ 215

Length = 390

>gnl|CDD|216480 pfam01403, Sema, Sema domain

 Score = 78.9 bits (195), Expect = 4e-18
 Identities = 31/51 (60%), Positives = 41/51 (80%), Gaps = 3/51 (5%)

Query: 45  AVYSRVARVCKSDKGGPHHF-GDRWTTFLKSRLNCSVPG--DYPFYFDEIR 92
           A++SRVARVCK+D GG  +   ++WTTFLK+RLNCSVPG    PFYF+E++
Sbjct: 202 AIHSRVARVCKNDPGGRSYLELNKWTTFLKARLNCSVPGREGIPFYFNELQ 252

The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor and human plexin A-3. Length = 435

>gnl|CDD|200503 cd11242, Sema_6, The Sema domain, a protein interacting module, of class 6 semaphorins (Sema6)

 Score = 76.0 bits (187), Expect = 6e-17
 Identities = 31/57 (54%), Positives = 41/57 (71%), Gaps = 1/57 (1%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDR-WTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNL 100
            V+SRVARVCK+D GG     ++ WT+FLK+RLNCSVPGD  FYFD ++   D + +
Sbjct: 202 VVFSRVARVCKNDMGGSPRVLEKQWTSFLKARLNCSVPGDSHFYFDVLQAVTDVIRI 258

Class 6 semaphorins (Sema6s) are membrane associated semaphorins. There are 6 subfamilies named 6A to 6D. Sema6s bind to plexin As in a neuropilin independent fashion. Sema6-plexin A signaling plays important roles in lamina-specific axon projections. Interactions between plexin A2, plexin A4, and Sema6A control lamina-restricted projection of hippocampal mossy fibers. Interactions between Sema6C, Sema6D and plexin A1 shape the stereotypic trajectories of sensory axons in the spinal cord. In addition to axon targeting, Sema6D-plexin A1 interactions influence a wide range of other biological processes. During cardiac development, Sema6D attracts or repels endothelial cells in the cardiac tube depending on the expression patterns of specific coreceptors in addition to plexin A1. Furthermore, Sema6D binds a receptor complex comprising of plexin A1, Trem2 (triggering receptor expressed on myeloid cells 2), and DAP12 on dendritic cells and osteoclasts to mediate T-cell-DC interactions and to control bone development, respectively. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 465

>gnl|CDD|200525 cd11264, Sema_5B, The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)

 Score = 75.0 bits (184), Expect = 1e-16
 Identities = 33/54 (61%), Positives = 41/54 (75%), Gaps = 4/54 (7%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR----LPE 95
           VYSRVARVCK+D GG     D WTTF+K+RLNCS PG+ PFY++E++    LPE
Sbjct: 197 VYSRVARVCKNDIGGRFLLEDTWTTFMKARLNCSRPGEIPFYYNELQSTFYLPE 250

Sema5B is expressed in regions of the basal telencephalon in rat. Sema5B is an inhibitory cue for corticofugal axons and acts as a source of repulsion for the appropriate guidance of cortical axons away from structures such as the ventricular zone as they navigate toward and within subcortical regions. In addition to its role as a guidance cue, Sema5B regulates the development and maintenance of synapse size and number in hippocampal neurons. In addition, the sema domain of Sema5B can be cleaved of the whole protein and exerts its function in regulation of synapse morphology. Sema5B belongs to the class 5 semaphorin family of proteins, which are transmembrane glycoproteins characterized by unique thrombospondin specific repeats in the extracellular region of the protein. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 437

>gnl|CDD|200528 cd11267, Sema_6B, The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)

 Score = 72.9 bits (179), Expect = 6e-16
 Identities = 32/57 (56%), Positives = 41/57 (71%), Gaps = 1/57 (1%)

Query: 46  VYSRVARVCKSDKGGPHHFGDR-WTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQ 101
           V SRVARVCK+D GG     ++ WT+FLK+RLNCSVPGD  FYF+ ++   D +NL 
Sbjct: 203 VVSRVARVCKNDMGGSQRVLEKQWTSFLKARLNCSVPGDSHFYFNVLQAVSDILNLG 259

Sema6B functions as repellents for axon growth; this repulsive activity is mediated by its receptor Plexin A4. Sema6B is expressed in CA3, and repels mossy fibers in a Plexin A4 dependent manner. In human, it was shown that peroxisome proliferator-activated receptors (PPARs) and 9-cis-retinoic acid receptor (RXR) regulate human semaphorin 6B (Sema6B) gene expression. Sema6B is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 466

>gnl|CDD|200524 cd11263, Sema_5A, The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

 Score = 72.0 bits (176), Expect = 1e-15
 Identities = 31/54 (57%), Positives = 40/54 (74%), Gaps = 4/54 (7%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR----LPE 95
           V+SR ARVCK+D GG     D WTTF+K+RLNCS PG+ PFY++E++    LPE
Sbjct: 197 VFSRAARVCKNDIGGRFLLEDTWTTFMKARLNCSRPGEIPFYYNELQSTFFLPE 250

Originally, mouse Sema5A was identified as a protein that induces inhibitory responses during optic nerve development. Recent studies show that Sema5A controls innate immunity in mice. It also has been identified as a candidate gene for causing idiopathic autism in humans. Plexin B3 functions as a binding partner and receptor for Sema5A. Furthermore, Sema5A is also implicated in cancer. The role of the Drosophila Sema5A ortholog, Dsema-5C, in tumorigenicity and metastasis has been reported. Sema5A is highly expressed in human pancreatic cancer cells and is associated with tumor growth, invasion and metastasis. Sema5A belongs to class 5 semaphorin family of proteins, which are transmembrane glycoproteins characterized by unique thrombospondin specific repeats in the extracellular region of the protein. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 436

>gnl|CDD|200530 cd11269, Sema_6D, The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)

 Score = 70.4 bits (172), Expect = 5e-15
 Identities = 32/57 (56%), Positives = 42/57 (73%), Gaps = 1/57 (1%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDR-WTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNL 100
           AVYSRVAR+CK+D GG     ++ WT+FLK+RLNCSVPGD  FYFD ++   D + +
Sbjct: 202 AVYSRVARICKNDMGGSQRVLEKHWTSFLKARLNCSVPGDSFFYFDVLQSITDIIEI 258

Sema6D is expressed predominantly in the nervous system during embryogenesis and it uses Plexin-A1 as a receptor. It displays repellent activity for dorsal root ganglion axons. Sema6D also acts as a regulator of late phase primary immune responses. In addition, Sema6D is overexpressed in gastric carcinoma, indicating that it may have an important role in the occurrence and development of the cancer. Sema6D is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 465

>gnl|CDD|200529 cd11268, Sema_6C, The Sema domain, a protein interacting module, of semaphorin 6C (Sema6C, also called semaphorin Y)

 Score = 67.4 bits (164), Expect = 5e-14
 Identities = 33/56 (58%), Positives = 37/56 (66%), Gaps = 1/56 (1%)

Query: 47  YSRVARVCKSDKGG-PHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQ 101
           +SRVARVCK D GG P      WT+FLK RLNCSVPGD  FYFD ++     VNL 
Sbjct: 203 FSRVARVCKRDMGGSPRALDRHWTSFLKLRLNCSVPGDSTFYFDVLQALTGPVNLH 258

Sema6C is highly expressed in adult brain and skeletal muscle and it shows growth cone collapsing activity. It may play a role in the maintenance and remodelling of neuronal connections. In adult skeletal muscle, this role includes prevention of motor neuron sprouting and uncontrolled motor neuron growth. The expression of Sema6C in adult skeletal muscle is down-regulated following denervation. Sema6C is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 465

>gnl|CDD|200500 cd11239, Sema_3, The Sema domain, a protein interacting module, of class 3 semaphorins

 Score = 67.0 bits (164), Expect = 7e-14
 Identities = 27/54 (50%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 41  TKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPF--YFDEIR 92
               A+YSRV R+CK+D GG     ++W+TFLK+RL CSVPG      YFDE+ 
Sbjct: 210 GSGKAIYSRVGRICKNDVGGQRSLVNKWSTFLKARLVCSVPGPDGIDTYFDELE 263

Class 3 semaphorins (Sema3s) are secreted regulator molecules involved in the development of the nervous system, vasculogenesis, angiogenesis,and tumorigenesis. There are 7 distinct subfamilies named Sema3A to 3G. Sema3s function as repellent signals during axon guidance by repelling neurons away from the source of Sema3s. However, Sema3s that are secreted by tumor cells play an inhibitory role in tumor growth and angiogenesis (specifically Sema3B and Sema3F). Sema3s functions by forming complexes with neuropilins and A-type plexins, where neuropilins serve as the ligand binding moiety and the plexins function as signal transduction component. Sema3s primarily inhibit the cell motility and migration of tumor and endothelial cells by inducing collapse of the actin cytoskeleton via neuropilins and plexins. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 471

>gnl|CDD|200531 cd11270, Sema_6E, The Sema domain, a protein interacting module, semaphorin 6E (sema6E)

 Score = 64.7 bits (157), Expect = 5e-13
 Identities = 30/57 (52%), Positives = 39/57 (68%), Gaps = 1/57 (1%)

Query: 47  YSRVARVCKSDKGG-PHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQD 102
           +SRVARVCK+D GG P      WT+FLK+RLNCSVPGD  FYFD ++   + + +  
Sbjct: 202 FSRVARVCKNDNGGSPRVLERYWTSFLKARLNCSVPGDSFFYFDVLQSLTNVMQINH 258

Sema6E is expressed predominantly in the nervous system during embryogenesis. It binds Plexin A1 and might utilize it as a receptor to repel axons of specific types during development. Sema6E acts as a repellent to dorsal root ganglion axons as well as sympathetic axons. Sema6E is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 462

>gnl|CDD|200527 cd11266, Sema_6A, The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)

 Score = 64.7 bits (157), Expect = 5e-13
 Identities = 28/56 (50%), Positives = 41/56 (73%), Gaps = 1/56 (1%)

Query: 46  VYSRVARVCKSDKGGPHHFGDR-WTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNL 100
           V+ RVA+VCK+D GG     ++ WT+FLK+RLNCSVPGD  FYF+ ++   D +++
Sbjct: 203 VFPRVAQVCKNDMGGSQRVLEKQWTSFLKARLNCSVPGDSHFYFNILQAVTDVIHI 258

In the cerebellum, Sema6A-plexin A2 signaling modulates granule cell migration by controlling centrosome positioning. Besides plexin A2, plexin A4 is also found to be a receptor of Sema6A. Interactions between plexin A2, plexin A4, and Sema6A control lamina-restricted projection of hippocampal mossy fibers. It is required for the clustering of boundary cap cells at the PNS/CNS interface and thus, prevents motoneurons from streaming out of the ventral spinal cord. At the dorsal root entry site, it organizes the segregation of dorsal roots. Sema6A may also be involved in axonal pathfinding processes in the periinfarct and homotopic contralateral cortex. Sema6A is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 466

>gnl|CDD|200514 cd11253, Sema_3E, The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E)

 Score = 61.8 bits (150), Expect = 4e-12
 Identities = 28/59 (47%), Positives = 39/59 (66%), Gaps = 5/59 (8%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPF--YFDEIRLPEDCVNLQ 101
           A+Y+RV RVC +D+GG     ++W+TFLK+RL CSVPG      +FDE+   ED   L+
Sbjct: 213 AIYTRVGRVCANDQGGQRMLVNKWSTFLKTRLICSVPGPNGIDTHFDEL---EDVFLLR 268

Sema3E is a secreted molecule implicated in axonal path finding and inhibition of developmental and postischemic angiogenesis. It is also highly expressed in metastatic cancer cells. Sema3E signaling, through its high affinity functional receptor Plexin D1, drives cancer cell invasiveness and metastatic spreading. Sema3E is a member of the class 3 semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 471

>gnl|CDD|200518 cd11257, Sema_4B, The Sema domain, a protein interacting module, of semaphorin 4B (Sema4B)

 Score = 61.4 bits (149), Expect = 6e-12
 Identities = 25/44 (56%), Positives = 32/44 (72%), Gaps = 1/44 (2%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGD-YPF 86
           N + SR+ARVCK D+GG      RWTTFLK++L CS+P D +PF
Sbjct: 216 NTIVSRIARVCKGDEGGERVLQKRWTTFLKAQLLCSLPDDGFPF 259

Sema4B, expressed in T and B cells, is an immune semaphorin. It functions as a negative regulatory of basophils through T cell-basophil contacts and it significantly inhibits IL-4 and IL-6 production from basophils in response to various stimuli, including IL-3 and papain. In addition, T cell-derived Sema4B suppresses basophil-mediated Th2 skewing and humoral memory responses. Sema4B may be also involved in lung cancer cell mobility by inducing the degradation of CLCP1 (CUB, LCCL-homology, coagulation factor V/VIII homology domains protein). Sema4B is characterized by a PDZ-binding motif at the carboxy-terminus, which mediates interaction with the post-synaptic density protein PSD-95/SAP90, which is thought to play a central role during synaptogenesis and in the structure and function of post-synaptic specializations of excitatory synapses. Sema4B belongs to class 4 transmembrane semaphorin family proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 464

