Psyllid ID: psy12771

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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-------150-------160
Protein Sequence
MYSFLGLPPLSFENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKIIL
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccHHHHccEEcEEcHHHHHHHHccccccccccEEEccccccccccccccccccccEEEcccccccccEEEEEEccccccccccEEEEccccccccEEEEEcccccccccccccccccccccccccccccccEEEEEcc
Secondary Structure Prediction (SSPRO)
cccHcccccccccccccccccccHHHHHHcccEEEEHHHHHHHcccccccHHHHHHHHHHcccccccccccccccccEEEcccccccccEEEEEEcccccccccEEEEEEEcccccccEEEEccccccccccccccEEEEHHccccHcccccHHHHHHcc
Coil and Loop (DISEMBL)
mysflglpplsfenqhnfpavppqlatfFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLthlgrhehvpgigsgiakcpydpndnstaiwvekgnpgnlpalysgtnaeftkadTVIFRTDllnfttgkkeytfKRTIKYDSKWLDSFKSLIAKIIL
Flexible Loop (DISEMBL)
MYSFLGLPPLSFENQHNFPAVPPQLATFFGVKKVVEEEeeeekkkergftkVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDllnfttgkkeytfkrtikydskwldsfKSLIAKIIL
Low Complexity Region (SEG)
MYSFLGLPPLSFENQHNFPAVPPQLATFFGvkkvveeeeeeekkkeRGFTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKIIL
Disordered region (IsUnstruct)
************************************************FTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKII*
Disordered Region (DISOPRED)
*YSFLGLPPLSFENQHNFPAVPPQLATFFGVK******************KVFFWKILENNLTHLG***********IAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDL************KRTIKYDSKWLDSFKSLIAKIIL
Disordered Region (DISEMBL)
MYSFLGLPPLSFENQHNFPAVPPQLATFFGVKK*************RGFTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKIIL
Disordered Region (DISPRO)
*YSFLGLPPLSFENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKIIL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYSFLGLPPLSFENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKIIL
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	160	2.2.26 [Sep-21-2011]
Q9XZC8	697	Semaphorin-2A OS=Schistoc	N/A	N/A	0.587	0.134	0.776	2e-42
Q24323	724	Semaphorin-2A OS=Drosophi	yes	N/A	0.581	0.128	0.741	5e-36
Q9P283	1151	Semaphorin-5B OS=Homo sap	yes	N/A	0.375	0.052	0.364	7e-06
Q60519	1093	Semaphorin-5B OS=Mus musc	yes	N/A	0.375	0.054	0.364	8e-06
Q60PR7	656	Semaphorin-2A OS=Caenorha	N/A	N/A	0.437	0.106	0.375	9e-06
Q5R7F5	1017	Semaphorin-6D OS=Pongo ab	no	N/A	0.362	0.057	0.356	4e-05
Q8NFY4	1073	Semaphorin-6D OS=Homo sap	no	N/A	0.362	0.054	0.356	4e-05
Q76KF0	1073	Semaphorin-6D OS=Mus musc	no	N/A	0.362	0.054	0.356	5e-05
Q95XP4	658	Semaphorin-2A OS=Caenorha	yes	N/A	0.493	0.120	0.349	5e-05
Q9H3T2	930	Semaphorin-6C OS=Homo sap	no	N/A	0.362	0.062	0.369	7e-05

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

 Score =  171 bits (432), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 73/94 (77%), Positives = 86/94 (91%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE+VPGIG GIAKCP+DP D+STA+WVE GNPG+LP LYSGTNAEFTKA
Sbjct: 128 VVYSNLTHLQRHEYVPGIGVGIAKCPFDPEDSSTAVWVENGNPGDLPGLYSGTNAEFTKA 187

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDS 150
           DTVIFRTDL N TTG++EY+FKRT+KYDSKWLD+
Sbjct: 188 DTVIFRTDLYNLTTGRREYSFKRTLKYDSKWLDN 221

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

 Score =  149 bits (377), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 69/93 (74%), Positives = 77/93 (82%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++  NLTHL R E+V G+G GIAKCPYDP DNSTAI+VE GNPG LP LYSGTNAEFTKA
Sbjct: 159 VIYANLTHLPRSEYVIGVGLGIAKCPYDPLDNSTAIYVENGNPGGLPGLYSGTNAEFTKA 218

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N +  + EY FKRT+KYDSKWLD
Sbjct: 219 DTVIFRTDLYNTSAKRLEYKFKRTLKYDSKWLD 251

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 = 50.1 bits (118), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 14/74 (18%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           +G+A+CPYDP  NSTA+   +G       LY+ T  +F+  D  I+R+      +G    
Sbjct: 224 NGVARCPYDPRHNSTAVISSQGE------LYAATVIDFSGRDPAIYRS----LGSGPP-- 271

Query: 136 TFKRTIKYDSKWLD 149
              RT +Y+SKWL+
Sbjct: 272 --LRTAQYNSKWLN 283

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 = 49.7 bits (117), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 14/74 (18%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           +G+A+CPYDP  NSTA+   +G       LY+ T  +F+  D  I+R+      +G    
Sbjct: 166 NGVARCPYDPRHNSTAVISSQGE------LYAATVIDFSGRDPAIYRS----LGSGPP-- 213

Query: 136 TFKRTIKYDSKWLD 149
              RT +Y+SKWL+
Sbjct: 214 --LRTAQYNSKWLN 225

May act as positive axonal guidance cues.

Mus musculus (taxid: 10090)

>sp|Q60PR7|SEM2A_CAEBR Semaphorin-2A OS=Caenorhabditis briggsae GN=mab-20 PE=3 SV=1

 Score = 49.7 bits (117), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 78  IAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTF 137
           I  C  DP  NSTA+ V+ GNP +  ++YSG        + +I+R  L     GK+ +  
Sbjct: 139 IGICVVDPTFNSTAVVVDNGNPEDASSVYSGIRTGMGGENHLIYRPPLTK--NGKQLHAS 196

Query: 138 KRTIKYDSKWLD 149
            RTI  D+KWL+
Sbjct: 197 IRTIYSDNKWLN 208

Regulates the formation or stabilization of cell-cell contacts at several stages of epithelial morphogenesis. In early embryonic development, required for proper ventral closure of the epidermis. During male tail morphogenesis, regulates precursor cell sorting and allows the formation of distinct sensory rays. Seems to control cell-cell contact formation through two parallel pathways, one involving efn-4 and one involving plx-2 and unc-129. May also be involved in axon guidance.

Caenorhabditis briggsae (taxid: 6238)

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

 Score = 47.4 bits (111), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 15/73 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CP+D    + A++ +         LYS T A+F  +D VI+R+          + 
Sbjct: 161 SGLARCPFDARQTNVALFADG-------KLYSATVADFLASDAVIYRS--------MGDG 205

Query: 136 TFKRTIKYDSKWL 148
           +  RTIKYDSKW+
Sbjct: 206 SALRTIKYDSKWI 218

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)

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

 Score = 47.0 bits (110), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 15/73 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CP+D    + A++ +         LYS T A+F  +D VI+R+          + 
Sbjct: 161 SGLARCPFDARQTNVALFADG-------KLYSATVADFLASDAVIYRS--------MGDG 205

Query: 136 TFKRTIKYDSKWL 148
           +  RTIKYDSKW+
Sbjct: 206 SALRTIKYDSKWI 218

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|Q76KF0|SEM6D_MOUSE Semaphorin-6D OS=Mus musculus GN=Sema6d PE=2 SV=1

 Score = 47.0 bits (110), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 15/73 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CP+D    + A++ +         LYS T A+F  +D VI+R+          + 
Sbjct: 161 SGLARCPFDARQTNVALFADG-------KLYSATVADFLASDAVIYRS--------MGDG 205

Query: 136 TFKRTIKYDSKWL 148
           +  RTIKYDSKW+
Sbjct: 206 SALRTIKYDSKWI 218

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.

Mus musculus (taxid: 10090)

>sp|Q95XP4|SEM2A_CAEEL Semaphorin-2A OS=Caenorhabditis elegans GN=mab-20 PE=1 SV=1

 Score = 47.0 bits (110), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 67  RHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLL 126
           R +  P    GI  C  DP  N TA+ V+ GNP +  ++YSG        + +I+R  L 
Sbjct: 134 RDQQEPRTEIGI--CVVDPTFNFTAVVVDSGNPEDATSVYSGIRTGMGGENHLIYRPPLT 191

Query: 127 NFTTGKKEYTFKRTIKYDSKWLD 149
               GK+ +   RTI  D+KWL+
Sbjct: 192 K--NGKQLHASIRTIYSDNKWLN 212

Regulates the formation or stabilization of cell-cell contacts at several stages of epithelial morphogenesis. In early embryonic development, required for proper ventral closure of the epidermis. During male tail morphogenesis, regulates precursor cell sorting and allows the formation of distinct sensory rays. Seems to control cell-cell contact formation through 2 parallel pathways, one involving efn-4 and one involving plx-2 and unc-129. May also be involved in axon guidance.