>gnl|CDD|200513 cd11252, Sema_3D, The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D)

 Score = 61.1 bits (148), Expect = 9e-12
 Identities = 27/54 (50%), Positives = 36/54 (66%), Gaps = 2/54 (3%)

Query: 41  TKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGD--YPFYFDEIR 92
           T   +V SRV RVCK+D GG     ++WTTFLK+RL CS+PG      +FDE++
Sbjct: 213 TSDKSVLSRVGRVCKNDVGGQRSLINKWTTFLKARLVCSIPGPDGADTHFDELQ 266

Sema3D is a secreted semaphorin expressed during the development of the nervous system. In zebrafish, Sema3D is expressed in the ventral tectum. It guides retinal axons along the dorsoventral axis of the tectum and guides the laterality of retinal ganglion cell (RGC) projections. Both Sema3D knockdown or its ubiquitous overexpression induced aberrant ipsilateral projections. Proper balance of Sema3D is needed at the midline for the progression of RGC axons from the chiasm midline into the contralateral optic tract. Sema3D is a member of the class 3 semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 474

>gnl|CDD|200501 cd11240, Sema_4, The Sema domain, a protein interacting module, of class 4 semaphorins (Sema4)

 Score = 60.5 bits (147), Expect = 1e-11
 Identities = 28/61 (45%), Positives = 34/61 (55%), Gaps = 6/61 (9%)

Query: 48  SRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDPYCAW 107
           SRVARVCK D GG      +WTTFLK++L CS P D    F+ +R   D   L     +W
Sbjct: 213 SRVARVCKGDLGGQRTLQKKWTTFLKAQLVCSQP-DSGLPFNVLR---DVFVLSPD--SW 266

Query: 108 D 108
           D
Sbjct: 267 D 267

Class 4 semaphorins (Sema4s) are transmembrane regulator molecules involved in the development of the nervous system, immune response, cytoskeletal organization, angiogenesis, and cell-cell interactions. There are 7 distinct subfamilies in class 4 semaphorins, named 4A to 4G. Several class 4 subfamilies play important roles in the immune system and are called "immune semaphorins". Sema4A plays critical roles in T cell-DC interactions in the immune response. Sema4D/CD100, expressed by lymphocytes, promotes the aggregation and survival of B lymphocytes and inhibits cytokine-induced migration of immune cells in vitro. It is required for normal activation of B and T lymphocytes. Sema4B negatively regulates basophil functions through T cell-basophil contacts and significantly inhibits IL-4 and IL-6 production from basophils in response to various stimuli, including IL-3 and papain. Sema4s not only influence the activation state of cells but also modulate their migration and survival. The effects of Sema4s on nonlymphoid cells are mediated by plexin D1 and plexin Bs. The Sema4G and Sema4C genes are expressed in the developing cerebellar cortex and are involved in neural tube closure and development of cerebellar granules cells through receptor plexin B2. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 456

>gnl|CDD|200515 cd11254, Sema_3F, The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)

 Score = 60.2 bits (146), Expect = 2e-11
 Identities = 26/50 (52%), Positives = 34/50 (68%), Gaps = 2/50 (4%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGD--YPFYFDEIR 92
           AV SR+ RVC +D GG     ++W+TFLK+RL CSVPG      +FDE+R
Sbjct: 213 AVLSRIGRVCLNDDGGHCCLVNKWSTFLKARLVCSVPGADGIETHFDELR 262

Sema3F is coexpressed with semaphorin3B. Both Sema3B and Sema3F proteins are candidate tumor suppressors that are down-regulated in highly metastatic tumors. Two receptor families, the neuropilins and plexins, have been implicated in mediating the actions of semaphorins 3B and 3F. Sema3F is a member of the class 3 semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 470

>gnl|CDD|200517 cd11256, Sema_4A, The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A)

 Score = 59.5 bits (144), Expect = 3e-11
 Identities = 22/39 (56%), Positives = 28/39 (71%)

Query: 48  SRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPF 86
           +RVARVCK+D GG      +WTTFLK++L CS  G +PF
Sbjct: 212 ARVARVCKNDVGGEKLLQKKWTTFLKAQLTCSQQGHFPF 250

Sema4A is expressed in immune cells and is thus termed an "immune semaphorin". It plays critical roles in T cell-DC interactions in the immune response. It has been reported to enhance activation and differentiation of T cells in vitro and generation of antigen-specific T cells in vivo. The function of Sema4A in the immune response implicates its role in infectious and noninfectious diseases. Sema4A exerts its function through three receptors, namely Plexin B, Plexin D1, and Tim-2. Sema4A belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. TThe Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 447

>gnl|CDD|200523 cd11262, Sema_4G, The Sema domain, a protein interacting module, of semaphorin 4G (Sema4G)

 Score = 59.0 bits (143), Expect = 4e-11
 Identities = 23/46 (50%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 48  SRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRL 93
           +RVARVCK D+GG      +WT+FLK+RL C +P +Y F F+ +R 
Sbjct: 213 ARVARVCKGDRGGKKTLQRKWTSFLKARLVCYIP-EYEFLFNVLRS 257

The Sema4G and Sema4C genes are expressed in the developing cerebellar cortex. Sema4G and Sema4C proteins specifically bind to Plexin B2 expressed in the cerebellar granule cells. Sema4G and Sema4C are involved in neural tube closure and cerebellar granule cell development through Plexin B2.Sema4G belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 457

>gnl|CDD|200519 cd11258, Sema_4C, The Sema domain, a protein interacting module, of semaphorin 4C (Sema4C)

 Score = 57.1 bits (138), Expect = 2e-10
 Identities = 24/47 (51%), Positives = 34/47 (72%), Gaps = 1/47 (2%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
           V +RVARVCK D GG      +WTTFLK+RL CS+P ++  YF++++
Sbjct: 212 VVARVARVCKGDLGGARTLQKKWTTFLKARLLCSIP-EWQLYFNQLK 257

Sema4C acts as a Plexin B2 ligand to regulate the development of cerebellar granule cells and to modulate ureteric branching in the developing kidney. The binding of Sema4C to Plexin B2 results the phosphorylation of downstream regulator ErbB-2 and the plexin protein itself. The cytoplasmic region of Sema4C binds a neurite-outgrowth-related protein SFAP75, suggesting that Sema4C may also play a role in neural function. Sema4C belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 458

>gnl|CDD|200511 cd11250, Sema_3B, The Sema domain, a protein interacting module, of semaphorin 3B (Sema3B)

 Score = 55.7 bits (134), Expect = 6e-10
 Identities = 24/48 (50%), Positives = 35/48 (72%), Gaps = 2/48 (4%)

Query: 47  YSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGD--YPFYFDEIR 92
           YSR+ ++C++D GG     ++WTTFLK+RL CSVPG+     +FDE+R
Sbjct: 216 YSRIGQICRNDMGGQRSLVNKWTTFLKARLVCSVPGNEGGDTHFDELR 263

Sema3B is coexpressed with semaphorin 3F and both proteins are candidate tumor suppressors. Both Sema3B and Sema3F show high levels of expression in normal tissues and low-grade tumors but are down-regulated in highly metastatic tumors in the lung, melanoma cells, bladder carcinoma cells and prostate carcinoma. They are upregulated by estrogen and inhibit cell motility and invasiveness through decreased FAK phosphorylation and inhibition of MMP-2 and MMP-9 expression. Two receptor families, the neuropilins (NP) and plexins, have been implicated in mediating the actions of semaphorins 3B and 3F. Sema3B is a member of the class 3 semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 471

>gnl|CDD|200521 cd11260, Sema_4E, The Sema domain, a protein interacting module, of semaphorin 4E (Sema4E)

 Score = 55.7 bits (134), Expect = 8e-10
 Identities = 23/36 (63%), Positives = 27/36 (75%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVP 81
           V SRVARVCK D GG      +WT+FLK+RL+CSVP
Sbjct: 209 VVSRVARVCKGDLGGQRTLQKKWTSFLKARLDCSVP 244

Sema4E is expressed in the epithelial cells that line the pharyngeal arches in zebrafish. It may act as a guidance molecule to restrict the branchiomotor axons to the mesenchymal cells. Gain-of-function and loss-of-function studies demonstrate that Sema4E is essential for the guidance of facial axons from the hindbrain into their pharyngeal arch targets and is sufficient for guidance of gill motor axons. Sema4E guides facial motor axons by a repulsive action. Sema4E belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 456

>gnl|CDD|200510 cd11249, Sema_3A, The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)

 Score = 54.2 bits (130), Expect = 2e-09
 Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 9/70 (12%)

Query: 25  FQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPG-- 82
           F+  +IDG +H         A ++R+ ++CK+D GG     ++WTTFLK+RL CSVPG  
Sbjct: 222 FRENAIDG-EHT------GKATHARIGQLCKNDFGGHRSLVNKWTTFLKARLICSVPGPN 274

Query: 83  DYPFYFDEIR 92
               +FDE++
Sbjct: 275 GIDTHFDELQ 284

Sema3A has been reported to inhibit the growth of certain experimental tumors and to regulate endothelial cell migration and apoptosis in vitro, as well as arteriogenesis in the muscle, skin vessel permeability, and tumor angiogenesis in vivo. The function of Sema3A is mediated through receptors neuropilin-1 (NP1) and plexins, although little is known about the requirement of specific plexins in its receptor complex. It is known however that Plexin-A4 is the receptor for Sema3A in the Toll-like receptor- and sepsis-induced cytokine storm during immune response. Sema3A is a member of the Class 3 semaphorin family of secreted proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 493

>gnl|CDD|200516 cd11255, Sema_3G, The Sema domain, a protein interacting module, of semaphorin 3G (Sema3G)

 Score = 54.1 bits (130), Expect = 2e-09
 Identities = 23/56 (41%), Positives = 36/56 (64%), Gaps = 2/56 (3%)

Query: 38  TQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPF--YFDEI 91
           T      A++SRV R+C +D GG     ++W+TF+K+RL CSVPG +    +FD++
Sbjct: 206 TAEDDDGAIHSRVGRLCANDAGGQRVLVNKWSTFIKARLVCSVPGPHGIQTHFDQL 261

Semaphorin 3G is identified as a primarily endothelial cell- expressed class 3 semaphorin that controls endothelial and smooth muscle cell functions in autocrine and paracrine manners, respectively. It is mainly expressed in the lung and kidney, and a little in the brain. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 474

>gnl|CDD|200520 cd11259, Sema_4D, The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

 Score = 52.9 bits (127), Expect = 6e-09
 Identities = 31/95 (32%), Positives = 48/95 (50%), Gaps = 10/95 (10%)

Query: 7   WSTPSLDEVNLCCRGSVRFQSTSIDGVD-HVWTQLTKKNAVYS--------RVARVCKSD 57
           ++ P L+E +      +R    S DG D  ++   T+ +  Y         R+ARVCK D
Sbjct: 171 YAIPWLNEPSFVFADVIRADPDSPDGEDDKIYFFFTEVSVEYEFVGKLLIPRIARVCKGD 230

Query: 58  KGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
           +GG      +WT+FLK+RL CS+P D    F+ + 
Sbjct: 231 QGGLRTLQKKWTSFLKARLICSIP-DKNLVFNVVN 264

Sema4D/CD100 is expressed in immune cells and plays critical roles in immune response; it is thus termed an "immune semaphorin". It is expressed by lymphocytes and promotes the aggregation and survival of B lymphocytes and inhibits cytokine-induced migration of immune cells in vitro. Sema4D/CD100 knock-out mice demonstrate that Sema4D is required for normal activation of B and T lymphocytes. Sema4D increases B-cell and DC function using either Plexin B1 or CD72 as receptors. The function of Sema4D in immune response implicates its role in infectious and noninfectious diseases. Sema4D belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 471

>gnl|CDD|200512 cd11251, Sema_3C, The Sema domain, a protein interacting module, of semaphorin 3C (Sema3C)

 Score = 53.0 bits (127), Expect = 6e-09
 Identities = 22/48 (45%), Positives = 32/48 (66%), Gaps = 2/48 (4%)

Query: 46  VYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGD--YPFYFDEI 91
           ++S +ARVC +D GG     ++WTTFLK+RL CSV  +     +FDE+
Sbjct: 214 IHSMIARVCPNDTGGQRSLVNKWTTFLKARLVCSVMDEDGTETHFDEL 261

Sema3C is a secreted semaphorin expressed in and adjacent to cardiac neural crest cells, and causes impaired migration of neural crest cells to the developing cardiac outflow tract, resulting in the interruption of the aortic arch and persistent truncus arteriosus. It has been proposed that Sema3C acts as a guidance molecule, regulating migration of neural crest cells that express semaphorin receptors such as plexin A2. Sema3C may also participate in tumor progression. The cleavage of Sema3C induced by ADAMTS1 promotes the migration of breast cancer cells. Sema3C is a member of the class 3 semaphorin family of secreted proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 470

>gnl|CDD|200495 cd09295, Sema, The Sema domain, a protein interacting module, of semaphorins and plexins

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 23/46 (50%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 38  TQLTKKNAVY-SRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPG 82
            +  KK  VY  R+ARVCK D GG H    + T+FLK+ LNCS P 
Sbjct: 194 VEYLKKGMVYVPRIARVCKLDVGGCHRLKKKLTSFLKADLNCSRPQ 239

Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors. Length = 392

>gnl|CDD|200504 cd11243, Sema_7A, The Sema domain, a protein interacting module, of semaphorin 7A (Sema7A, also called CD108)

 Score = 47.9 bits (114), Expect = 3e-07
 Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 2/46 (4%)

Query: 48  SRVARVCKSDKGG-PHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
           SRVAR+CK D+GG       +W+TFLK+RL C  P   P  F+ ++
Sbjct: 189 SRVARLCKEDQGGTSSLSTSKWSTFLKARLVCGDPAT-PMNFNRLQ 233

Sema7A plays regulatory roles in both immune and nervous systems. Unlike other semaphorins, which act as repulsive guidance cues, Sema7A enhances central and peripheral axon growth and is required for proper axon tract formation during embryonic development. Sema7A also plays a critical role in the negative regulation of T cell activation and function. Sema7A is a membrane-anchored member of the semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 414

>gnl|CDD|200522 cd11261, Sema_4F, The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)

 Score = 47.2 bits (112), Expect = 6e-07
 Identities = 19/33 (57%), Positives = 20/33 (60%)

Query: 49  RVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVP 81
           RVARVC  D GG      RWTTFLK+ L C  P
Sbjct: 217 RVARVCAGDLGGRKTLQQRWTTFLKADLLCPGP 249

Sema4F plays role in heterotypic cell-cell contacts and controls cell proliferation and suppresses tumorigenesis. In neurofibromatosis type 1 (NF1) patients, reduced Sema4F level disrupts Schwann cell/axonal interactions. Experiments using a yeast two-hybrid system show that the extreme C-terminus of Sema4F interacts with the PDZ domains of post-synaptic density protein SAP90/PSD-95, indicating possible functional involvement of Semas4F at glutamatergic synapses. Recent work also suggests a role for Sema4F in the injury response of intramedullary axotomized motoneuron. Sema4F belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulator molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. Length = 460

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	148
KOG3611|consensus	737		100.0
smart00630	390	Sema semaphorin domain.	100.0
PF01403	433	Sema: Sema domain; InterPro: IPR001627 The Sema do	99.95

>KOG3611|consensus

Probab=100.00  E-value=4.4e-40  Score=306.44  Aligned_cols=124  Identities=37%  Similarity=0.621  Sum_probs=112.8

Q ss_pred             cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEe--------cCceeeeeeecccccCCCCCcccCcceehhhhhhhc
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLT--------KKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLN   77 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~--------~~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~   77 (148)
                      +|+++|||||+||.|.-|         .|+|||||+        +++++|||||||||||+||++.|+++|||||||||+
T Consensus       209 ~~dskwLneP~FV~a~~i---------~~~vyFFFrE~a~e~~~~~~~v~sRVARVCknD~GG~~~l~~~WTSFLKARL~  279 (737)
T KOG3611|consen  209 KYDSKWLNEPNFVGAFDI---------GDHVYFFFREIAVENNNCGKAVYSRVARVCKNDVGGRRVLEKKWTSFLKARLN  279 (737)
T ss_pred             cCCchhccCCcEEEeeee---------CCEEEEEecccccccCcccceEEeeeeeEeccCCCCceEcccchhHhhhhhee
Confidence            799999999999999776         389999997        468999999999999999999999999999999999


Q ss_pred             CCCCCCCCccCccccceeeecc--C----------------CCceeEEeee-eccccccCCCCeeeeecCCCeeeecCC-
Q psy6150          78 CSVPGDYPFYFDEIRLPEDCVN--L----------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPYQE-  137 (148)
Q Consensus        78 Cs~pg~~~~~Fn~lqdv~~l~~--~----------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~q~-  137 (148)
                      ||+||+.+||||+||+||.+..  .                .++.|+|+|. |++   +|+|||++.+++.++|+||++ 
T Consensus       280 CSvp~~~~fyFn~lq~v~~~~~~~~~~~~YgvFtt~~n~~~~SAVC~f~l~dI~~---vF~G~fk~q~~~~~~W~pv~~~  356 (737)
T KOG3611|consen  280 CSVPGDSPFYFNELQSVFLLVSLGGRDVFYAVFSTSSNSIPGSAVCAFSLSDIRA---VFDGPFKEQKGPNSAWLPVPGD  356 (737)
T ss_pred             cccCCCCCCcccccceeeeccccCCCceEEEEEcccccCcceeEEecCCHHHHHH---HhCCccccccCCcccceeccCC
Confidence            9999999999999999985332  2                2334999999 999   999999999999999999999 


Q ss_pred             Ccee
Q psy6150         138 RTLE  141 (148)
Q Consensus       138 ~~~~  141 (148)
                      +||.
T Consensus       357 ~vP~  360 (737)
T KOG3611|consen  357 KVPK  360 (737)
T ss_pred             cCCC
Confidence            9985

>smart00630 Sema semaphorin domain

Probab=100.00  E-value=4.5e-34  Score=248.58  Aligned_cols=123  Identities=35%  Similarity=0.644  Sum_probs=108.8

Q ss_pred             cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEec--------CceeeeeeecccccCCCCCcccCcceehhhhhhhc
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLN   77 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~   77 (148)
                      +++++||++|+||++..         .+|+|||||.+        ++.++||||||||||.||+++|+++||||+||||+
T Consensus       130 ~~~~~~l~~~~FV~sf~---------~~~~vYFff~e~~~e~~~~~~~~~SRVaRVCk~D~Gg~~~l~~~wtSflka~L~  200 (390)
T smart00630      130 LYDSKWLNEPNFVYAFE---------SGDFVYFFFRETAVEDDNCGKAVHSRVARVCKNDVGGPRSLDKKWTSFLKARLE  200 (390)
T ss_pred             ccCcccccCCcEEEEEE---------cCCEEEEEEEEEccccCcCCceeeeeeeeecccCcCccccccccccEEEEEEEE
Confidence            35789999999999843         57899999974        67899999999999999999999999999999999


Q ss_pred             CCCCCCCCccCccccceeeeccC-------------------CCceeEEeee-eccccccCCCCeeeeecCCCeeeec-C
Q psy6150          78 CSVPGDYPFYFDEIRLPEDCVNL-------------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPY-Q  136 (148)
Q Consensus        78 Cs~pg~~~~~Fn~lqdv~~l~~~-------------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~-q  136 (148)
                      |+.||+.+++||+||||+.+..+                   +++.|||+|. |++   +|+|+|++-+..+.+|.++ .
T Consensus       201 Cs~~g~~~~~fn~lQ~v~~~~~g~~~~~vlygvFst~~~~~~~SAvC~f~l~~I~~---~F~~~~~~~~~~~~~~~~~~~  277 (390)
T smart00630      201 CSVPGESPFYFNELQAAFLLPPGSESDDVLYGVFSTSSNPIPGSAVCAFSLKDINA---VFNGPFKECETSTSQWLPYSR  277 (390)
T ss_pred             ecCCCcCCccchhhhheeecccCCCCCCEEEEEEeCCCCCCCccEEEEeEHHHHHH---HHhhhhhhccCcCcceecccC
Confidence            99999889999999999965531                   3445999999 999   9999999999999999988 6


Q ss_pred             CCce
Q psy6150         137 ERTL  140 (148)
Q Consensus       137 ~~~~  140 (148)
                      +.+|
T Consensus       278 ~~vp  281 (390)
T smart00630      278 GKVP  281 (390)
T ss_pred             CcCC
Confidence            6665

>PF01403 Sema: Sema domain; InterPro: IPR001627 The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance

Probab=99.95  E-value=3.5e-28  Score=210.75  Aligned_cols=131  Identities=33%  Similarity=0.569  Sum_probs=113.4

Q ss_pred             cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEec--------CceeeeeeecccccCCCCCcccCcceehhhhhhhc
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLN   77 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~   77 (148)
                      .++..||++|.|+.+..+.+...-  .+++|||||.+        ++..+||||||||+|.||.+.+.++||||+||||+
T Consensus       158 ~~~~~~~~~p~fv~~~~~~~v~~f--~~~~vYF~f~e~~~~~~~~~~~~~srvaRvCk~D~g~~~~~e~~wttf~karL~  235 (433)
T PF01403_consen  158 QYDSKWLNEPSFVSSFEIGYVYGF--SDDFVYFFFRERASEYDSCGKPYYSRVARVCKNDPGGYSYLEPLWTTFLKARLN  235 (433)
T ss_dssp             CCCTTSSSSTEEEEEEEEEECEEE--ETTEEEEEEEEEESSSSTSSCCEEEEEEEEETTSSTBSSSCCTBESSEEEEEEE
T ss_pred             cccccccccccccccccccccccc--CCcEEEEEEEeeccccccccccceeeeeeccccCCccccchhhcccccccccee
Confidence            346789999999999888655543  67899999973        47889999999999999998777999999999999


Q ss_pred             CCCCC-CCCccCccccceeeeccCCC-------------------ceeEEeee-eccccccCCCCeeeeecCCCeeeecC
Q psy6150          78 CSVPG-DYPFYFDEIRLPEDCVNLQD-------------------PYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPYQ  136 (148)
Q Consensus        78 Cs~pg-~~~~~Fn~lqdv~~l~~~~~-------------------~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~q  136 (148)
                      |+.|+ ..+++||+||+++.+.++.+                   +.|+|+|. |.+   +|+|++...++++.+|.++.
T Consensus       236 C~~~~~~~~~~fn~lq~~~~~~~~~~~~~vlyavFt~~~~~~~~SAvC~ysl~~I~~---~F~g~~~~~~~~~~~~~~~~  312 (433)
T PF01403_consen  236 CSVPGDGSPFYFNELQAVFVSKPGSGDDDVLYAVFTTSWNSSPGSAVCAYSLSDINQ---AFNGPFKCCDGSTSKWLPYP  312 (433)
T ss_dssp             CEETTCSCTEECHEEEEEEEEECTTTTSEEEEEEEEESSSSSSCEEEEEEEHHHHHH---HHCSHBEECCSCHTTBCCTT
T ss_pred             ccccCcCCCchhhhhhhhccccccccCCceEEEEEEecccccCCceEEEEEHHHHHH---HhhcchhhcccccCcccccc
Confidence            99998 67899999999997776433                   34999999 999   99999999999999999977


Q ss_pred             CCcee
Q psy6150         137 ERTLE  141 (148)
Q Consensus       137 ~~~~~  141 (148)
                      +.+|+
T Consensus       313 ~~~~~  317 (433)
T PF01403_consen  313 NSVPS  317 (433)
T ss_dssp             SCCCS
T ss_pred             CcccC
Confidence            66654

Sema domains also occur in a hepatocyte growth factor receptor, in SEX protein [] and in viral proteins. CD100 (also called SEMA4D) is associated with PTPase and serine kinase activity. CD100 increases PMA, CD3 and CD2 induced T cell proliferation, increases CD45 induced T cell adhesion, induces B cell homotypic adhesion and down-regulates B cell expression of CD23. The Sema domain is characterised by a conserved set of cysteine residues, which form four disulphide bonds to stabilise the structure. The Sema domain fold is a variation of the beta propeller topology, with seven blades radially arranged around a central axis. Each blade contains a four- stranded (strands A to D) antiparallel beta sheet. The inner strand of each blade (A) lines the channel at the centre of the propeller, with strands B and C of the same repeat radiating outward, and strand D of the next repeat forming the outer edge of the blade. The large size of the Sema domain is not due to a single inserted domain but results from the presence of additional secondary structure elements inserted in most of the blades. The Sema domain uses a 'loop and hook' system to close the circle between the first and the last blades. The blades are constructed sequentially with an N-terminal beta- strand closing the circle by providing the outermost strand (D) of the seventh (C-terminal) blade. The beta-propeller is further stabilised by an extension of the N terminus, providing an additional, fifth beta-strand on the outer edge of blade 6 [, , ]. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0005515 protein binding; PDB: 3NVX_A 3NVQ_A 3OL2_A 1OLZ_B 3OKT_A 3AL9_B 3OKY_A 3AL8_B 3NVN_A 3OKW_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	148
3okw_A	565	Mouse Semaphorin 6a, Extracellular Domains 1-2 Leng		1e-10
3afc_A	556	Mouse Semaphorin 6a Extracellular Domain Length = 5		1e-10
1q47_A	495	Structure Of The Semaphorin 3a Receptor-Binding Mod		1e-07
4gz8_A	667	Mouse Semaphorin 3a, Domains Sema-Psi-Ig Length = 6		1e-07
4gza_G	538	Complex Of Mouse Plexin A2 - Semaphorin 3a - Neurop		1e-07
1olz_A	663	The Ligand-Binding Face Of The Semaphorins Revealed		1e-06