Caenorhabditis elegans (taxid: 6239)

>sp|Q9H3T2|SEM6C_HUMAN Semaphorin-6C OS=Homo sapiens GN=SEMA6C PE=2 SV=4

 Score = 46.6 bits (109), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 15/73 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG A+CP+D   ++ AI+ E        +LYS T A+F  +D V++R      + G +  
Sbjct: 164 SGQARCPFDATQSNVAIFAEG-------SLYSATAADFQASDAVVYR------SLGPQPP 210

Query: 136 TFKRTIKYDSKWL 148
              R+ KYDSKWL
Sbjct: 211 L--RSAKYDSKWL 221

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)

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	160
212283364	716	semaphorin 2a [Polyrhachis vicina]	0.581	0.129	0.806	7e-42
345497365	724	PREDICTED: semaphorin-2A-like [Nasonia v	0.581	0.128	0.817	7e-42
307184882	690	Semaphorin-2A [Camponotus floridanus]	0.581	0.134	0.806	8e-42
321469350	771	hypothetical protein DAPPUDRAFT_51392 [D	0.581	0.120	0.784	1e-41
328782173	734	PREDICTED: semaphorin-2A [Apis mellifera	0.581	0.126	0.806	1e-41
383860772	733	PREDICTED: semaphorin-2A-like [Megachile	0.581	0.126	0.806	1e-41
350414357	734	PREDICTED: semaphorin-2A-like isoform 1	0.581	0.126	0.795	2e-41
307192922	594	Semaphorin-2A [Harpegnathos saltator]	0.581	0.156	0.806	4e-41
350414359	711	PREDICTED: semaphorin-2A-like isoform 2	0.581	0.130	0.795	4e-41
340715165	711	PREDICTED: semaphorin-2A-like isoform 1	0.581	0.130	0.795	5e-41

>gi|212283364|gb|ACJ23177.1| semaphorin 2a [Polyrhachis vicina]

 Score =  174 bits (442), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 75/93 (80%), Positives = 86/93 (92%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE+VPG+G GIAKCPYDP DNSTA+WVEKGNPG+LPALYSGTNAEFTKA
Sbjct: 143 VIYSNLTHLPRHEYVPGVGMGIAKCPYDPADNSTAVWVEKGNPGDLPALYSGTNAEFTKA 202

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N TTG+K ++FKRT+KYDSKWLD
Sbjct: 203 DTVIFRTDLYNLTTGRKAFSFKRTLKYDSKWLD 235

Source: Polyrhachis vicina

Species: Polyrhachis vicina

Genus: Polyrhachis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345497365|ref|XP_001599891.2| PREDICTED: semaphorin-2A-like [Nasonia vitripennis]

 Score =  174 bits (442), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 76/93 (81%), Positives = 85/93 (91%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE+VPG+G GIAKCPYDP DNSTA+WVEKGNPG+LPALYSGTNAEFTKA
Sbjct: 151 VIYSNLTHLTRHEYVPGVGIGIAKCPYDPADNSTAVWVEKGNPGDLPALYSGTNAEFTKA 210

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL NFTT  K Y+FKRT+KYDSKWLD
Sbjct: 211 DTVIFRTDLYNFTTTDKAYSFKRTLKYDSKWLD 243

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307184882|gb|EFN71160.1| Semaphorin-2A [Camponotus floridanus]

 Score =  174 bits (442), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 75/93 (80%), Positives = 86/93 (92%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE+VPG+G GIAKCPYDP DNSTA+WVEKGNPG+LPALYSGTNAEFTKA
Sbjct: 117 VIYSNLTHLPRHEYVPGVGMGIAKCPYDPADNSTAVWVEKGNPGDLPALYSGTNAEFTKA 176

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N TTG+K ++FKRT+KYDSKWLD
Sbjct: 177 DTVIFRTDLYNLTTGRKAFSFKRTLKYDSKWLD 209

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321469350|gb|EFX80330.1| hypothetical protein DAPPUDRAFT_51392 [Daphnia pulex]

 Score =  174 bits (441), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 73/93 (78%), Positives = 88/93 (94%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++  NLTHLGR+E+VPG+G GIAKCP+DP+DNSTA+WVE+GNPG+LPALYSGTNAEFTKA
Sbjct: 196 VINANLTHLGRNEYVPGVGMGIAKCPFDPSDNSTAVWVERGNPGDLPALYSGTNAEFTKA 255

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           D VIFRTDL N+TTG++E+TFKRT+KYDSKWLD
Sbjct: 256 DAVIFRTDLYNYTTGRREFTFKRTLKYDSKWLD 288

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328782173|ref|XP_392426.3| PREDICTED: semaphorin-2A [Apis mellifera] gi|380020174|ref|XP_003693969.1| PREDICTED: semaphorin-2A-like [Apis florea]

 Score =  174 bits (441), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 75/93 (80%), Positives = 85/93 (91%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE VPG+G GIAKCPYDP DNSTA+WVEKGNPG+LPALYSGTNAEFTKA
Sbjct: 161 VIYSNLTHLPRHEFVPGVGMGIAKCPYDPADNSTAVWVEKGNPGDLPALYSGTNAEFTKA 220

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N TTG+K ++FKRT+KYDSKWLD
Sbjct: 221 DTVIFRTDLYNLTTGRKAFSFKRTLKYDSKWLD 253

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383860772|ref|XP_003705863.1| PREDICTED: semaphorin-2A-like [Megachile rotundata]

 Score =  174 bits (440), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 75/93 (80%), Positives = 85/93 (91%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE VPG+G GIAKCPYDP DNSTA+WVEKGNPG+LPALYSGTNAEFTKA
Sbjct: 161 VIYSNLTHLPRHEFVPGVGMGIAKCPYDPADNSTAVWVEKGNPGDLPALYSGTNAEFTKA 220

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N TTG+K ++FKRT+KYDSKWLD
Sbjct: 221 DTVIFRTDLYNLTTGRKAFSFKRTLKYDSKWLD 253

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350414357|ref|XP_003490290.1| PREDICTED: semaphorin-2A-like isoform 1 [Bombus impatiens]

 Score =  173 bits (438), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 74/93 (79%), Positives = 85/93 (91%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE VPG+G GIAKCPYDP DNSTA+WVEKGNPG+LPALYSGTNAEFTKA
Sbjct: 161 VIYSNLTHLPRHEFVPGVGMGIAKCPYDPADNSTAVWVEKGNPGDLPALYSGTNAEFTKA 220

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N TTG++ ++FKRT+KYDSKWLD
Sbjct: 221 DTVIFRTDLYNLTTGRRAFSFKRTLKYDSKWLD 253

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307192922|gb|EFN75947.1| Semaphorin-2A [Harpegnathos saltator]

 Score =  172 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 75/93 (80%), Positives = 85/93 (91%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE VPG+G GIAKCPYDP DNSTA+WVEKGNPG+LPALYSGTNAEFTKA
Sbjct: 21  VIYSNLTHLPRHEFVPGVGMGIAKCPYDPADNSTAVWVEKGNPGDLPALYSGTNAEFTKA 80

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N TTG+K ++FKRT+KYDSKWLD
Sbjct: 81  DTVIFRTDLYNLTTGRKAFSFKRTLKYDSKWLD 113

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350414359|ref|XP_003490291.1| PREDICTED: semaphorin-2A-like isoform 2 [Bombus impatiens] gi|350414361|ref|XP_003490292.1| PREDICTED: semaphorin-2A-like isoform 3 [Bombus impatiens]

 Score =  172 bits (437), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 74/93 (79%), Positives = 85/93 (91%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE VPG+G GIAKCPYDP DNSTA+WVEKGNPG+LPALYSGTNAEFTKA
Sbjct: 138 VIYSNLTHLPRHEFVPGVGMGIAKCPYDPADNSTAVWVEKGNPGDLPALYSGTNAEFTKA 197

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N TTG++ ++FKRT+KYDSKWLD
Sbjct: 198 DTVIFRTDLYNLTTGRRAFSFKRTLKYDSKWLD 230

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340715165|ref|XP_003396089.1| PREDICTED: semaphorin-2A-like isoform 1 [Bombus terrestris] gi|340715167|ref|XP_003396090.1| PREDICTED: semaphorin-2A-like isoform 2 [Bombus terrestris]

 Score =  172 bits (435), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 74/93 (79%), Positives = 84/93 (90%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           ++ +NLTHL RHE VPG+G GIAKCPYDP DNSTA+WVEKGNPG LPALYSGTNAEFTKA
Sbjct: 138 VIYSNLTHLPRHEFVPGVGMGIAKCPYDPADNSTAVWVEKGNPGELPALYSGTNAEFTKA 197

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           DTVIFRTDL N TTG++ ++FKRT+KYDSKWLD
Sbjct: 198 DTVIFRTDLYNLTTGRRAFSFKRTLKYDSKWLD 230

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	160
FB|FBgn0011260	724	Sema-2a "Sema-2a" [Drosophila	0.581	0.128	0.741	3.9e-33
FB|FBgn0264273	785	Sema-2b "Semaphorin-2b" [Droso	0.581	0.118	0.709	4.7e-32
UNIPROTKB|H0YMV0	219	SEMA6D "Semaphorin-6D" [Homo s	0.362	0.264	0.383	9.7e-06
ZFIN|ZDB-GENE-070912-187	1101	sema5b "sema domain, seven thr	0.375	0.054	0.391	1.4e-05
FB|FBgn0250876	1093	Sema-5c "Semaphorin-5c" [Droso	0.462	0.067	0.340	1.7e-05
WB|WBGene00003111	658	mab-20 [Caenorhabditis elegans	0.493	0.120	0.349	1.9e-05
UNIPROTKB|F1NSD7	991	SEMA5B "Uncharacterized protei	0.375	0.060	0.378	4.1e-05
ZFIN|ZDB-GENE-050513-1	801	sema3fa "semaphorin 3fa" [Dani	0.456	0.091	0.370	5.2e-05
UNIPROTKB|F1NJN3	983	SEMA5A "Uncharacterized protei	0.5	0.081	0.346	5.2e-05
UNIPROTKB|A6NM95	597	SEMA6D "Semaphorin-6D" [Homo s	0.362	0.097	0.383	5.9e-05