>pdb|3OKW|A Chain A, Mouse Semaphorin 6a, Extracellular Domains 1-2 Length = 565

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 41/62 (66%), Gaps = 1/62 (1%)
Query: 41  TKKNAVYSRVARVCKSDKGGPHHFGDR-WTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVN 99
           T    V+ RVA+VCK+D GG     ++ WT+FLK+RLNCSVPGD  FYF+ ++   D + 
Sbjct: 230 TMGKVVFPRVAQVCKNDMGGSQRVLEKQWTSFLKARLNCSVPGDSHFYFNILQAVTDVIR 289
Query: 100 LQ 101
           + 
Sbjct: 290 IN 291

>pdb|3AFC|A Chain A, Mouse Semaphorin 6a Extracellular Domain Length = 556

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 41/62 (66%), Gaps = 1/62 (1%)
Query: 41  TKKNAVYSRVARVCKSDKGGPHHFGDR-WTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVN 99
           T    V+ RVA+VCK+D GG     ++ WT+FLK+RLNCSVPGD  FYF+ ++   D + 
Sbjct: 231 TMGKVVFPRVAQVCKNDMGGSQRVLEKQWTSFLKARLNCSVPGDSHFYFNILQAVTDVIR 290
Query: 100 LQ 101
           + 
Sbjct: 291 IN 292

>pdb|1Q47|A Chain A, Structure Of The Semaphorin 3a Receptor-Binding Module Length = 495

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 9/70 (12%)
Query: 25  FQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDY 84
           F+  +IDG +H         A ++R+ ++CK+D GG     ++WTTFLK+RL CSVPG  
Sbjct: 222 FRENAIDG-EH------SGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPN 274
Query: 85  PF--YFDEIR 92
               +FDE++
Sbjct: 275 GIDTHFDELQ 284

>pdb|4GZ8|A Chain A, Mouse Semaphorin 3a, Domains Sema-Psi-Ig Length = 667

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 9/70 (12%)
Query: 25  FQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDY 84
           F+  +IDG +H         A ++R+ ++CK+D GG     ++WTTFLK+RL CSVPG  
Sbjct: 230 FRENAIDG-EH------SGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPN 282
Query: 85  PF--YFDEIR 92
               +FDE++
Sbjct: 283 GIDTHFDELQ 292

>pdb|4GZA|G Chain G, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1 Length = 538

Iteration: 1
 Score = 52.0 bits (123), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 9/70 (12%)
Query: 25  FQSTSIDGVDHVWTQLTKKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDY 84
           F+  +IDG +H         A ++R+ ++CK+D GG     ++WTTFLK+RL CSVPG  
Sbjct: 230 FRENAIDG-EH------SGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPN 282
Query: 85  PF--YFDEIR 92
               +FDE++
Sbjct: 283 GIDTHFDELQ 292

>pdb|1OLZ|A Chain A, The Ligand-Binding Face Of The Semaphorins Revealed By The High Resolution Crystal Structure Of Sema4d Length = 663

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 52/106 (49%), Gaps = 13/106 (12%)
Query: 7   WSTPSLDEVNLCCRGSVRFQSTSIDGVD-HVWTQLTKKNAVYS--------RVARVCKSD 57
           ++ P L+E +      +R    S DG D  V+   T+ +  Y         R+ARVCK D
Sbjct: 180 YAIPWLNEPSFVFADVIRKSPDSPDGEDDRVYFFFTEVSVEYEFVFRVLIPRIARVCKGD 239
Query: 58  KGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDCVNLQDP 103
           +GG      +WT+FLK+RL CS P D    F+ +R   D   L+ P
Sbjct: 240 QGGLRTLQKKWTSFLKARLICSRP-DSGLVFNVLR---DVFVLRSP 281

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	148
3nvx_A	383	Protein A39; beta-propeller, viral protein; HET: N	2e-13
1olz_A	663	Semaphorin 4D; developmental protein, CD100, beta-	7e-11
1q47_A	495	Semaphorin 3A; beta propeller, signaling protein;	4e-10
3oky_B	565	Putative uncharacterized protein; transmembrane, l	6e-09
3oky_B	565	Putative uncharacterized protein; transmembrane, l	4e-05
3nvq_A	590	Semaphorin-7A; beta-propeller, signaling, signalin	6e-09
4fww_A	527	Macrophage-stimulating protein receptor; beta-prop	9e-05
2uzx_B	727	Hepatocyte growth factor receptor; signaling prote	1e-04
3nvn_B	476	Plexin-C1; beta-propeller, signaling, viral protei	1e-04
3nvn_B	476	Plexin-C1; beta-propeller, signaling, viral protei	5e-04
3ol2_B	528	Plexin-B1; beta-propeller, signalling, extacellula	2e-04
3ol2_B	528	Plexin-B1; beta-propeller, signalling, extacellula	7e-04

>3nvx_A Protein A39; beta-propeller, viral protein; HET: NAG; 2.00A {Vaccinia virus} PDB: 3nvn_A* Length = 383

 Score = 65.6 bits (159), Expect = 2e-13
 Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 44  NAVYSRVARVCKSDKGGPHHF-GDRWTTFLKSRLNCSVPGDYPFY 87
                 +A++C +D+GGP      RW+TFLK  L C + G     
Sbjct: 172 IVKIPYIAQMCLNDEGGPSSLSSHRWSTFLKVELECDIDGRSYRQ 216

>1olz_A Semaphorin 4D; developmental protein, CD100, beta-propeller, PSI domain, IG-like domain, extracellular receptor, neurogenesis; 2.0A {Homo sapiens} SCOP: b.1.1.4 b.69.12.1 g.16.2.1 PDB: 3ol2_A* Length = 663

 Score = 58.2 bits (139), Expect = 7e-11
 Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
             +  R+ARVCK D+GG      +WT+FLK+RL CS P      F+ +R
Sbjct: 226 RVLIPRIARVCKGDQGGLRTLQKKWTSFLKARLICSRPDS-GLVFNVLR 273

>1q47_A Semaphorin 3A; beta propeller, signaling protein; HET: NAG; 2.80A {Mus musculus} SCOP: b.69.12.1 Length = 495

 Score = 55.8 bits (133), Expect = 4e-10
 Identities = 21/50 (42%), Positives = 30/50 (60%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRL 93
            A ++R+ ++CK+D GG     ++WTTFLK+RL CSVPG          L
Sbjct: 234 KATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDEL 283

>3oky_B Putative uncharacterized protein; transmembrane, ligand, SEMA-domain, cell-CELL signalling, SI protein; HET: NAG; 2.19A {Mus musculus} PDB: 3okw_A* 3afc_A* 3al8_A* Length = 565

 Score = 52.4 bits (124), Expect = 6e-09
 Identities = 27/49 (55%), Positives = 35/49 (71%), Gaps = 1/49 (2%)

Query: 44  NAVYSRVARVCKSDKGGPHHF-GDRWTTFLKSRLNCSVPGDYPFYFDEI 91
             V+ RVA+VCK+D GG       +WT+FLK+RLNCSVPGD  FYF+ +
Sbjct: 233 KVVFPRVAQVCKNDMGGSQRVLEKQWTSFLKARLNCSVPGDSHFYFNIL 281

>3oky_B Putative uncharacterized protein; transmembrane, ligand, SEMA-domain, cell-CELL signalling, SI protein; HET: NAG; 2.19A {Mus musculus} PDB: 3okw_A* 3afc_A* 3al8_A* Length = 565

 Score = 41.3 bits (95), Expect = 4e-05
 Identities = 10/35 (28%), Positives = 15/35 (42%)

Query: 105 CAWDLKLRKDCVNLQDPYCAWDLKLRKCVPYQERT 139
           C    K +K C+  +DPYC W  +   C      +
Sbjct: 500 CERHGKCKKTCIASRDPYCGWVRESGSCAHLSPLS 534

>3nvq_A Semaphorin-7A; beta-propeller, signaling, signaling protein-protein binding; HET: NAG NDG; 2.40A {Homo sapiens} Length = 590

 Score = 52.3 bits (124), Expect = 6e-09
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 44  NAVYSRVARVCKSDKGGPHHF-GDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
               SRVA++C+ D+GG       +W TFLK+ L CS        F+ ++
Sbjct: 212 PLNVSRVAQLCRGDQGGESSLSVSKWNTFLKAMLVCSDAAT-NKNFNRLQ 260

>4fww_A Macrophage-stimulating protein receptor; beta-propeller, cysteine-knot, receptor tyrosine kinase, MAC stimulating protein, N-glycosylation; HET: NAG BMA; 1.85A {Homo sapiens} Length = 527

 Score = 40.4 bits (93), Expect = 9e-05
 Identities = 5/49 (10%), Positives = 19/49 (38%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
           +A+++R+AR+  ++     +           +L      +    +  ++
Sbjct: 233 SALHTRLARLSATEPELGDYRELVLDCRFAPKLVPRGSPEGGQPYPVLQ 281

>2uzx_B Hepatocyte growth factor receptor; signaling protein/receptor, leucine rich repeat, receptor ectodomain, signaling protein, ATP-binding; 2.8A {Homo sapiens} PDB: 2uzy_B 1shy_B 1ssl_A Length = 727

 Score = 39.6 bits (91), Expect = 1e-04
 Identities = 7/55 (12%), Positives = 19/55 (34%), Gaps = 14/55 (25%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSV------PGDYPFYFDEIR 92
              ++R+ R C  + G          ++++  L C +             F+ ++
Sbjct: 251 QTFHTRIIRFCSINSG--------LHSYMEMPLECILTEKRKKRSTKKEVFNILQ 297

>3nvn_B Plexin-C1; beta-propeller, signaling, viral protein-signaling protein C; HET: NDG NAG; 2.26A {Homo sapiens} PDB: 3nvq_B* Length = 476

 Score = 39.6 bits (91), Expect = 1e-04
 Identities = 7/27 (25%), Positives = 13/27 (48%)

Query: 113 KDCVNLQDPYCAWDLKLRKCVPYQERT 139
            +C+   DP+C W   L++C    +  
Sbjct: 428 SECLTATDPHCGWCHSLQRCTFQGDCV 454

>3nvn_B Plexin-C1; beta-propeller, signaling, viral protein-signaling protein C; HET: NDG NAG; 2.26A {Homo sapiens} PDB: 3nvq_B* Length = 476

 Score = 38.0 bits (87), Expect = 5e-04
 Identities = 5/45 (11%), Positives = 12/45 (26%), Gaps = 9/45 (20%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYF 88
              +  +AR+ +S                ++ L+C          
Sbjct: 224 ATGWPSMARIAQST---------EVLFQGQASLDCGHGHPDGRRL 259

>3ol2_B Plexin-B1; beta-propeller, signalling, extacellular, signaling protein; HET: NAG BMA; 2.99A {Homo sapiens} Length = 528

 Score = 39.3 bits (90), Expect = 2e-04
 Identities = 9/25 (36%), Positives = 13/25 (52%)

Query: 113 KDCVNLQDPYCAWDLKLRKCVPYQE 137
             C+  +DPYC W + L +C    E
Sbjct: 473 ASCLAHRDPYCGWCVLLGRCSRRSE 497

>3ol2_B Plexin-B1; beta-propeller, signalling, extacellular, signaling protein; HET: NAG BMA; 2.99A {Homo sapiens} Length = 528

 Score = 37.8 bits (86), Expect = 7e-04
 Identities = 8/53 (15%), Positives = 18/53 (33%), Gaps = 8/53 (15%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPED 96
            A  + V+RVC  D+         + ++++  L C            +    +
Sbjct: 226 RAFRAYVSRVCLRDQ--------HYYSYVELPLACEGGRYGLIQAAAVATSRE 270

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	148
3oky_B	565	Putative uncharacterized protein; transmembrane, l	100.0
1q47_A	495	Semaphorin 3A; beta propeller, signaling protein;	100.0
4gz8_A	667	Semaphorin-3A; multi-domain, cell-CELL signaling,	100.0
3nvq_A	590	Semaphorin-7A; beta-propeller, signaling, signalin	99.98
1olz_A	663	Semaphorin 4D; developmental protein, CD100, beta-	99.98
3nvx_A	383	Protein A39; beta-propeller, viral protein; HET: N	99.96
2uzx_B	727	Hepatocyte growth factor receptor; signaling prote	99.84
3ol2_B	528	Plexin-B1; beta-propeller, signalling, extacellula	99.81
3al9_A	539	Plexin-A2; beta-propeller, membrane protein, signa	99.79
4fww_A	527	Macrophage-stimulating protein receptor; beta-prop	99.78
3oky_A	681	Plexin-A2; transmembrane, ligand, SEMA-domain, cel	99.68
3nvn_B	476	Plexin-C1; beta-propeller, signaling, viral protei	98.76

>3oky_B Putative uncharacterized protein; transmembrane, ligand, SEMA-domain, cell-CELL signalling, SI protein; HET: NAG; 2.19A {Mus musculus} PDB: 3okw_A* 3afc_A* 3al8_A*

Probab=100.00  E-value=3.8e-38  Score=285.13  Aligned_cols=124  Identities=31%  Similarity=0.536  Sum_probs=110.0

Q ss_pred             cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEe--------cCceeeeeeecccccCCCC-CcccCcceehhhhhhh
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLT--------KKNAVYSRVARVCKSDKGG-PHHFGDRWTTFLKSRL   76 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~--------~~k~~~sRVaRVCknD~GG-~~~L~~kWTTFlKArL   76 (148)
                      +|+++|||||+||+|..+         +|+|||||+        ++|.++||||||||||.|| ++.|+++|||||||||
T Consensus       196 ~~~s~wLneP~FV~a~~~---------~d~VYFfF~E~a~E~~~~~k~~~sRVARVCk~D~GG~~r~L~~~WtSFlKarL  266 (565)
T 3oky_B          196 KHDSKWLKEPYFVQAVDY---------GDYIYFFFREIAVEYNTMGKVVFPRVAQVCKNDMGGSQRVLEKQWTSFLKARL  266 (565)
T ss_dssp             TTCTTTCSSCEEEEEEEE---------TTEEEEEEEEECGGGSSSSCCEEEEEEEEETTCCCCCSSSSTTBCSSCEEEEB
T ss_pred             ccchhhhcCCceeEEEee---------CCEEEEEEccccccccccCcceeeeEeeeCCCCCCCcccccccceeEEEEEEE
Confidence            589999999999998543         789999997        4678999999999999999 6899999999999999


Q ss_pred             cCCCCCCCCccCccccceeeec--c----------------CCCceeEEeee-eccccccCCCCeeeeecCCCeeeec-C
Q psy6150          77 NCSVPGDYPFYFDEIRLPEDCV--N----------------LQDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPY-Q  136 (148)
Q Consensus        77 ~Cs~pg~~~~~Fn~lqdv~~l~--~----------------~~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~-q  136 (148)
                      +|++||+.++|||+||+|+.+.  +                .+++.|||+|. |++   +|+|||++.++++.+|+++ +
T Consensus       267 ~Cs~pg~~~~~fn~lQav~~~~~~~~~~~~YgvFtt~~~~~~~SAVC~y~l~dI~~---~F~G~fk~~~~~~~~W~~~~~  343 (565)
T 3oky_B          267 NCSVPGDSHFYFNILQAVTDVIRINGRDVVLATFSTPYNSIPGSAVCAYDMLDIAN---VFTGRFKEQKSPDSTWTPVPD  343 (565)
T ss_dssp             CCEECSSSCEECCEEEEECCCEEETTEEEEEEEEECCSSSSCCEEEEEEEHHHHHH---HTTSCBEEESSTTSCEEECCG
T ss_pred             EcCCCCCCCccccceeeeeeeeccCCCCEEEEEEccCCCCCCccEEeeccHHHHHH---HhcCCcccccCCCcceEecCC
Confidence            9999999899999999986332  1                23556999999 999   9999999999999999997 7


Q ss_pred             CCcee
Q psy6150         137 ERTLE  141 (148)
Q Consensus       137 ~~~~~  141 (148)
                      ++||+
T Consensus       344 ~~vP~  348 (565)
T 3oky_B          344 ERVPK  348 (565)
T ss_dssp             GGSCS
T ss_pred             CcCCC
Confidence            87764

>1q47_A Semaphorin 3A; beta propeller, signaling protein; HET: NAG; 2.80A {Mus musculus} SCOP: b.69.12.1

Probab=100.00  E-value=1.7e-35  Score=262.57  Aligned_cols=130  Identities=28%  Similarity=0.459  Sum_probs=113.6

Q ss_pred             cccCCCCCCCceeeeeeeEeecCCCCC-CceEEEEEec--------CceeeeeeecccccCCCCCcccCcceehhhhhhh
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTSIDG-VDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRL   76 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~-ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL   76 (148)
                      +++..||++|+||++..|   +.+.+. +|+|||||.+        ++.++||||||||||.||+++|+++||||+||||
T Consensus       190 ~~d~~~l~~p~FV~s~~i---~~~~~~~~~~VYFff~e~~~e~~~~~~~~~SRVaRvCk~D~GG~~~l~~~wtSflka~L  266 (495)
T 1q47_A          190 QHDSRWLNDPRFISAHLI---PESDNPEDDKVYFFFRENAIDGEHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARL  266 (495)
T ss_dssp             SSCTTTCSSCEEEEEEEE---CCSSSGGGCEEEEEEEEECCCCSSCCCCEEEEEEEEETTCCCBSSSSBTBCSSCEEEEB
T ss_pred             ccCcccccCcceEEEEEe---cccccCCCCEEEEEEEeecccccccCcceEEEEEEECCCCCCccccchhccceEEEEEE
Confidence            367999999999999887   433333 7899999973        6789999999999999999999999999999999


Q ss_pred             cCCCCCCC--CccCccccceeeeccC-------------------CCceeEEeee-eccccccCCCCeeeeecCCCeeee
Q psy6150          77 NCSVPGDY--PFYFDEIRLPEDCVNL-------------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVP  134 (148)
Q Consensus        77 ~Cs~pg~~--~~~Fn~lqdv~~l~~~-------------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~  134 (148)
                      +|+.||+.  +++||+||+++.+..+                   +++.|||+|. |++   +|+|||++.++++.+|.+
T Consensus       267 ~Cs~~g~~g~~~~fn~lq~v~~~~~~~~~~~vlygvFst~~~~~~~SAvC~f~l~~I~~---~F~g~~~~~~~~~~~w~~  343 (495)
T 1q47_A          267 ICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRR---VFLGPYAHRDGPNYQWVP  343 (495)
T ss_dssp             CCEECCTTSCCEECCEEEEEEEECCSSTTCCEEEEEEECSCSSSCCEEEEEECHHHHHH---HHTSCBEECSSTTBCCEE
T ss_pred             EccCCCCCCCccccCceeeEEEeccCCCCCcEEEEEEecCCCCCCCcEEEEeEHHHHHH---HHhhhhhhccCCccceee
Confidence            99999874  7999999999965432                   2334999999 999   999999999999999999


Q ss_pred             cCCCcee
Q psy6150         135 YQERTLE  141 (148)
Q Consensus       135 ~q~~~~~  141 (148)
                      |+|++|.
T Consensus       344 ~~g~vp~  350 (495)
T 1q47_A          344 YQGRVPY  350 (495)
T ss_dssp             CCSCCCS
T ss_pred             ecCccCC
Confidence            9999875

>4gz8_A Semaphorin-3A; multi-domain, cell-CELL signaling, plexin, glycosilate extracellular, signaling protein; HET: NAG BMA MAN; 3.30A {Mus musculus}

Probab=100.00  E-value=1e-33  Score=259.62  Aligned_cols=131  Identities=27%  Similarity=0.441  Sum_probs=114.8

Q ss_pred             cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEec--------CceeeeeeecccccCCCCCcccCcceehhhhhhhc
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLN   77 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~   77 (148)
                      ++++.||+||.||++..|..  .+.+.+|+|||||++        ++.++||||||||||.||++.|+++||||+||||+
T Consensus       198 ~~~s~~l~~P~FV~s~~i~~--~~~~~~d~VYFFFrE~a~e~~~~~k~~~SRVaRVCknD~GG~~~L~~~wtSFlKarL~  275 (667)
T 4gz8_A          198 QHDSRWLNDPRFISAHLIPE--SDNPEDDKVYFFFRENAIDGEHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLI  275 (667)
T ss_dssp             SSCTTTCSSCEEEEEEEECC--SSSTTSCEEEEEEEEECCCC-CCCCCEEEEEEEEETTCCCCSSSSTTBCSSCEEEEEC
T ss_pred             ecccccccCCcceeeeeecc--cccCCCCEEEEEEEEEeeccCCcccceeeeeeeeCCCCCCCccccccceeeEEEEEEE
Confidence            57899999999999988832  234457899999973        57899999999999999999999999999999999


Q ss_pred             CCCCCC--CCccCccccceeeeccC-------------------CCceeEEeee-eccccccCCCCeeeeecCCCeeeec
Q psy6150          78 CSVPGD--YPFYFDEIRLPEDCVNL-------------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPY  135 (148)
Q Consensus        78 Cs~pg~--~~~~Fn~lqdv~~l~~~-------------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~  135 (148)
                      |+.||+  ++++||+||+++.+...                   +++.|||+|. |++   +|+|||++.+++..+|.++
T Consensus       276 Cs~pg~~~~~~~fn~Lq~v~~~~~~~~~~~vlYaVFtt~~~~~~~SAVC~FsL~dI~~---~F~g~~k~~~~~~~~w~~~  352 (667)
T 4gz8_A          276 CSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRR---VFLGPYAHRDGPNYQWVPY  352 (667)
T ss_dssp             CEECCTTSCCEECCEEEEEEEECCSCTTCCEEEEEEECSCSSSCCEEEEEEEHHHHHH---HHHSCBEECSSTTBCCEEC
T ss_pred             eecCCCCcccchhHhhhheeEccCCCCCCcEEEEEecCCCCCCCCcEEEEEEcHHHHH---HHhhhhhcccCCCcccccc
Confidence            999987  67899999999865432                   2345999999 999   9999999999999999999


Q ss_pred             CCCcee
Q psy6150         136 QERTLE  141 (148)
Q Consensus       136 q~~~~~  141 (148)
                      .+++|.
T Consensus       353 ~~~vp~  358 (667)
T 4gz8_A          353 QGRVPY  358 (667)
T ss_dssp             CSCCCS
T ss_pred             cCCcCC
Confidence            999875

>3nvq_A Semaphorin-7A; beta-propeller, signaling, signaling protein-protein binding; HET: NAG NDG; 2.40A {Homo sapiens}

Probab=99.98  E-value=1.8e-33  Score=255.58  Aligned_cols=106  Identities=21%  Similarity=0.332  Sum_probs=92.1

Q ss_pred             CCCCCCCceeeeeeeEeecCCCCCCceEEEEEec--------CceeeeeeecccccCCCCCcc-cCcceehhhhhhhcCC
Q psy6150           9 TPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHH-FGDRWTTFLKSRLNCS   79 (148)
Q Consensus         9 ~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~-L~~kWTTFlKArL~Cs   79 (148)
                      ++|||||+||+|..|   +++.+.||||||||++        ++.++||||||||||.||.+. |+++|||||||||+|+
T Consensus       172 ~~wL~eP~FV~s~~i---~~~~~~~d~VYFFFrE~a~e~~~~~~~~~SRVARVCknD~GG~~~ll~~~WTSFlKarL~Cs  248 (590)
T 3nvq_A          172 DTVMQNPQFIKATIV---HQDQAYDDKIYYFFREDNPDKNPEAPLNVSRVAQLCRGDQGGESSLSVSKWNTFLKAMLVCS  248 (590)
T ss_dssp             TTSCSSCEEEEEEEE---CCSSGGGCEEEEEEEEECSCCCTTSCSEEEEEEEEETTCCCBSSTTTTTBCSCCEEEEBCCB
T ss_pred             cchhcCCceeEEEec---cccCCCCCEEEEEecccccccccccceeeeeeeeecCCCccccchhhhcceeEEEEEEEECC
Confidence            689999999999999   5555568999999984        356799999999999999885 5999999999999999


Q ss_pred             CCCCCCccCccccceeeeccCC------------------CceeEEeee-eccccccCCCC
Q psy6150          80 VPGDYPFYFDEIRLPEDCVNLQ------------------DPYCAWDLK-LRKDCVNLQDP  121 (148)
Q Consensus        80 ~pg~~~~~Fn~lqdv~~l~~~~------------------~~~c~ysl~-i~~~~~~f~Gp  121 (148)
                      .||+ ++|||+||||+.++.+.                  ++.|||+|. |++   +|+|+
T Consensus       249 ~pg~-~~~FN~LQ~a~~~~~~~~~~~~~vlYgVFt~~~~~SAVCafsl~dI~~---~F~~~  305 (590)
T 3nvq_A          249 DAAT-NKNFNRLQDVFLLPDPSGQWRDTRVYGVFSNPWNYSAVCVYSLGDIDK---VFRTS  305 (590)
T ss_dssp             CTTT-CCBCCEEEEEEEECCTTCCGGGCEEEEEEECTTCCEEEEEEEHHHHHH---HHHHC
T ss_pred             CCCC-CCCccceeeEEEccccCCCCCCCEEEEEEecCCCCceEEEeeHHHHHH---HHhcC
Confidence            9986 78999999999766532                  234999999 999   99976