FB|FBgn0011260 Sema-2a "Sema-2a" [Drosophila melanogaster (taxid:7227)]

 Score = 369 (135.0 bits), Expect = 3.9e-33, P = 3.9e-33
 Identities = 69/93 (74%), Positives = 77/93 (82%)

Query:    57 ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
             ++  NLTHL R E+V G+G GIAKCPYDP DNSTAI+VE GNPG LP LYSGTNAEFTKA
Sbjct:   159 VIYANLTHLPRSEYVIGVGLGIAKCPYDPLDNSTAIYVENGNPGGLPGLYSGTNAEFTKA 218

Query:   117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
             DTVIFRTDL N +  + EY FKRT+KYDSKWLD
Sbjct:   219 DTVIFRTDLYNTSAKRLEYKFKRTLKYDSKWLD 251

GO:0007629 "flight behavior" evidence=IMP

GO:0042756 "drinking behavior" evidence=IMP

GO:0030534 "adult behavior" evidence=NAS;IMP

GO:0007632 "visual behavior" evidence=IMP

GO:0005576 "extracellular region" evidence=ISS;NAS

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

GO:0016201 "synaptic target inhibition" evidence=NAS;IMP

GO:0007431 "salivary gland development" evidence=IMP

GO:0016020 "membrane" evidence=IEA

GO:0004872 "receptor activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0070983 "dendrite guidance" evidence=IGI

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

 Score = 360 (131.8 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 66/93 (70%), Positives = 77/93 (82%)

Query:    57 ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
             ++  NLTHL R ++VPGIG GI KCPYDP DNSTA++VE GNP  LPALY+GTNAEFTKA
Sbjct:   214 VINANLTHLPRSQYVPGIGLGIGKCPYDPADNSTAVYVENGNPFGLPALYAGTNAEFTKA 273

Query:   117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
             D+VIFR+DL N T G+KE  FKRT+KYDSK LD
Sbjct:   274 DSVIFRSDLYNLTNGRKEANFKRTVKYDSKLLD 306

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|H0YMV0 SEMA6D "Semaphorin-6D" [Homo sapiens (taxid:9606)]

 Score = 106 (42.4 bits), Expect = 9.7e-06, P = 9.7e-06
 Identities = 28/73 (38%), Positives = 42/73 (57%)

Query:    76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
             SG+A+CP+D    + A++ +    G L   YS T A+F  +D VI+R+       G  + 
Sbjct:   161 SGLARCPFDARQTNVALFAD----GKL---YSATVADFLASDAVIYRS------MG--DG 205

Query:   136 TFKRTIKYDSKWL 148
             +  RTIKYDSKW+
Sbjct:   206 SALRTIKYDSKWI 218

GO:0030215 "semaphorin receptor binding" evidence=IEA

ZFIN|ZDB-GENE-070912-187 sema5b "sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B" [Danio rerio (taxid:7955)]

 Score = 115 (45.5 bits), Expect = 1.4e-05, P = 1.4e-05
 Identities = 29/74 (39%), Positives = 41/74 (55%)

Query:    76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
             +G+A+CPYDP  NSTA+  E G       LY+ T  +F+  D VI+R+       G    
Sbjct:   178 NGVARCPYDPRHNSTAVVTESGE------LYAATVIDFSGRDPVIYRS-----LGGMPPL 226

Query:   136 TFKRTIKYDSKWLD 149
                RT +Y+SKWL+
Sbjct:   227 ---RTAQYNSKWLN 237

GO:0016020 "membrane" evidence=IEA

GO:0004872 "receptor activity" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

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

 Score = 114 (45.2 bits), Expect = 1.7e-05, P = 1.7e-05
 Identities = 32/94 (34%), Positives = 49/94 (52%)

Query:    55 WKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFT 114
             W+ +EN LT       V G+ SG+ KCP+ P  NST++    G       L+ GT  +F+
Sbjct:   157 WRQMEN-LT-------VTGVDSGVVKCPFHPQANSTSLLQSNGQ------LFVGTATDFS 202

Query:   115 KADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWL 148
              +D  I RT +    + K+   F RT +Y++ WL
Sbjct:   203 GSDVAILRTGV---ESNKR---FLRTKQYNNNWL 230

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

WB|WBGene00003111 mab-20 [Caenorhabditis elegans (taxid:6239)]

 Score = 111 (44.1 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 29/83 (34%), Positives = 42/83 (50%)

Query:    67 RHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLL 126
             R +  P    GI  C  DP  N TA+ V+ GNP +  ++YSG        + +I+R  L 
Sbjct:   134 RDQQEPRTEIGI--CVVDPTFNFTAVVVDSGNPEDATSVYSGIRTGMGGENHLIYRPPLT 191

Query:   127 NFTTGKKEYTFKRTIKYDSKWLD 149
                 GK+ +   RTI  D+KWL+
Sbjct:   192 K--NGKQLHASIRTIYSDNKWLN 212

GO:0030155 "regulation of cell adhesion" evidence=IGI;IMP

GO:0045138 "tail tip morphogenesis" evidence=IGI;IMP

GO:0016331 "morphogenesis of embryonic epithelium" evidence=IMP

GO:0010172 "embryonic body morphogenesis" evidence=IMP

GO:0032956 "regulation of actin cytoskeleton organization" evidence=IMP

GO:0030334 "regulation of cell migration" evidence=IMP

GO:0007413 "axonal fasciculation" evidence=IMP

GO:0007411 "axon guidance" evidence=IMP

GO:0009986 "cell surface" evidence=IDA

UNIPROTKB|F1NSD7 SEMA5B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 110 (43.8 bits), Expect = 4.1e-05, P = 4.1e-05
 Identities = 28/74 (37%), Positives = 41/74 (55%)

Query:    76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
             +G+A+CPYDP  NSTA+   +G       LY+ T  +F+  D  I+R+ L N        
Sbjct:    65 NGVARCPYDPRHNSTAVITSRGE------LYAATVIDFSGRDPAIYRS-LGNVPP----- 112

Query:   136 TFKRTIKYDSKWLD 149
                RT +Y+SKWL+
Sbjct:   113 --LRTAQYNSKWLN 124

GO:0004872 "receptor activity" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

ZFIN|ZDB-GENE-050513-1 sema3fa "semaphorin 3fa" [Danio rerio (taxid:7955)]

 Score = 108 (43.1 bits), Expect = 5.2e-05, P = 5.2e-05
 Identities = 33/89 (37%), Positives = 46/89 (51%)

Query:    72 PG-IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTT 130
             PG + SG  KCPYDP  NS +  +  G       LY+G   +F   D+ IFRT       
Sbjct:   201 PGKVDSGKGKCPYDPKLNSVSALIN-GQ------LYAGVYIDFMGTDSAIFRT------L 247

Query:   131 GKKEYTFKRTIKYDSKWLDSFKSLIAKII 159
             GK  +T  RT +Y+S+WL     + A++I
Sbjct:   248 GK--HTAMRTDQYNSRWLHDPTFVHAQLI 274

GO:0016020 "membrane" evidence=IEA

GO:0004872 "receptor activity" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0001755 "neural crest cell migration" evidence=IGI

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

 Score = 109 (43.4 bits), Expect = 5.2e-05, P = 5.2e-05
 Identities = 35/101 (34%), Positives = 50/101 (49%)

Query:    49 FTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSG 108
             FT +   + L NNLT +  H+ +    SG+A+CPY P  NSTA+    G       LY+ 
Sbjct:    45 FTPICTNRTL-NNLTEI--HDQI----SGMARCPYSPQHNSTALLTSSGE------LYAA 91

Query:   109 TNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
             T  +F   D  I+R+       G       RT +Y+SKWL+
Sbjct:    92 TAMDFPGRDPAIYRS------LGALPPL--RTAQYNSKWLN 124

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

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

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|A6NM95 SEMA6D "Semaphorin-6D" [Homo sapiens (taxid:9606)]

 Score = 106 (42.4 bits), Expect = 5.9e-05, P = 5.9e-05
 Identities = 28/73 (38%), Positives = 42/73 (57%)

Query:    76 SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
             SG+A+CP+D    + A++ +    G L   YS T A+F  +D VI+R+       G  + 
Sbjct:   161 SGLARCPFDARQTNVALFAD----GKL---YSATVADFLASDAVIYRS------MG--DG 205