>1olz_A Semaphorin 4D; developmental protein, CD100, beta-propeller, PSI domain, IG-like domain, extracellular receptor, neurogenesis; 2.0A {Homo sapiens} SCOP: b.1.1.4 b.69.12.1 g.16.2.1 PDB: 3ol2_A*

Probab=99.98  E-value=2.4e-33  Score=256.01  Aligned_cols=132  Identities=28%  Similarity=0.453  Sum_probs=110.5

Q ss_pred             cccCCCCCCCceeeeeeeEeecCCCC-CCceEEEEEec--------CceeeeeeecccccCCCCCcccCcceehhhhhhh
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTSID-GVDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRL   76 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d-~ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL   76 (148)
                      .++++||++|.||++.+|....++.+ .+|+|||||++        +|.++||||||||||.||++.|+++||||+||||
T Consensus       179 e~~~~~L~~p~FV~s~~i~~~~~~~~~~~~~VYFff~e~~~e~~~~~k~~~SRVaRvCk~D~GG~~~l~~~wtSflka~L  258 (663)
T 1olz_A          179 EYAIPWLNEPSFVFADVIRKSPDSPDGEDDRVYFFFTEVSVEYEFVFRVLIPRIARVCKGDQGGLRTLQKKWTSFLKARL  258 (663)
T ss_dssp             CSSTTTCSSCEEEEEEEECCCC----CCCCEEEEEEEEECSSCBCSSCCEEEEEEEEETTCCCCSSSSTTSCSSCEEEEE
T ss_pred             cchhhhccCCceeEeeeeeccccccccCCCEEEEEEeeccccccccCcceeeEEEEECCCCCCcccccccccceEEEEeE
Confidence            46899999999999988844333333 47999999983        5789999999999999999999999999999999


Q ss_pred             cCCCCCCCCccCccccceeeeccC-------------------CCceeEEeee-eccccccCC-CCeeee---ecCCCee
Q psy6150          77 NCSVPGDYPFYFDEIRLPEDCVNL-------------------QDPYCAWDLK-LRKDCVNLQ-DPYCAW---DLKLRKC  132 (148)
Q Consensus        77 ~Cs~pg~~~~~Fn~lqdv~~l~~~-------------------~~~~c~ysl~-i~~~~~~f~-Gp~~~~---~~~~~~w  132 (148)
                      +|+.|+ .+++||+|||++.+..+                   +++.|||+|. |++   +|+ |+|++.   +.++.+|
T Consensus       259 ~Cs~~~-~~~~fn~lq~~~~~~~~~~~~~vlygvFst~~~~~~~SAvC~f~l~~I~~---~F~~g~~~~~~~~~~~~~~w  334 (663)
T 1olz_A          259 ICSRPD-SGLVFNVLRDVFVLRSPGLKVPVFYALFTPQLNNVGLSAVCAYNLSTAEE---VFSHGKYMQSTTVEQSHTKW  334 (663)
T ss_dssp             CCEEGG-GTEECCEEEEEEEECCTTCSSCEEEEEEECSSSCSSEEEEEEEEHHHHHH---HHHHSCBEEEECCSTTCCEE
T ss_pred             EecCCC-CCcccCceeeEEEeccCCCCCCEEEEEEccCCCCCCCcEEEEEEHHHHHH---HHhhccccccccccCCCcee
Confidence            999995 47899999999966432                   2234999999 999   998 999986   5678899


Q ss_pred             eecCCCcee
Q psy6150         133 VPYQERTLE  141 (148)
Q Consensus       133 v~~q~~~~~  141 (148)
                      ++|+++||+
T Consensus       335 ~~~~~~vp~  343 (663)
T 1olz_A          335 VRYNGPVPK  343 (663)
T ss_dssp             EECCSCCCS
T ss_pred             EecCCCCCC
Confidence            999999873

>3nvx_A Protein A39; beta-propeller, viral protein; HET: NAG; 2.00A {Vaccinia virus} PDB: 3nvn_A*

Probab=99.96  E-value=1.7e-31  Score=233.01  Aligned_cols=113  Identities=20%  Similarity=0.397  Sum_probs=90.7

Q ss_pred             CCCCCCCceeeeeeeEeecCCCCCCceEEEEEec-----CceeeeeeecccccCCCCCcccC-cceehhhhhhhcCCCCC
Q psy6150           9 TPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK-----KNAVYSRVARVCKSDKGGPHHFG-DRWTTFLKSRLNCSVPG   82 (148)
Q Consensus         9 ~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~-----~k~~~sRVaRVCknD~GG~~~L~-~kWTTFlKArL~Cs~pg   82 (148)
                      +.|||||+||++...   +  .+.||||||||++     .+.++||||||||||.||+++|+ +||||||||||+|++||
T Consensus       137 d~wLn~P~FV~s~~~---~--~~dddkVYFFFrE~a~e~~~~~~SRVARVCknD~GG~~~L~~~kWTSFLKArL~Cs~pG  211 (383)
T 3nvx_A          137 DNVIPKDGLRGAFVD---K--DGTYDKVYILFTDTIGSKRIVKIPYIAQMCLNDEGGPSSLSSHRWSTFLKVELECDIDG  211 (383)
T ss_dssp             TTSSCTTCCSEEEEE---E--ETTEEEEEEEEEEEECSSSCEEEEEEEEEETTCCCCSSGGGTTBCSSCEEEEECCEETT
T ss_pred             ccccCCcceeEEEcc---c--cCCCCEEEEEEEeecccccceeeehhhhcCccCCCCcccchhcceeeEEEEEEECCCCC
Confidence            689999999987432   2  2346999999984     23578999999999999999885 99999999999999998


Q ss_pred             CCCccCccccceeeeccC--------------CCceeEEeee-eccccccCCCCeeeeecCCCeeeecCCCcee
Q psy6150          83 DYPFYFDEIRLPEDCVNL--------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPYQERTLE  141 (148)
Q Consensus        83 ~~~~~Fn~lqdv~~l~~~--------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~q~~~~~  141 (148)
                      +.  +||.+|+++ +...              +++.|+|+|. |++   +|+||+         |..|+++||+
T Consensus       212 ~~--~~nllq~~~-~~~~~~~vlYgvFss~~~~SAVC~ysl~dI~~---~F~g~~---------~~~~~~~vP~  270 (383)
T 3nvx_A          212 RS--YRQIIHSRT-IKTDNDTILYVFFDSPYSKSALCTYSMNTIKQ---SFSTSK---------LEGYTKQLPS  270 (383)
T ss_dssp             EE--CCEEEEEEE-EECSSCEEEEEEEECSSSEEEEEEEEHHHHHH---HHHHCC---------BTTCCSCCCS
T ss_pred             cc--cccEEEEEE-ecCCCCcEEEEEecCCCCCcEEEeeeHHHHHH---HhcCCc---------ccccCCCCCC
Confidence            63  789999987 3332              2455999999 999   999984         4456666654

>2uzx_B Hepatocyte growth factor receptor; signaling protein/receptor, leucine rich repeat, receptor ectodomain, signaling protein, ATP-binding; 2.8A {Homo sapiens} PDB: 2uzy_B 1shy_B 1ssl_A

Probab=99.84  E-value=2.7e-22  Score=184.55  Aligned_cols=107  Identities=8%  Similarity=0.166  Sum_probs=80.7

Q ss_pred             cCCCC--CCCceeeeeeeEeecCCCCCCceEEEEEec-----CceeeeeeecccccCCCCCcccCcceehhhhhhhcCCC
Q psy6150           8 STPSL--DEVNLCCRGSVRFQSTSIDGVDHVWTQLTK-----KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSV   80 (148)
Q Consensus         8 ~~~wL--~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~-----~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~Cs~   80 (148)
                      +..|+  ++|.||++         .+.+|+|||||.+     ++.++||||||||||.        +||||+||||+|+.
T Consensus       217 ~~~~~~~~~~~fV~~---------f~~~~~vYF~f~e~~~~~~~~~~SRvaRvCk~D~--------~wtSflka~L~Cs~  279 (727)
T 2uzx_B          217 LPEFRDSYPIKYVHA---------FESNNFIYFLTVQRETLDAQTFHTRIIRFCSINS--------GLHSYMEMPLECIL  279 (727)
T ss_dssp             CGGGTTTSCEEEEEE---------EEETTEEEEEEEEBSSTTCSSBCCEEEEECCSSS--------CCCSCEEEEEEEEE
T ss_pred             ccccccccCCCceee---------eecCCEEEEEEeeccccccccceeEEEEEecCCC--------CeeEEEEEEEEecC
Confidence            34566  67778775         2358899999984     5789999999999998        59999999999999


Q ss_pred             CCC------CCccCccccceeeeccC-----------C---------------------CceeEEeee-eccccccCCCC
Q psy6150          81 PGD------YPFYFDEIRLPEDCVNL-----------Q---------------------DPYCAWDLK-LRKDCVNLQDP  121 (148)
Q Consensus        81 pg~------~~~~Fn~lqdv~~l~~~-----------~---------------------~~~c~ysl~-i~~~~~~f~Gp  121 (148)
                      ||+      .+++||+||+++.+.++           +                     ++.|||+|. |++   +|+||
T Consensus       280 ~~~~~~r~~~~~~fn~lQa~~~~~~g~~La~~l~i~~~~~vlygVFs~~~~~~~~~~~~SAvC~f~l~~I~~---~F~~~  356 (727)
T 2uzx_B          280 TEKRKKRSTKKEVFNILQAAYVSKPGAQLARQIGASLNDDILFAVFAQSKPDSAEPMDRSAMCAFPIKYVND---FFNKI  356 (727)
T ss_dssp             C---------CEEECEEEEEEEECCCHHHHHHHTCCTTCCEEEEEEEEECTTSSCEEEEEEEEEEEHHHHHH---HHTCC
T ss_pred             CCcccccccCCcCcCceeEEeecCCchhhhhhccCCCCCCEEEEEEcCCccccCCCCCCcEEEEEEHHHHHH---HHhhh
Confidence            985      46799999999855321           1                     123999999 999   99999


Q ss_pred             eeeeecCCCeeee
Q psy6150         122 YCAWDLKLRKCVP  134 (148)
Q Consensus       122 ~~~~~~~~~~wv~  134 (148)
                      |++-....+.|++
T Consensus       357 ~~~~~~~~~~~~~  369 (727)
T 2uzx_B          357 VNKNNVRCLQHFY  369 (727)
T ss_dssp             ----CEECCHHHH
T ss_pred             HhhcCcccccccc
Confidence            9986556777863

>3ol2_B Plexin-B1; beta-propeller, signalling, extacellular, signaling protein; HET: NAG BMA; 2.99A {Homo sapiens}

Probab=99.81  E-value=3.1e-21  Score=173.14  Aligned_cols=103  Identities=15%  Similarity=0.231  Sum_probs=83.5

Q ss_pred             ccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEec------CceeeeeeecccccCCCCCcccCcceehhhhhhhcCCC
Q psy6150           7 WSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSV   80 (148)
Q Consensus         7 ~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~Cs~   80 (148)
                      |.+.|  +|.||++..         .+|+|||||.+      ++..++|||||||||.        +||||+||||+|+.
T Consensus       194 ~~~~~--~~~FV~aF~---------~~~~VYF~f~e~~~~~~~~~~~sRvaRvCk~D~--------~w~Sy~k~~L~C~g  254 (528)
T 3ol2_B          194 RLSEY--SHHFVSAFA---------RGASAYFLFLRRDLQAQSRAFRAYVSRVCLRDQ--------HYYSYVELPLACEG  254 (528)
T ss_dssp             CHHHH--CCEEEEEEE---------ETTEEEEEEEEECTTSTTCCEEEEEEEEESSCS--------SCTTCEEEEEESTT
T ss_pred             ccccC--CCcEEEEEe---------cCCEEEEEEEEEcccccccccccceeeeeCCCC--------CeeEEEEEEEecCC
Confidence            45677  999999832         47899999973      3688999999999998        79999999999994


Q ss_pred             CCCCCccCccccceeeeccC--------------------------------CCceeEEeee-eccccccCCCCeee-e-
Q psy6150          81 PGDYPFYFDEIRLPEDCVNL--------------------------------QDPYCAWDLK-LRKDCVNLQDPYCA-W-  125 (148)
Q Consensus        81 pg~~~~~Fn~lqdv~~l~~~--------------------------------~~~~c~ysl~-i~~~~~~f~Gp~~~-~-  125 (148)
                      +     +||+||+++.++.+                                +++.|||+|. |++   +|+||+++ + 
T Consensus       255 ~-----~fn~lQaa~~~~~g~~l~~~vly~vFs~~~~~~~~~~~~~~~~p~~~SAVC~f~l~~I~~---~f~~~~~~Cy~  326 (528)
T 3ol2_B          255 G-----RYGLIQAAAVATSREVAHGEVLFAAFSSAAPPTVGRPPSAAAGASGASALCAFPLDEVDR---LANRTRDACYT  326 (528)
T ss_dssp             T-----TSCEEEEEEEEEC---CCCSEEEEEEECBCCC-----CCBCCGGGCCEEEEEEEHHHHHH---HHHHHHHHHHH
T ss_pred             C-----CCCceeEEEEccCCCccCCCEEEEEEecCCCCccccccccccCCCCccEEEEEEHHHHHH---HHhhhhhhhhc
Confidence            3     79999999966532                                3456999999 999   99999987 2 


Q ss_pred             ------ecCCCeeeecC
Q psy6150         126 ------DLKLRKCVPYQ  136 (148)
Q Consensus       126 ------~~~~~~wv~~q  136 (148)
                            ++....|+|+.
T Consensus       327 ~~~~~~~~~~~~~~p~~  343 (528)
T 3ol2_B          327 REGRAEDGTEVAYIEYD  343 (528)
T ss_dssp             STTTCSSSCCCEEECTT
T ss_pred             cccccccCCcccceecC
Confidence                  23456788764

>3al9_A Plexin-A2; beta-propeller, membrane protein, signaling protein; HET: NAG; 2.10A {Mus musculus} PDB: 3al8_B*

Probab=99.79  E-value=4.5e-21  Score=171.48  Aligned_cols=97  Identities=12%  Similarity=0.257  Sum_probs=75.7

Q ss_pred             CCceeeeeeeEeecCCCCCCceEEEEEec-------------CceeeeeeecccccCCCCCcccCcceehhhhhhhcCCC
Q psy6150          14 EVNLCCRGSVRFQSTSIDGVDHVWTQLTK-------------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSV   80 (148)
Q Consensus        14 ~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~-------------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~Cs~   80 (148)
                      +|.||++         .+.++.|||||.+             ++.++||||||||||.        +||||+||||+|+.
T Consensus       210 ~~~fV~a---------F~~~~~VYF~~~e~~~~~~~~e~~~~~~~~~SRvaRvCk~D~--------~wtSflka~L~Cs~  272 (539)
T 3al9_A          210 DIFYIYG---------FASGGFVYFLTVQPETPDGMAINSAGDLFYTSRIVRLCKDDP--------KFHSYVSLPFGCTR  272 (539)
T ss_dssp             CCEEEEE---------EEETTEEEEEEEEECCC----------CBEEEEEEEEESSCT--------TCTTCEEEEEEEEE
T ss_pred             CcceEEE---------EecCCEEEEEEEecccccccccccccccceeeEEEEEcCCcc--------ccceEEEEEeecCC
Confidence            5566765         2457899999973             3678999999999995        89999999999999


Q ss_pred             CCCCCccCccccceeeeccC--------------------------------CCceeEEeee-eccccccCCCC----ee
Q psy6150          81 PGDYPFYFDEIRLPEDCVNL--------------------------------QDPYCAWDLK-LRKDCVNLQDP----YC  123 (148)
Q Consensus        81 pg~~~~~Fn~lqdv~~l~~~--------------------------------~~~~c~ysl~-i~~~~~~f~Gp----~~  123 (148)
                      ||.   +||+||+++.+.++                                +++.|||+|. |++   +|+|+    |+
T Consensus       273 ~g~---~fn~lqa~~~~~~g~~La~~l~~~~~~~vlygvFs~~~~~~~~~~~~SAvC~f~l~~I~~---~F~~~~~~cf~  346 (539)
T 3al9_A          273 AGV---EYRLLQAAYLAKPGEALAQAFNISSDEDVLFAIFSKGQKQYHHPPDDSALCAFPIRAINL---QIKERLQSCYH  346 (539)
T ss_dssp             TTE---EEEEEEEEEEECCCHHHHHHHTCCTTSCEEEEEEEEBSBCSSSCCSCEEEEEEEHHHHHH---HHHHHHHHHHT
T ss_pred             CCc---CcchhheeeeccccccchhhcccCCCCCEEEEEEecCccccCCCCCCCEEEEEEHHHHHH---HHHhhHHhhhc
Confidence            974   89999999854321                                2345999999 999   99998    44


Q ss_pred             eeecCCCeee
Q psy6150         124 AWDLKLRKCV  133 (148)
Q Consensus       124 ~~~~~~~~wv  133 (148)
                      .-..+..+|.
T Consensus       347 ~~~~~~~~w~  356 (539)
T 3al9_A          347 GEGNLELNWL  356 (539)
T ss_dssp             TCSBCCCHHH
T ss_pred             cCCcccccee
Confidence            4444566675

>4fww_A Macrophage-stimulating protein receptor; beta-propeller, cysteine-knot, receptor tyrosine kinase, MAC stimulating protein, N-glycosylation; HET: NAG BMA; 1.85A {Homo sapiens}

Probab=99.78  E-value=1.3e-20  Score=165.96  Aligned_cols=97  Identities=10%  Similarity=0.099  Sum_probs=76.7

Q ss_pred             CCceEEEEEe-------cCceeeeeeecccccCCCCCcccCcceehhhhhhhcCCCCCCC--------CccCccccceee
Q psy6150          32 GVDHVWTQLT-------KKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDY--------PFYFDEIRLPED   96 (148)
Q Consensus        32 ~ddkvY~ff~-------~~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~Cs~pg~~--------~~~Fn~lqdv~~   96 (148)
                      .+++|||||.       .++.++||||||||||.|        |+||+|+||+|+.++..        +++||.||+++.
T Consensus       214 ~~~~vYF~f~e~~~~~~~~~~~~SRvaRVCk~D~~--------~~Sy~e~~L~C~~~~~~~~~~~~~~~~~yn~lQ~a~~  285 (527)
T 4fww_A          214 TGAFVYFLTVQPASVTDDPSALHTRLARLSATEPE--------LGDYRELVLDCRFAPKLVPRGSPEGGQPYPVLQVAHS  285 (527)
T ss_dssp             ETTEEEEEEEEESSTTSCTTSEEEEEEEEESSSSC--------CTTCEEEEEEEEECC----------CEEECEEEEEEE
T ss_pred             cCCEEEEEEEEEccccCCCcccceeeeEEcccCCC--------cceEEEEEEEeeccccccccccccCCcccceeeeEee
Confidence            4678999997       367899999999999976        99999999999988653        356999999874


Q ss_pred             ecc--------------------------------CCCceeEEeee-eccccccCCCCeeeeecCCCeeeecCCCc
Q psy6150          97 CVN--------------------------------LQDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPYQERT  139 (148)
Q Consensus        97 l~~--------------------------------~~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~q~~~  139 (148)
                      .+.                                .+++.|||+|. |++   +|+|++.+-.....+|..+.+++
T Consensus       286 ~~~g~~La~~l~~~~~~~vly~vFs~~~~~~~~~~~~SAvC~f~m~~I~~---~F~~~~~~c~~~~~~~~~~~~~~  358 (527)
T 4fww_A          286 APVGAQLATELSIAEGQEVLFGVFVTGKDGGPGVGPNSVVCAFPIDLLDT---LIDEGVERCCESPVHPGLRRGLD  358 (527)
T ss_dssp             EECCHHHHHHHTSCTTCEEEEEEEECCC----CCSCSCEEEEEEHHHHHH---HHHHHHHHHHSSSCCTTCBCCCT
T ss_pred             cCccchhhhhcccCCCCCEEEEEEeCccCCCCCCCCccEEEEEEHHHHHH---HHHhhhhhcccCCCCCCceeccC
Confidence            321                                12567999999 999   99999988777777775555544

>3oky_A Plexin-A2; transmembrane, ligand, SEMA-domain, cell-CELL signalling, SI protein; HET: NAG; 2.19A {Mus musculus} PDB: 3okt_A* 4gza_A

Probab=99.68  E-value=2.3e-18  Score=158.50  Aligned_cols=89  Identities=13%  Similarity=0.272  Sum_probs=72.6

Q ss_pred             CCCceEEEEEecC-------------ceeeeeeecccccCCCCCcccCcceehhhhhhhcCCCCCCCCccCccccceeee
Q psy6150          31 DGVDHVWTQLTKK-------------NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIRLPEDC   97 (148)
Q Consensus        31 d~ddkvY~ff~~~-------------k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~Cs~pg~~~~~Fn~lqdv~~l   97 (148)
                      +.++.|||||.+.             +..+||||||||+|        .+||||+||||+|+.+|.   +||.||+++.+
T Consensus       217 ~~~~fVYFlf~q~~~~~~~~~~~~~~~~~~SRVaRvCk~D--------~~wtSylka~L~C~~~g~---~fn~lQaa~~~  285 (681)
T 3oky_A          217 ASGGFVYFLTVQPETPDGMAINSAGDLFYTSRIVRLCKDD--------PKFHSYVSLPFGCTRAGV---EYRLLQAAYLA  285 (681)
T ss_dssp             EETTEEEEEEEEECCC----------CCEEEEEEEEESSC--------TTCTTCEEEEEEEEETTE---EECEEEEEEEE
T ss_pred             EcCCEEEEEEEeecccccccccccccceeeEEEEEecCCC--------CCeeEEEEEEEecCCCCc---CCCceeEEEec
Confidence            3467899998641             46889999999999        499999999999999874   79999999965


Q ss_pred             ccC--------------------------------CCceeEEeee-eccccccCCCC----eeeeecCCCeee
Q psy6150          98 VNL--------------------------------QDPYCAWDLK-LRKDCVNLQDP----YCAWDLKLRKCV  133 (148)
Q Consensus        98 ~~~--------------------------------~~~~c~ysl~-i~~~~~~f~Gp----~~~~~~~~~~wv  133 (148)
                      .++                                +++.|||+|. |++   +|+|+    |+.....+..|.
T Consensus       286 ~pg~~LA~~lg~~~~~~vlygVFs~~~~~~~~~~~~SAVCaF~l~~I~~---~f~~~~~~Cy~~~~~~~~~w~  355 (681)
T 3oky_A          286 KPGEALAQAFNISSDEDVLFAIFSKGQKQYHHPPDDSALCAFPIRAINL---QIKERLQSCYHGEGNLELNWL  355 (681)
T ss_dssp             CCCHHHHHHHTCCTTSCEEEEEEESBSSCSSSCCSCEEEEEEEHHHHHH---HHHHHHHHHHTTCSBCCCHHH
T ss_pred             cCcchhhhhcccCccCCEEEEEEecCCcCCCCCCCceEEEEEEHHHHHH---HHhhhhhhhhcCCCCCCcccc
Confidence            321                                3445999999 999   99998    887776677775

>3nvn_B Plexin-C1; beta-propeller, signaling, viral protein-signaling protein C; HET: NDG NAG; 2.26A {Homo sapiens} PDB: 3nvq_B*

Probab=98.76  E-value=2.8e-09  Score=95.41  Aligned_cols=70  Identities=9%  Similarity=-0.012  Sum_probs=53.2

Q ss_pred             cccCCCCC---CC-ceeeeeeeEeecCCCCCCceEEEEEe----cCc--eeeeeeecccccCCCCCcccCcceehhhhhh
Q psy6150           6 TWSTPSLD---EV-NLCCRGSVRFQSTSIDGVDHVWTQLT----KKN--AVYSRVARVCKSDKGGPHHFGDRWTTFLKSR   75 (148)
Q Consensus         6 ~~~~~wL~---~P-~Fv~~~~i~f~~~s~d~ddkvY~ff~----~~k--~~~sRVaRVCknD~GG~~~L~~kWTTFlKAr   75 (148)
                      ++++.||+   +| +||.+         .+.++.|||+|.    .++  ..+||||||||+|.        + ++|+||+
T Consensus       185 ~~~~~~~~~~~~~~~fV~a---------f~~~~~vyf~~y~y~~~s~~~~~~sriaRvCk~D~--------~-~sy~e~~  246 (476)
T 3nvn_B          185 ELGRLKLCEGAGSLHFVDA---------FLWNGSIYFPYYPYNYTSGAATGWPSMARIAQSTE--------V-LFQGQAS  246 (476)
T ss_dssp             TTSEEEBCTTSCCEEECCC---------EECSSEEEEEEEEEETTTTEECSCCEEEEEESSSS--------C-CEEEEEE
T ss_pred             hhcceeeccCCCCceeeee---------hhcCceeEEEEEeeccccCCccceeeEEEEeecCC--------C-cEEEEEE
Confidence            45667888   77 77765         235678898764    244  58999999999996        2 7899999


Q ss_pred             hcCCCCCCCCccCcccccee
Q psy6150          76 LNCSVPGDYPFYFDEIRLPE   95 (148)
Q Consensus        76 L~Cs~pg~~~~~Fn~lqdv~   95 (148)
                      |+|+.++..  .||.||++.
T Consensus       247 L~C~~~~~~--~y~ll~slg  264 (476)
T 3nvn_B          247 LDCGHGHPD--GRRLLLSSS  264 (476)
T ss_dssp             ECCCSSCSS--CCCEEEEEE
T ss_pred             EeccCCCCC--CcceEEecC
Confidence            999997643  388888775