Query:   136 TFKRTIKYDSKWL 148
             +  RTIKYDSKW+
Sbjct:   206 SALRTIKYDSKWI 218

GO:0004872 "receptor activity" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q24323	SEM2A_DROME	No assigned EC number	0.7419	0.5812	0.1284	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	160
cd11238	452	cd11238, Sema_2A, The Sema domain, a protein inter	2e-45
cd11235	437	cd11235, Sema_semaphorin, The Sema domain, a prote	1e-19
cd11265	433	cd11265, Sema_5C, The Sema domain, a protein inter	4e-11
pfam01403	435	pfam01403, Sema, Sema domain	8e-11
cd11237	446	cd11237, Sema_1A, The Sema domain, a protein inter	1e-09
cd11264	437	cd11264, Sema_5B, The Sema domain, a protein inter	1e-08
cd11242	465	cd11242, Sema_6, The Sema domain, a protein intera	3e-08
cd11239	471	cd11239, Sema_3, The Sema domain, a protein intera	5e-08
cd11269	465	cd11269, Sema_6D, The Sema domain, a protein inter	9e-08
cd11254	470	cd11254, Sema_3F, The Sema domain, a protein inter	1e-07
cd11241	438	cd11241, Sema_5, The Sema domain, a protein intera	2e-07
cd11270	462	cd11270, Sema_6E, The Sema domain, a protein inter	5e-07
cd11263	436	cd11263, Sema_5A, The Sema domain, a protein inter	7e-07
cd11266	466	cd11266, Sema_6A, The Sema domain, a protein inter	1e-06
cd11268	465	cd11268, Sema_6C, The Sema domain, a protein inter	2e-06
cd11267	466	cd11267, Sema_6B, The Sema domain, a protein inter	3e-06
smart00630	390	smart00630, Sema, semaphorin domain	5e-05
cd11249	493	cd11249, Sema_3A, The Sema domain, a protein inter	6e-04
cd11240	456	cd11240, Sema_4, The Sema domain, a protein intera	0.001
cd11250	471	cd11250, Sema_3B, The Sema domain, a protein inter	0.002
cd11257	464	cd11257, Sema_4B, The Sema domain, a protein inter	0.002

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

 Score =  153 bits (389), Expect = 2e-45
 Identities = 63/93 (67%), Positives = 75/93 (80%), Gaps = 3/93 (3%)

Query: 57  ILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKA 116
           +L+ NL HL   E+VPG G+GI KCPYDP+DNSTA+WVE GNPG+LPALYSGT  EFTKA
Sbjct: 94  VLDANLLHLP--EYVPGPGNGIGKCPYDPDDNSTAVWVEWGNPGDLPALYSGTRTEFTKA 151

Query: 117 DTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           +TVI+R  L N T G+ E +F RT+KYDSKWLD
Sbjct: 152 NTVIYRPPLYNNTKGRHE-SFMRTLKYDSKWLD 183

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

 Score = 84.0 bits (208), Expect = 1e-19
 Identities = 34/85 (40%), Positives = 44/85 (51%), Gaps = 15/85 (17%)

Query: 65  LGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTD 124
           +   E V    SG  KCPYDP+ NSTA++ +         LYSGT+A+F   D VI+RT 
Sbjct: 91  VETFELVGKEESGRGKCPYDPDHNSTALFADGE-------LYSGTSADFLGTDPVIYRTL 143

Query: 125 LLNFTTGKKEYTFKRTIKYDSKWLD 149
             N           RT  +DSKWL+
Sbjct: 144 GHN--------PPLRTEYHDSKWLN 160

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 = 59.8 bits (145), Expect = 4e-11
 Identities = 29/79 (36%), Positives = 43/79 (54%), Gaps = 12/79 (15%)

Query: 71  VPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTT 130
           V    SG+AKCPY P+ N TA+    G       L+ G+  +F+ +D+ I+RT       
Sbjct: 102 VTEWDSGVAKCPYSPHANITALLSSSGQ------LFVGSPTDFSGSDSAIYRTL------ 149

Query: 131 GKKEYTFKRTIKYDSKWLD 149
           G    +F RT +Y+SKWL+
Sbjct: 150 GTSNKSFLRTKQYNSKWLN 168

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|216480 pfam01403, Sema, Sema domain

 Score = 58.5 bits (142), Expect = 8e-11
 Identities = 28/89 (31%), Positives = 34/89 (38%), Gaps = 15/89 (16%)

Query: 60  NNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTV 119
           N          V     G   CPYDP  NST++ +  G       LYSGT  +F+  D  
Sbjct: 91  NLGDRCLFSLDVDKEEDGCGDCPYDPLGNSTSV-LVDGE------LYSGTVIDFSGRDPS 143

Query: 120 IFRTDLLNFTTGKKEYTFKRTIKYDSKWL 148
           I R            Y   RT  +DSK L
Sbjct: 144 IRRL--------LGSYDGLRTEFHDSKLL 164

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

 Score = 55.4 bits (134), Expect = 1e-09
 Identities = 28/75 (37%), Positives = 38/75 (50%), Gaps = 20/75 (26%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
            G   CPYDP  NSTA++ + G       LYS T A+F+ AD +I+R  L          
Sbjct: 105 DGQGLCPYDPKHNSTAVYAD-GQ------LYSATVADFSGADPLIYREPL---------- 147

Query: 136 TFKRTIKYDSKWLDS 150
              RT +YD K L++
Sbjct: 148 ---RTERYDLKQLNA 159

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

 Score = 52.3 bits (125), Expect = 1e-08
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 14/74 (18%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           +G+A+CPYDP  NSTA+   +G       LY+ T  +F+  D  I+R+ L +        
Sbjct: 107 NGVARCPYDPRHNSTAVITSRGE------LYAATVIDFSGRDPAIYRS-LGSVPP----- 154

Query: 136 TFKRTIKYDSKWLD 149
              RT +Y+SKWL+
Sbjct: 155 --LRTAQYNSKWLN 166

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

 Score = 51.4 bits (123), Expect = 3e-08
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 15/73 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CP+D    + A++ +         LYS T  +F  +D VI+R+          + 
Sbjct: 113 SGMARCPFDAKQANVALFADG-------KLYSATVTDFLASDAVIYRS--------LGDS 157

Query: 136 TFKRTIKYDSKWL 148
              RT+KYDSKWL
Sbjct: 158 PTLRTVKYDSKWL 170

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

 Score = 50.8 bits (122), Expect = 5e-08
 Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 15/75 (20%)

Query: 74  IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKK 133
           + SG  KCP+DPN    ++ ++         LYSGT  +F   D  IFR      + G +
Sbjct: 116 LESGRGKCPFDPNQPFASVLIDG-------ELYSGTAIDFMGRDAAIFR------SLGHR 162

Query: 134 EYTFKRTIKYDSKWL 148
            Y   RT +YDS+WL
Sbjct: 163 HYI--RTEQYDSRWL 175

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

 Score = 50.0 bits (119), Expect = 9e-08
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 15/73 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CP+D    + A++ +         LYS T A+F  +D VI+R+            
Sbjct: 113 SGLARCPFDARQTNVALFADG-------KLYSATVADFLASDAVIYRSMGDGSAL----- 160

Query: 136 TFKRTIKYDSKWL 148
              RTIKYDSKW+
Sbjct: 161 ---RTIKYDSKWI 170

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

 Score = 49.8 bits (119), Expect = 1e-07
 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 16/80 (20%)

Query: 71  VPG-IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFT 129
            P  + SG  KCPYDP  +S +  +          LY+G   +F   D  IFR      T
Sbjct: 112 EPDKLESGKGKCPYDPKQDSVSALING-------ELYAGVYIDFMGTDAAIFR------T 158

Query: 130 TGKKEYTFKRTIKYDSKWLD 149
            GK+     RT +Y+S+WL+
Sbjct: 159 MGKQ--PAMRTDQYNSRWLN 176

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

 Score = 49.1 bits (117), Expect = 2e-07
 Identities = 33/103 (32%), Positives = 47/103 (45%), Gaps = 25/103 (24%)

Query: 49  FTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSG 108
           F+ V   + L N LT +          SG+A+CPY P  NSTA+    G       LY+G
Sbjct: 87  FSPVCTIRKLSN-LTQI-LDTI-----SGVARCPYSPAHNSTALISASG------ELYAG 133

Query: 109 TNAEFTKADTVIFRT--DLLNFTTGKKEYTFKRTIKYDSKWLD 149
           T  +F+  D  I+R+                 RT +Y+SKWL+
Sbjct: 134 TVYDFSGRDPAIYRSLGGKPPL----------RTAQYNSKWLN 166

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

 Score = 47.8 bits (113), Expect = 5e-07
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 14/73 (19%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
            G A+CP++   ++  ++      G+    YS T  +F  +D VI+R+       G+   
Sbjct: 110 IGQARCPFESRQSNVGLFAG----GDF---YSATMTDFLASDAVIYRS------LGESSP 156

Query: 136 TFKRTIKYDSKWL 148
              RT+KYDSKWL
Sbjct: 157 VL-RTVKYDSKWL 168

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

 Score = 47.3 bits (112), Expect = 7e-07
 Identities = 31/90 (34%), Positives = 44/90 (48%), Gaps = 20/90 (22%)

Query: 60  NNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTV 119
           NNLT +  H+ +    SG+A+CPY P  NSTA+    G       LY+ T  +F   D  
Sbjct: 97  NNLTEI--HDQI----SGMARCPYSPQHNSTALLTSSGE------LYAATAMDFPGRDPA 144

Query: 120 IFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
           I+R+               RT +Y+SKWL+
Sbjct: 145 IYRS--------LGILPPLRTAQYNSKWLN 166

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

 Score = 46.6 bits (110), Expect = 1e-06
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 15/73 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CPYD    + A++ +         LYS T  +F   D VI+R+          + 
Sbjct: 113 SGMARCPYDAKHANVALFADG-------KLYSATVTDFLAIDAVIYRS--------LGDS 157

Query: 136 TFKRTIKYDSKWL 148
              RT+K+DSKWL
Sbjct: 158 PTLRTVKHDSKWL 170

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

 Score = 46.2 bits (109), Expect = 2e-06
 Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 15/73 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG A+CP+D   ++ AI+ E        +LYS T A+F  +D V++R      + G +  
Sbjct: 112 SGQARCPFDATQSNVAIFAEG-------SLYSATAADFQASDAVVYR------SLGPQPP 158

Query: 136 TFKRTIKYDSKWL 148
              R+ KYDSKWL
Sbjct: 159 L--RSAKYDSKWL 169

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

 Score = 45.2 bits (107), Expect = 3e-06
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 15/72 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CPYDP   + A++ +         L++ T  +F   D VI+R+          + 
Sbjct: 113 SGMARCPYDPKHANVALFADG-------MLFTATVTDFLAIDAVIYRS--------LGDS 157

Query: 136 TFKRTIKYDSKW 147
              RT+K+DSKW
Sbjct: 158 PALRTVKHDSKW 169

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|214747 smart00630, Sema, semaphorin domain

 Score = 42.0 bits (99), Expect = 5e-05
 Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 101 NLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFK 152
           NL  LY GT A+F+ +D  I R+  +    G       RT+ YDSKWL+   
Sbjct: 90  NLGELYVGTVADFSGSDPAIPRSLSVRRLKGTSGV-SLRTVLYDSKWLNEPN 140

Length = 390

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

 Score = 38.8 bits (90), Expect = 6e-04
 Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 15/84 (17%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           +G  K PYDP   + ++ ++         LYSGT A+F   D  IFR      T G    
Sbjct: 139 NGRGKSPYDPKLLTASLLIDG-------ELYSGTAADFMGRDFAIFR------TLGHHHP 185

Query: 136 TFKRTIKYDSKWLDSFKSLIAKII 159
              RT ++DS+WL+  + + A +I
Sbjct: 186 I--RTEQHDSRWLNDPRFISAHLI 207

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

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 7/48 (14%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRT 123
            G  +CP+DP    TAI V+         LYS T   F  ++ VI R 
Sbjct: 112 DGKGRCPFDPAQRYTAIMVDG-------ELYSATVNNFLGSEPVISRN 152

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

 Score = 37.2 bits (86), Expect = 0.002
 Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 15/76 (19%)

Query: 77  GIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYT 136
           G  K PYDP   + ++ V          LYSG   +    D  IFR      + G++   
Sbjct: 119 GKGKSPYDPRHTAASVLVGD-------ELYSGVATDLMGRDFTIFR------SLGQRPSL 165

Query: 137 FKRTIKYDSKWLDSFK 152
             RT ++DS+WL+  K
Sbjct: 166 --RTEQHDSRWLNEPK 179

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

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 7/47 (14%)

Query: 77  GIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRT 123
           G  +CP+DP   STAI V+         LY+GT + F   D +I+R+
Sbjct: 120 GKGRCPFDPEYKSTAIMVDG-------ELYTGTVSNFQGNDPIIYRS 159

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	160
KOG3611|consensus	737		99.96
PF01403	433	Sema: Sema domain; InterPro: IPR001627 The Sema do	99.63
smart00630	390	Sema semaphorin domain.	99.42

>KOG3611|consensus

Probab=99.96  E-value=4.1e-30  Score=242.99  Aligned_cols=131  Identities=34%  Similarity=0.520  Sum_probs=108.0

Q ss_pred             CcccCCCCCCCc-cccccCCCCCccchhhcccccccchhhHHHHhhhcccccceEEeeecCcccccCCCc----------
Q psy12771          1 MYSFLGLPPLSF-ENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLTHLGRHE----------   69 (160)
Q Consensus         1 ~~~~~~~~~~~~-~~~~~~p~~~~~~~~~~~~~~~i~~~~~~~kk~~~~~~~nfirvL~~~N~ThL~~~e----------   69 (160)
                      ||++. |.+++. .+.+.|+++.+.+           .+|.-+.|+ ..+|.||||+|+..|.+||+.|.          
T Consensus        77 vf~l~-l~~~~~~~~~~~W~~~~~~~-----------~~C~~kgk~-~~eC~N~irvL~~~~~~~L~vCGT~Af~P~C~~  143 (737)
T KOG3611|consen   77 VFRLS-LENISEVQAKLEWKSSESDR-----------EECRMKGKD-ETECRNYIRVLAPRNNGHLYVCGTNAFNPVCRN  143 (737)
T ss_pred             EEEEe-cCccccccceeeccCChhhh-----------hhhcccCCC-hhHccceeEEEeecCCCeEEEeecccCCcchhh
Confidence            46666 777775 6667777777666           344333333 46789999999999999996221          


Q ss_pred             -------c-CCccCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeecccccccCCCCccccceec
Q psy12771         70 -------H-VPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTI  141 (160)
Q Consensus        70 -------~-v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe  141 (160)
                             . +.+.++|+|+|||||++|+||+++++       +|||||++||+|+|++|||++      |++  +.|||+
T Consensus       144 ~~~~~~~~~~~~~~~g~g~CP~dP~~nstav~~~~-------~Lys~t~~dF~g~d~~I~Rs~------g~~--~~lrT~  208 (737)
T KOG3611|consen  144 YNVTTLQESVQRLESGIGRCPYDPKHNSTAVFVDG-------ELYSGTVADFLGSDALIYRSL------GKN--PTLRTV  208 (737)
T ss_pred             hccccccccCccccCCceeCCCCCCcCceEEEECC-------EEEEEecccccCCCceEEEec------CCC--CCceec
Confidence                   1 35689999999999999999999998       899999999999999999987      765  679999


Q ss_pred             cCccCCCCCCCeeEEEec
Q psy12771        142 KYDSKWLDSFKSLIAKII  159 (160)
Q Consensus       142 ~~dskWLneP~FV~S~~I  159 (160)
                      ++|++|||||+||+|+.|
T Consensus       209 ~~dskwLneP~FV~a~~i  226 (737)
T KOG3611|consen  209 KYDSKWLNEPNFVGAFDI  226 (737)
T ss_pred             cCCchhccCCcEEEeeee
Confidence            999999999999999987

>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=99.63  E-value=1.3e-16  Score=140.39  Aligned_cols=112  Identities=29%  Similarity=0.364  Sum_probs=90.2

Q ss_pred             cccchhhHHHHhhhc--------ccccceEEeeecCcccccCCC--------------cc--------CCccCcccccCC
Q psy12771         33 KVVEEEEEEEKKKER--------GFTKVFFWKILENNLTHLGRH--------------EH--------VPGIGSGIAKCP   82 (160)
Q Consensus        33 ~~i~~~~~~~kk~~~--------~~~~nfirvL~~~N~ThL~~~--------------e~--------v~~~esG~gkCP   82 (160)
                      ..+.|..+.+.+++|        ..|.|||++|+..|.+||..|              ..        .....+|.++||
T Consensus        34 ~~~~~~~~~~~~~~C~~~~~~~~~~c~N~i~vL~~~~~~~Li~CGT~~~~p~C~~~~l~~~~~l~~~~~~~~~~~~~~~~  113 (433)
T PF01403_consen   34 QRTGWTSDCEDCEECQPKGKSNETECNNYIKVLLVYNDNRLIVCGTNAFQPICRLRNLSNISCLFSLSPDESPSGQGVCP  113 (433)
T ss_dssp             EEEEEEEEHHHCHHHCSTTTTTTTTSSEBEEEEEEESSSEEEEEESTTTSCEEEEEETTTCEEEEEEEECCEEEGTTTS-
T ss_pred             ccccCccccccccccCCCcccccccCcceeEEEEecCCCEEEEcCccccccCccEeccccccceeeeecccccCCeeecc
Confidence            345566555555554        468899999999999888522              11        134579999999


Q ss_pred             CCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeecccccccCCCCccccceeccCccCCCCCCCeeEEEec
Q psy12771         83 YDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus        83 ydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLneP~FV~S~~I  159 (160)
                      |+|..+.+++++++       +||+|+..||.|.+++|+|.+      +.+  ..++|+.++++||++|+||+++.|
T Consensus       114 ~~p~~~~~~~~~~~-------~lyvgt~~~~~~~~~~i~R~~------~~~--~~l~~~~~~~~~~~~p~fv~~~~~  175 (433)
T PF01403_consen  114 YDPNQSSVALVVNG-------ELYVGTTYDFSGSSPIISRSL------GSQ--PPLRTEQYDSKWLNEPSFVSSFEI  175 (433)
T ss_dssp             SSTTSCEEEEEETT-------EEEEEEESSTTSSSEEEEEEE------TSS--STEESCCCCTTSSSSTEEEEEEEE
T ss_pred             cccCCCcceecccc-------cEEEeeeccccCCCcceeecc------ccc--cccccccccccccccccccccccc
Confidence            99999999999965       899999999999999999987      443  689999999999999999999875

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 ....