---

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	148
d1q47a_	495	b.69.12.1 (A:) Semaphorin 3a {Mouse (Mus musculus)	5e-15
d1olza2	478	b.69.12.1 (A:3-480) Semaphorin 4d {Human (Homo sap	3e-14
d1shyb1	476	b.69.12.1 (B:40-515) Hepatocyte growth factor rece	6e-08
d1olza3	56	g.16.2.1 (A:481-536) Semaphorin 4d {Human (Homo sa	5e-04

>d1q47a_ b.69.12.1 (A:) Semaphorin 3a {Mouse (Mus musculus) [TaxId: 10090]} Length = 495

class: All beta proteins
fold: 7-bladed beta-propeller
superfamily: Sema domain
family: Sema domain
domain: Semaphorin 3a
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.6 bits (167), Expect = 5e-15
 Identities = 23/51 (45%), Positives = 35/51 (68%), Gaps = 2/51 (3%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGD--YPFYFDEIR 92
            A ++R+ ++CK+D GG     ++WTTFLK+RL CSVPG      +FDE++
Sbjct: 234 KATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQ 284

>d1olza2 b.69.12.1 (A:3-480) Semaphorin 4d {Human (Homo sapiens) [TaxId: 9606]} Length = 478

class: All beta proteins
fold: 7-bladed beta-propeller
superfamily: Sema domain
family: Sema domain
domain: Semaphorin 4d
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.3 bits (161), Expect = 3e-14
 Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 45  AVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYPFYFDEIR 92
            +  R+ARVCK D+GG      +WT+FLK+RL CS P      F+ +R
Sbjct: 225 VLIPRIARVCKGDQGGLRTLQKKWTSFLKARLICSRPDS-GLVFNVLR 271

>d1shyb1 b.69.12.1 (B:40-515) Hepatocyte growth factor receptor {Human (Homo sapiens) [TaxId: 9606]} Length = 476

class: All beta proteins
fold: 7-bladed beta-propeller
superfamily: Sema domain
family: Sema domain
domain: Hepatocyte growth factor receptor
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 6e-08
 Identities = 8/55 (14%), Positives = 20/55 (36%), Gaps = 14/55 (25%)

Query: 44  NAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDYP------FYFDEIR 92
              ++R+ R C  + G          ++++  L C +    P        F+ ++
Sbjct: 233 QTFHTRIIRFCSINSG--------LHSYMEMPLECILTELVPRGSTKKEVFNILQ 279

>d1olza3 g.16.2.1 (A:481-536) Semaphorin 4d {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: Trefoil/Plexin domain-like
superfamily: Plexin repeat
family: Plexin repeat
domain: Semaphorin 4d
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 5e-04
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 113 KDCVNLQDPYCAWDLKLRKCVPYQE 137
           +DCV  +DPYCAW      CV   +
Sbjct: 9   EDCVLARDPYCAWSPPTATCVALHQ 33

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	148
d1q47a_	495	Semaphorin 3a {Mouse (Mus musculus) [TaxId: 10090]	99.97
d1olza2	478	Semaphorin 4d {Human (Homo sapiens) [TaxId: 9606]}	99.96
d1shyb1	476	Hepatocyte growth factor receptor {Human (Homo sap	99.87

>d1q47a_ b.69.12.1 (A:) Semaphorin 3a {Mouse (Mus musculus) [TaxId: 10090]}

class: All beta proteins
fold: 7-bladed beta-propeller
superfamily: Sema domain
family: Sema domain
domain: Semaphorin 3a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.97  E-value=5.2e-32  Score=236.34  Aligned_cols=131  Identities=27%  Similarity=0.441  Sum_probs=113.2

Q ss_pred             cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEec--------CceeeeeeecccccCCCCCcccCcceehhhhhhhc
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLN   77 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~   77 (148)
                      .+++.||++|.||++..|..  .....+|+|||||++        ++.++||||||||||.||++.|+++||||+||||+
T Consensus       190 ~~~~~~l~~p~Fv~s~~i~~--~~~~~~~~vYfff~e~~~e~~~~~~~~~sRvaRVCk~D~GG~~~l~~~wtSf~ka~L~  267 (495)
T d1q47a_         190 QHDSRWLNDPRFISAHLIPE--SDNPEDDKVYFFFRENAIDGEHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLI  267 (495)
T ss_dssp             SSCTTTCSSCEEEEEEEECC--SSSGGGCEEEEEEEEECCCCSSCCCCEEEEEEEEETTCCCBSSSSBTBCSSCEEEEBC
T ss_pred             hhhhhhcCCccceeeeeecc--ccCCCCCEEEEEEEEEehhcCCCCceeEEEEEEecccCcCccccccccccEEEEEEEE
Confidence            46788999999999988843  223347899999984        56789999999999999999999999999999999


Q ss_pred             CCCCCC--CCccCccccceeeeccC-------------------CCceeEEeee-eccccccCCCCeeeeecCCCeeeec
Q psy6150          78 CSVPGD--YPFYFDEIRLPEDCVNL-------------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPY  135 (148)
Q Consensus        78 Cs~pg~--~~~~Fn~lqdv~~l~~~-------------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~  135 (148)
                      |+.||+  .+++||+||+++.+..+                   +++.|+|+|. |++   +|+|+|++.+....+|.+|
T Consensus       268 Cs~~g~~~~~~~fn~lq~~~~~~~~~~~~~vlygvFst~~~~~~~SAvC~fsl~~I~~---~F~g~~~~~~~~~~~~~~~  344 (495)
T d1q47a_         268 CSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRR---VFLGPYAHRDGPNYQWVPY  344 (495)
T ss_dssp             CEECCTTSCCEECCEEEEEEEECCSSTTCCEEEEEEECSCSSSCCEEEEEECHHHHHH---HHTSCBEECSSTTBCCEEC
T ss_pred             eecCCCCCccccchhhheeEEeccCCCCCcEEEEEeeccCCCCCceEEEEeEHHHHHH---HhhhhhhhhcCCCcccccc
Confidence            999987  57999999999865421                   2345999999 999   9999999999999999999


Q ss_pred             CCCcee
Q psy6150         136 QERTLE  141 (148)
Q Consensus       136 q~~~~~  141 (148)
                      .+++|.
T Consensus       345 ~~~~p~  350 (495)
T d1q47a_         345 QGRVPY  350 (495)
T ss_dssp             CSCCCS
T ss_pred             cCCCCc
Confidence            998875

>d1olza2 b.69.12.1 (A:3-480) Semaphorin 4d {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: 7-bladed beta-propeller
superfamily: Sema domain
family: Sema domain
domain: Semaphorin 4d
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=5.8e-30  Score=222.99  Aligned_cols=132  Identities=27%  Similarity=0.433  Sum_probs=107.9

Q ss_pred             cccCCCCCCCceeeeeeeEeecCC-CCCCceEEEEEe--------cCceeeeeeecccccCCCCCcccCcceehhhhhhh
Q psy6150           6 TWSTPSLDEVNLCCRGSVRFQSTS-IDGVDHVWTQLT--------KKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRL   76 (148)
Q Consensus         6 ~~~~~wL~~P~Fv~~~~i~f~~~s-~d~ddkvY~ff~--------~~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL   76 (148)
                      .++..||++|+|+++..|...... .+.+|+|||||.        +++.++||||||||+|.||++.|+++||||+||||
T Consensus       177 ~~~~~~l~~p~fv~~~~i~~~~~~~f~~~~~vYFff~e~~~e~~~~~~~~~SRvaRvCk~D~GG~~~l~~~wtSy~ka~L  256 (478)
T d1olza2         177 EYAIPWLNEPSFVFADVIRKSPDSPDGEDDRVYFFFTEVSVEYEFVFRVLIPRIARVCKGDQGGLRTLQKKWTSFLKARL  256 (478)
T ss_dssp             CSSTTTCSSCEEEEEEEECCCC----CCCCEEEEEEEEECSSCBCSSCCEEEEEEEEETTCCCCSSSSTTSCSSCEEEEE
T ss_pred             hhhhhcccCCceEEEeeecccccccccCCCEEEEEEEEEeccCCCCCceeeeeeehhccCCcCCccccccceeEEEEEEE
Confidence            356789999999999887332222 233789999997        36789999999999999999999999999999999


Q ss_pred             cCCCCCCCCccCccccceeeeccCC-------------------CceeEEeee-eccccccCC-CCeeeeec---CCCee
Q psy6150          77 NCSVPGDYPFYFDEIRLPEDCVNLQ-------------------DPYCAWDLK-LRKDCVNLQ-DPYCAWDL---KLRKC  132 (148)
Q Consensus        77 ~Cs~pg~~~~~Fn~lqdv~~l~~~~-------------------~~~c~ysl~-i~~~~~~f~-Gp~~~~~~---~~~~w  132 (148)
                      +|+.+++ +++||+|||++.+..+.                   ++.|||+|+ |++   +|+ |+|+...+   ...+|
T Consensus       257 ~Cs~~~~-~~~yn~lq~a~~~~~~~~~~~vly~vFst~~~~~~~SAvC~fsl~~I~~---~F~~~~~~~~~~~~~~~~~~  332 (478)
T d1olza2         257 ICSRPDS-GLVFNVLRDVFVLRSPGLKVPVFYALFTPQLNNVGLSAVCAYNLSTAEE---VFSHGKYMQSTTVEQSHTKW  332 (478)
T ss_dssp             CCEEGGG-TEECCEEEEEEEECCTTCSSCEEEEEEECSSSCSSEEEEEEEEHHHHHH---HHHHSCBEEEECCSTTCCEE
T ss_pred             EeccCCC-CCCCcceeEEEEecCCCCCCcEEEEEEcCCCCCCCccEEEEeEHHHHHH---HHhhcchhhccCCCCCcccc
Confidence            9999875 78999999999655432                   224999999 999   997 99998754   66789


Q ss_pred             eecCCCcee
Q psy6150         133 VPYQERTLE  141 (148)
Q Consensus       133 v~~q~~~~~  141 (148)
                      ..+.+.+|.
T Consensus       333 ~~~~~~~~~  341 (478)
T d1olza2         333 VRYNGPVPK  341 (478)
T ss_dssp             EECCSCCCS
T ss_pred             cccCCcCCc
Confidence            998887764

>d1shyb1 b.69.12.1 (B:40-515) Hepatocyte growth factor receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: 7-bladed beta-propeller
superfamily: Sema domain
family: Sema domain
domain: Hepatocyte growth factor receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=6.8e-24  Score=183.67  Aligned_cols=94  Identities=11%  Similarity=0.219  Sum_probs=73.7

Q ss_pred             CCCceEEEEEec-----CceeeeeeecccccCCCCCcccCcceehhhhhhhcCCCCCCC------CccCccccceeeecc
Q psy6150          31 DGVDHVWTQLTK-----KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGDY------PFYFDEIRLPEDCVN   99 (148)
Q Consensus        31 d~ddkvY~ff~~-----~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~Cs~pg~~------~~~Fn~lqdv~~l~~   99 (148)
                      +.+|+|||||.+     ++.++||||||||||.|        ||||+||||+|+.|+..      .++||+|||++...+
T Consensus       215 ~~~~~vYF~f~e~~~~~~~~~~SRvaRVCk~D~~--------wtSy~ka~L~Cs~p~~~p~~~~~~~~fN~lQ~~~v~~p  286 (476)
T d1shyb1         215 ESNNFIYFLTVQRETLDAQTFHTRIIRFCSINSG--------LHSYMEMPLECILTELVPRGSTKKEVFNILQAAYVSKP  286 (476)
T ss_dssp             EETTEEEEEEECCSSTTCSCCCEEEEEEECCTTC--------CCSCEEEEEEEECC---------CCBCCCCCEEEEECC
T ss_pred             ccCCEEEEEEEeccccccccceeEEEEEeccCCC--------cceEEEEEEEEecCCcccccCCCCcccceeeEEEecCc
Confidence            457999999984     67889999999999965        99999999999999764      389999999874321


Q ss_pred             C--------------------------------CCceeEEeee-eccccccCCCCeeeeecCCCeeeec
Q psy6150         100 L--------------------------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPY  135 (148)
Q Consensus       100 ~--------------------------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~  135 (148)
                      +                                +++.|||+|. |++   +|+|+|+........|++.
T Consensus       287 g~~La~~l~~~~~~~vlygvFsts~~~~~~~~~~SAVC~fsl~dI~~---~F~~~~~~~~~~~~~~~~~  352 (476)
T d1shyb1         287 GAQLARQIGASLNDDILFGVFAQSKPDSAEPMDRSAMCAFPIKYVND---FFNKIVNKNNVRCLQHFYG  352 (476)
T ss_dssp             CHHHHHHHTCCTTCCEEEEEEEEECTTSSSEEEEEEEEEEEHHHHHH---HHHCC----CBCCCTTTSC
T ss_pred             chhhhhhcCCCCCCCEEEEEEcCCcCCCCCCCCCcEEEEEEHHHHHH---HHhhhhhccccCCCceeeC
Confidence            0                                1456999999 999   9999999998888888754