>smart00630 Sema semaphorin domain

Probab=99.42  E-value=3.4e-13  Score=119.48  Aligned_cols=86  Identities=26%  Similarity=0.230  Sum_probs=67.4

Q ss_pred             ccccceEEeeecCcccccCCCccCCccCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeeccccc
Q psy12771         48 GFTKVFFWKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLN  127 (160)
Q Consensus        48 ~~~~nfirvL~~~N~ThL~~~e~v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~  127 (160)
                      ..|.||||+|+.+|.+||+.|..    -.-.++|-+-.-         +       +||+||+.||.|++++|+|++   
T Consensus        57 ~dc~N~irll~~~~~~~L~~CGT----~a~~p~C~~~~l---------~-------~ly~gt~~~~~~~~~~i~r~~---  113 (390)
T smart00630       57 TDCVNYIRLLLDYNDDRLLVCGT----NAFQPVCRLINL---------G-------ELYVGTVADFSGSDPAIPRSL---  113 (390)
T ss_pred             ccCcceEEEEEEcCCCEEEEeCC----CCCCCceeEEec---------C-------ceEEEEecccCCCCcceeccc---
Confidence            46789999999999999998752    122455654322         1       599999999999999999997   


Q ss_pred             ccCCCCc-----cccceeccCccCCCCCCCeeEEEec
Q psy12771        128 FTTGKKE-----YTFKRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus       128 ~~~G~~~-----~~~LRTe~~dskWLneP~FV~S~~I  159 (160)
                         |.+.     ...|||++++++|||+|+||+||.+
T Consensus       114 ---~~r~l~~~~~~~l~t~~~~~~~l~~~~FV~sf~~  147 (390)
T smart00630      114 ---SVRRLKGTSGVSLRTVLYDSKWLNEPNFVYAFES  147 (390)
T ss_pred             ---cccccccccCceeeccccCcccccCCcEEEEEEc
Confidence               3321     1379999999999999999999853

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	160
3afc_A	556	Mouse Semaphorin 6a Extracellular Domain Length = 5		6e-05
3okw_A	565	Mouse Semaphorin 6a, Extracellular Domains 1-2 Leng		1e-04

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 15/73 (20%)
Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CPYD    + A++ +         LYS T  +F   D VI+R+          + 
Sbjct: 146 SGMARCPYDAKHANIALFADG-------KLYSATVTDFLAIDAVIYRS--------LGDS 190
Query: 136 TFKRTIKYDSKWL 148
              RT+K+DSKWL
Sbjct: 191 PTLRTVKHDSKWL 203

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 15/73 (20%)
Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           SG+A+CPYD    + A++ +         LYS T  +F   D VI+R+ L +  T     
Sbjct: 145 SGMARCPYDAKHANIALFADG-------KLYSATVTDFLAIDAVIYRS-LGDSPT----- 191
Query: 136 TFKRTIKYDSKWL 148
              RT+K+DSKWL
Sbjct: 192 --LRTVKHDSKWL 202

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	160
3oky_B	565	Putative uncharacterized protein; transmembrane, l	5e-08
1q47_A	495	Semaphorin 3A; beta propeller, signaling protein;	8e-08
3nvq_A	590	Semaphorin-7A; beta-propeller, signaling, signalin	1e-06
1olz_A	663	Semaphorin 4D; developmental protein, CD100, beta-	2e-06
3nvn_B	476	Plexin-C1; beta-propeller, signaling, viral protei	4e-05
3ol2_B	528	Plexin-B1; beta-propeller, signalling, extacellula	7e-04

>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 = 50.1 bits (118), Expect = 5e-08
 Identities = 27/95 (28%), Positives = 40/95 (42%), Gaps = 21/95 (22%)

Query: 55  WKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFT 114
                + L   G         SG+A+CPYD    + A++ +         LYS T  +F 
Sbjct: 130 RNYRVDTLETFGDEF------SGMARCPYDAKHANIALFAD-------GKLYSATVTDFL 176

Query: 115 KADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
             D VI+R+          +    RT+K+DSKWL 
Sbjct: 177 AIDAVIYRS--------LGDSPTLRTVKHDSKWLK 203

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

 Score = 49.6 bits (117), Expect = 8e-08
 Identities = 24/95 (25%), Positives = 40/95 (42%), Gaps = 15/95 (15%)

Query: 55  WKILENNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFT 114
           +  + ++              +G  K PYDP   + ++ ++         LYSGT A+F 
Sbjct: 118 YIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDGE-------LYSGTAADFM 170

Query: 115 KADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
             D  IFRT           +   RT ++DS+WL+
Sbjct: 171 GRDFAIFRTLG--------HHHPIRTEQHDSRWLN 197

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

 Score = 46.2 bits (108), Expect = 1e-06
 Identities = 9/54 (16%), Positives = 17/54 (31%), Gaps = 7/54 (12%)

Query: 74  IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLN 127
           +G      P+ P++NS  ++           +YS    +        FR     
Sbjct: 119 LGEMRGYAPFSPDENSLVLFEG-------DEVYSTIRKQEYNGKIPRFRRIRGE 165

>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 = 45.5 bits (106), Expect = 2e-06
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 17/86 (19%)

Query: 64  HLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRT 123
           +L   + +     G  +CP+DP  + T++ V+         LYSGT+  F  ++ +I R 
Sbjct: 118 NLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVD-------GELYSGTSYNFLGSEPIISRN 170

Query: 124 DLLNFTTGKKEYTFKRTIKYDSKWLD 149
              +           RT +Y   WL+
Sbjct: 171 SSHS---------PLRT-EYAIPWLN 186

>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 = 41.5 bits (96), Expect = 4e-05
 Identities = 13/89 (14%), Positives = 20/89 (22%), Gaps = 7/89 (7%)

Query: 61  NLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVI 120
            L +L R+    G           P   STA  V +    N   L       +   +   
Sbjct: 104 PLGNLSRNSLRNGTE----VVSCHPQ-GSTAGVVYRAGRNNRWYLAVAAT--YVLPEPET 156

Query: 121 FRTDLLNFTTGKKEYTFKRTIKYDSKWLD 149
                   +        K T        +
Sbjct: 157 ASRCNPAASDHDTAIALKDTEGRSLATQE 185

>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 = 19/95 (20%), Positives = 27/95 (28%), Gaps = 6/95 (6%)

Query: 60  NNLTHLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEF--TKAD 117
             L  L      PG          DP   ST   V +G  G  P L+ G           
Sbjct: 109 GQLEQLLLRPERPG--DTQYVAANDPAV-STVGLVAQGLAGE-PLLFVGRGYTSRGVGGG 164

Query: 118 TVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFK 152
                T  L     +  ++++ T K     L  + 
Sbjct: 165 IPPITTRALWPPDPQAAFSYEETAKLAVGRLSEYS 199

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	160
3oky_B	565	Putative uncharacterized protein; transmembrane, l	99.98
3nvq_A	590	Semaphorin-7A; beta-propeller, signaling, signalin	99.92
1q47_A	495	Semaphorin 3A; beta propeller, signaling protein;	99.9
4gz8_A	667	Semaphorin-3A; multi-domain, cell-CELL signaling,	99.89
1olz_A	663	Semaphorin 4D; developmental protein, CD100, beta-	99.87
3nvx_A	383	Protein A39; beta-propeller, viral protein; HET: N	99.75
3ol2_B	528	Plexin-B1; beta-propeller, signalling, extacellula	99.39
3al9_A	539	Plexin-A2; beta-propeller, membrane protein, signa	98.83
2uzx_B	727	Hepatocyte growth factor receptor; signaling prote	98.7
3nvn_B	476	Plexin-C1; beta-propeller, signaling, viral protei	97.71
4fww_A	527	Macrophage-stimulating protein receptor; beta-prop	97.6

>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=99.98  E-value=1.2e-33  Score=259.03  Aligned_cols=110  Identities=29%  Similarity=0.382  Sum_probs=93.5

Q ss_pred             cchhhHHHHhhhc-------ccccceEEeeecCcccccCCC-----------------ccCCccCcccccCCCCCCCCCe
Q psy12771         35 VEEEEEEEKKKER-------GFTKVFFWKILENNLTHLGRH-----------------EHVPGIGSGIAKCPYDPNDNST   90 (160)
Q Consensus        35 i~~~~~~~kk~~~-------~~~~nfirvL~~~N~ThL~~~-----------------e~v~~~esG~gkCPydP~~nsT   90 (160)
                      |+|+++++++++|       .+|.||||||+++|.|||+.|                 +.+.+.++|+|||||||.+++|
T Consensus        80 i~W~~~~~~~~~C~~kGK~~~eC~NyIrvL~~~n~~~L~~CGTnAf~P~C~~~~~~~l~~~~~~~~G~~~CPydP~~~~t  159 (565)
T 3oky_B           80 LTWKSRQADVDTCRMKGKHKDECHNFIKVLLKKNDDTLFVCGTNAFNPSCRNYRVDTLETFGDEFSGMARCPYDAKHANI  159 (565)
T ss_dssp             EECCCCHHHHHHHHHTTCCTTTSSCBEEEEEEEETTEEEEEECTTTSCEEEEEETTTCCBCSCCEECTTTSCSSTTSCCE
T ss_pred             EEEeCCHHHhhhhhhcCCChHHcCceEEEEeecCCCEEEEeccCCCCcceEEEecccccccccccCCceeCCCCCCCCce
Confidence            4444444444443       588999999999999999622                 2245678999999999999999


Q ss_pred             eEEecCCCCCCCCccceeecccccCCCceEeecccccccCCCCccccceeccCccCCCCCCCeeEEEec
Q psy12771         91 AIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus        91 al~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLneP~FV~S~~I  159 (160)
                      ||+++|       +|||||++||+|+|++|||++      |++  +.|||+++|++|||||+||+|+.+
T Consensus       160 al~~~g-------~LYsgt~~dF~g~d~~I~Rs~------g~~--~~lRT~~~~s~wLneP~FV~a~~~  213 (565)
T 3oky_B          160 ALFADG-------KLYSATVTDFLAIDAVIYRSL------GDS--PTLRTVKHDSKWLKEPYFVQAVDY  213 (565)
T ss_dssp             EEEETT-------EEEEEEESSTTCCCEEEEEEC------TTS--CCEECCTTCTTTCSSCEEEEEEEE
T ss_pred             EEEECC-------EEEEEEecccCCCCceEEecC------CCC--CceeeeccchhhhcCCceeEEEee
Confidence            999997       999999999999999999998      765  679999999999999999999875

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

Probab=99.92  E-value=2.7e-26  Score=211.32  Aligned_cols=103  Identities=16%  Similarity=0.135  Sum_probs=85.9

Q ss_pred             hhhHHHHhhhc---ccccceEEeeecCcccccCCC---------c-----cCCccCcccccCCCCCCCCCeeEEecCCCC
Q psy12771         37 EEEEEEKKKER---GFTKVFFWKILENNLTHLGRH---------E-----HVPGIGSGIAKCPYDPNDNSTAIWVEKGNP   99 (160)
Q Consensus        37 ~~~~~~kk~~~---~~~~nfirvL~~~N~ThL~~~---------e-----~v~~~esG~gkCPydP~~nsTal~vdgg~p   99 (160)
                      |...+++|++|   .+|.||||||+++|.| |+.|         .     .+...++|+|||||||++++|+|++||   
T Consensus        66 ~~~~~~~~~~C~~k~eC~NyIrvl~~~~~~-l~~CGT~Af~P~C~~~~~~~~~~~~~g~g~cP~dP~~~~t~~~~~g---  141 (590)
T 3nvq_A           66 TVNIGSTKGSCLDKRDCENYITLLERRSEG-LLACGTNARHPSCWNLVNGTVVPLGEMRGYAPFSPDENSLVLFEGD---  141 (590)
T ss_dssp             EEECCSCSSCCSSCSSCCCBEEEEEEETTE-EEEEECTTTCCEEEEESSSCEEEEEECTTSSCSSTTSCCCEEEETT---
T ss_pred             ecCCHHHhhhhhccccccceEEEeeecCCc-EEEeecCCCCCCeeEEeeeeccccccccccccCCCCCCceEEEecC---
Confidence            44444566665   6899999999999998 7622         1     123568999999999999999999998   


Q ss_pred             CCCCccceeec-ccccCCCceEeecccccccCCCCccccceeccCccCCCCCCCeeEEEec
Q psy12771        100 GNLPALYSGTN-AEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus       100 ~~~~eLYSgT~-tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLneP~FV~S~~I  159 (160)
                          +|||||+ .||+|++|+|+|++      |.   ..|||+   ++|||||+||+|+.|
T Consensus       142 ----~LYs~t~~~~f~g~~p~i~R~~------g~---~~lrt~---~~wL~eP~FV~s~~i  186 (590)
T 3nvq_A          142 ----EVYSTIRKQEYNGKIPRFRRIR------GE---SELYTS---DTVMQNPQFIKATIV  186 (590)
T ss_dssp             ----EEEECSCSSTTCCSCCCCEEEE------SS---SCEECC---TTSCSSCEEEEEEEE
T ss_pred             ----ceeeeeeeccccCCCceeEEcC------CC---Cccccc---cchhcCCceeEEEec
Confidence                9999995 79999999999998      65   369998   589999999999876

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

Probab=99.90  E-value=1.1e-24  Score=195.69  Aligned_cols=97  Identities=33%  Similarity=0.473  Sum_probs=84.7

Q ss_pred             ccccceEEeeecCcccccCCCc-------------------cC-----CccCcccccCCCCCCCCCeeEEecCCCCCCCC
Q psy12771         48 GFTKVFFWKILENNLTHLGRHE-------------------HV-----PGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLP  103 (160)
Q Consensus        48 ~~~~nfirvL~~~N~ThL~~~e-------------------~v-----~~~esG~gkCPydP~~nsTal~vdgg~p~~~~  103 (160)
                      ..|.||||+|+++|.+||+.|.                   .+     .+.++|+++|||||.++++++++++       
T Consensus        87 ~~C~N~ikvL~~~~~~~L~~CGT~a~~p~C~~~~l~~~~~~~~~~l~~~~~~~g~~~cp~dp~~~~~~l~~~~-------  159 (495)
T 1q47_A           87 KECANFIKVLEAYNQTHLYACGTGAFHPICTYIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDG-------  159 (495)
T ss_dssp             TTSSCBEEEEEECSSSEEEEEECCSSSCEEEEEECCSCTTSCCCEEEEEEEEECTTTSCSSTTSCCEEEEETT-------
T ss_pred             ccCcceEEEEEecCCCeEEEeecCCCCceEEEEecCcccccceeeccccccccCceeCCCCCCcCeeEEEeCC-------
Confidence            5689999999999999996321                   11     1345899999999999999999986       


Q ss_pred             ccceeecccccCCCceEeecccccccCCCCccccceeccCccCCCCCCCeeEEEec
Q psy12771        104 ALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus       104 eLYSgT~tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLneP~FV~S~~I  159 (160)
                      +||+||..||.|.+++|+|++      |.+  ..|||+++|++|||+|+||+|+.|
T Consensus       160 ~LY~gt~~d~~g~~~~i~rsl------~~~--~~lrT~~~d~~~l~~p~FV~s~~i  207 (495)
T 1q47_A          160 ELYSGTAADFMGRDFAIFRTL------GHH--HPIRTEQHDSRWLNDPRFISAHLI  207 (495)
T ss_dssp             EEEEEEECSTTSCCEEEEEEE------SSS--CCEECCSSCTTTCSSCEEEEEEEE
T ss_pred             eEEEEEeccCCCCCcceeeec------Ccc--ccccccccCcccccCcceEEEEEe
Confidence            899999999999999999997      654  789999999999999999999875

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

Probab=99.89  E-value=6.3e-24  Score=197.49  Aligned_cols=131  Identities=28%  Similarity=0.344  Sum_probs=100.7

Q ss_pred             cccCCCCCCCccccccCCCCCccchhhcccccccchhhHHHHhhhcccccceEEeeecCcccccCCCcc-----------
Q psy12771          2 YSFLGLPPLSFENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLTHLGRHEH-----------   70 (160)
Q Consensus         2 ~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~i~~~~~~~kk~~~~~~~nfirvL~~~N~ThL~~~e~-----------   70 (160)
                      |.+. +..++..+.+.||+.+..+..|           ..+-|.....|.||||+|+.+|.+||+.|..           
T Consensus        61 y~Ls-~~~l~~~~~i~w~~~~~d~~~C-----------~~kGk~~~~eC~NyikvL~~~~~~~LivCGTnafqp~C~~~~  128 (667)
T 4gz8_A           61 FSFN-LVNIKDFQKIVWPVSYTRRDEC-----------KWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIE  128 (667)
T ss_dssp             EEEE-TTCTTSEEEEECCCCHHHHHHH-----------HHTTCCTTTTSSCBEEEEEEEETTEEEEEECCSSSCEEEEEE
T ss_pred             EEEc-hhhcccceEEecCCChhhHhhc-----------ccCCCCccccCCCeEEEEEECCCCeEEECCCCCCCceEEEEE
Confidence            3443 4455555666666655555333           2222222346889999999999999963210           


Q ss_pred             -------------CCccCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeecccccccCCCCcccc
Q psy12771         71 -------------VPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTF  137 (160)
Q Consensus        71 -------------v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~~~~G~~~~~~  137 (160)
                                   ....++|+++|||||.+++|+++++|       +||+||++||+|.+++|+|++      +.+  ..
T Consensus       129 l~~~~~~~~~~~~~~~~~sg~g~cP~dP~~~~tal~~dg-------~LYsGT~~df~g~d~~I~Rsl------~~~--~~  193 (667)
T 4gz8_A          129 VGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDG-------ELYSGTAADFMGRDFAIFRTL------GHH--HP  193 (667)
T ss_dssp             CCSSSSCCCCEECCSCCEECTTTSCSSSSSCCEEEEETT-------EEEEEEECSTTSCCEEEEEES------CSS--CC
T ss_pred             CCCccccceeecccccccCcceECCCCCccceEEEeecC-------eEEEEeccccCCCCceEEecC------CCC--Cc
Confidence                         13457899999999999999999998       899999999999999999997      554  68


Q ss_pred             ceeccCccCCCCCCCeeEEEec
Q psy12771        138 KRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus       138 LRTe~~dskWLneP~FV~S~~I  159 (160)
                      +||+.++++||+||+||+++.|
T Consensus       194 lrT~~~~s~~l~~P~FV~s~~i  215 (667)
T 4gz8_A          194 IRTEQHDSRWLNDPRFISAHLI  215 (667)
T ss_dssp             EECCSSCTTTCSSCEEEEEEEE
T ss_pred             ceeeecccccccCCcceeeeee
Confidence            9999999999999999999876

>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=99.87  E-value=8.2e-23  Score=189.13  Aligned_cols=95  Identities=25%  Similarity=0.397  Sum_probs=82.1

Q ss_pred             ccccceEEeeecCcccccCCCc-----------------cCCccCcccccCCCCCCCCCeeEEecCCCCCCCCccceeec
Q psy12771         48 GFTKVFFWKILENNLTHLGRHE-----------------HVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTN  110 (160)
Q Consensus        48 ~~~~nfirvL~~~N~ThL~~~e-----------------~v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~  110 (160)
                      ..|.|||++|+++|.+||+.|.                 .+.+.++|+++|||||.+++++++++|       +||+||.
T Consensus        85 ~dc~N~i~vL~~~~~~~L~~CGTna~qp~C~~~~l~~~~~~~~~~~g~~~cp~dp~~~~~~vi~~g-------~Ly~gt~  157 (663)
T 1olz_A           85 TECLNYIRVLQPLSATSLYVCGTNAFQPACDHLNLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVDG-------ELYSGTS  157 (663)
T ss_dssp             TTSSCBEEEEEECSSSEEEEEECTTTSCEEEEEETTTTEECCCCEECTTTSCSSTTSCEEEEEETT-------EEEEEEE
T ss_pred             cccceeEEEEEEcCCCeEEEeeccCCCcEEEEeecCccccccccccCCccCCCCCCCCeeEEEeCC-------eEEEEEe
Confidence            4678999999999999986332                 134578999999999999999999987       8999999


Q ss_pred             ccccCCCceEeecccccccCCCCccccceeccCccCCCCCCCeeEEEec
Q psy12771        111 AEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus       111 tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLneP~FV~S~~I  159 (160)
                      .||.|.+|+|+|++      ..   ..|||| +|++|||||+||+|+.|
T Consensus       158 ~~~~g~~p~i~Rs~------~~---~~lrTe-~~~~~L~~p~FV~s~~i  196 (663)
T 1olz_A          158 YNFLGSEPIISRNS------SH---SPLRTE-YAIPWLNEPSFVFADVI  196 (663)
T ss_dssp             SSTTSCSEEEEEEC------SS---CCBCCC-SSTTTCSSCEEEEEEEE
T ss_pred             ccccCCCceEEecc------cc---cccccc-chhhhccCCceeEeeee
Confidence            99999999999987      22   469998 58999999999999865

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

Probab=99.75  E-value=1.1e-18  Score=154.26  Aligned_cols=93  Identities=11%  Similarity=-0.089  Sum_probs=73.0

Q ss_pred             cccccceEEeeecCcc--cccCCCc-------------cCCccCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecc
Q psy12771         47 RGFTKVFFWKILENNL--THLGRHE-------------HVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNA  111 (160)
Q Consensus        47 ~~~~~nfirvL~~~N~--ThL~~~e-------------~v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~t  111 (160)
                      ...|.||||||+..|.  +||+.|.             .....++|+|+|||||.++++.+ .+|       +|||||++
T Consensus        43 ~~eC~NyIrVL~~~~~~~~~L~vCGTNAf~P~C~~~~~~~~~~~~g~G~~Pf~ps~~s~~~-~~g-------~LYsat~~  114 (383)
T 3nvx_A           43 GLTNNNYITTSIKVEDADKDTLVCGTNNGNPKCWKIDGSDDPKHRGRGYAPYQNSKVTIIS-YNE-------CVLSDINI  114 (383)
T ss_dssp             ECCSSCBEEEEEEC----CCEEEEECGGGSCEEEETTSCBCTTCCCBTTBCSSSCCCCEEE-ETT-------EEEECSCS
T ss_pred             hhHhcceEEEEEEccCCCCeEEEecCCCCCCceEeecCcccccccccccCCCCCCcceEEe-cCC-------eEEEEEcc
Confidence            3689999999999775  8885221             11345789999999999986644 455       89999999


Q ss_pred             cccCCCceEeecccccccCCCCccccceeccCccCCCCCCCeeEEEe
Q psy12771        112 EFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKI  158 (160)
Q Consensus       112 DF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLneP~FV~S~~  158 (160)
                      | .|++|+|+|++      |.+ .+.|||+   ++|||||+||+|+.
T Consensus       115 d-~G~~p~i~R~~------g~~-~~~LrT~---d~wLn~P~FV~s~~  150 (383)
T 3nvx_A          115 S-KEGIKRWRRFD------GPC-GYDLYTA---DNVIPKDGLRGAFV  150 (383)
T ss_dssp             S-TTCCCCCEECS------BTT-BSCEECC---TTSSCTTCCSEEEE
T ss_pred             c-CCCCceEEecC------CCC-Ccccccc---ccccCCcceeEEEc
Confidence            9 79999999997      652 1579998   57999999999974

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

Probab=99.39  E-value=5.6e-14  Score=127.87  Aligned_cols=142  Identities=15%  Similarity=0.021  Sum_probs=94.8

Q ss_pred             CcccCCCCCCCccccccCCCCCccchhhcccccccchhhHHHHhhhcccccceEEeeecCcccccCCCcc----------
Q psy12771          1 MYSFLGLPPLSFENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLTHLGRHEH----------   70 (160)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~i~~~~~~~kk~~~~~~~nfirvL~~~N~ThL~~~e~----------   70 (160)
                      ||++.  +++..+.++.|-++.+.+ .|.  ......+|.. +    +.+.||||+|+ .|.+||+.|..          
T Consensus        39 ly~Ls--~~L~~~~~~~tGP~~d~~-~C~--p~~~~~~C~~-~----~~tdN~nkvL~-~~~~~L~~CGSafqg~C~~~~  107 (528)
T 3ol2_B           39 LFQLS--PGLQLEATVSTGPVLDSR-DCL--PPVMPDECPQ-A----QPTNNPNQLLL-VSPGALVVCGSVHQGVCEQRR  107 (528)
T ss_dssp             EEEEC--TTCCEEEEEECCCEEECT-TSC--SSCCTTTCTT-C----EEECCCEEEEE-ECSSEEEEEESSGGGCEEEEE
T ss_pred             EEEcC--CCcccceEeccCCCCCCc-CCC--CCcccccccc-c----CcccceEEEEE-EcCCeEEEcccCcCceeEEEe
Confidence            35554  477777777777765554 444  2112233322 1    24689999999 57799974321          


Q ss_pred             ------CCccCcccccCCC----CCCCCCeeEEecCCCCCCCCccceeecccccC---CCceEe-eccccccc-CCC--C
Q psy12771         71 ------VPGIGSGIAKCPY----DPNDNSTAIWVEKGNPGNLPALYSGTNAEFTK---ADTVIF-RTDLLNFT-TGK--K  133 (160)
Q Consensus        71 ------v~~~esG~gkCPy----dP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G---~dpvI~-Rs~l~~~~-~G~--~  133 (160)
                            +...++|+++|||    ||.++.+++++++  |.+..+||+||..||.|   .+|+|+ |++..... .+-  .
T Consensus       108 l~~~~~~~~~~~~~~~~~~va~~dp~~s~v~vi~~~--~~~~~~LyvGt~~d~~~~~~~~p~Is~R~L~~~~~~~~F~~~  185 (528)
T 3ol2_B          108 LGQLEQLLLRPERPGDTQYVAANDPAVSTVGLVAQG--LAGEPLLFVGRGYTSRGVGGGIPPITTRALWPPDPQAAFSYE  185 (528)
T ss_dssp             TTEEEEEEECCSSCCGGGCCSCSSTTSCEEEEEEEC--TTSCEEEEEEECCCC---CCCCCSEEEEESSCSSGGGTTCEE
T ss_pred             cCCcceeeeeccCCCcCCcccCCCCCCCeEEEEeeC--CCCceEEEEEEeccCCCccCCCcceEEeecCCcccccccccc
Confidence                  1234699999999    9999999999985  23447999999999997   799999 88721000 000  0


Q ss_pred             ccccceeccCccCCCCCCCeeEEEe
Q psy12771        134 EYTFKRTIKYDSKWLDSFKSLIAKI  158 (160)
Q Consensus       134 ~~~~LRTe~~dskWLneP~FV~S~~  158 (160)
                      ....|||+ ++++|  +|+||+||.
T Consensus       186 ~~~~l~t~-~~~~~--~~~FV~aF~  207 (528)
T 3ol2_B          186 ETAKLAVG-RLSEY--SHHFVSAFA  207 (528)
T ss_dssp             EEEECCCS-CHHHH--CCEEEEEEE
T ss_pred             ccceeEec-ccccC--CCcEEEEEe
Confidence            01469997 67889  999999985

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

Probab=98.83  E-value=2.2e-09  Score=97.31  Aligned_cols=105  Identities=8%  Similarity=-0.020  Sum_probs=68.4

Q ss_pred             cceEEeeec-CcccccCCCcc-------------C---Cc--cCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecc
Q psy12771         51 KVFFWKILE-NNLTHLGRHEH-------------V---PG--IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNA  111 (160)
Q Consensus        51 ~nfirvL~~-~N~ThL~~~e~-------------v---~~--~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~t  111 (160)
                      .|++++|.. .|.+||+.|..             +   ..  ...|.+.||+||..+.+++++.++  ...++||+||..
T Consensus        81 dN~nkvLl~~~~~~~L~~CGS~~qg~C~~~~l~~~~~~~~~~~~~~~~v~~~~p~~stv~vv~~~~--~~~~~Lyvgt~~  158 (539)
T 3al9_A           81 NNVNKLLIIDYSENRLLACGSLYQGVCKLLRLDDLFILVEPSHKKEHYLSSVNKTGTMYGVIVRSE--GEDGKLFIGTAV  158 (539)
T ss_dssp             CCCEEEEEEEGGGTEEEEEESSTTTCEEEEETTTCCEEECCCSSGGGCCCCCCCSSSEEEEEECCT--TSCEEEEEEECC
T ss_pred             CceEEEEEEecCCCeEEEeecCCCCCceeEecccccccccccccCcccccCCCCCCCeEEEEeecC--CCCccEEEEEec
Confidence            688887776 78888863211             1   11  123456899999999999999432  122489999999


Q ss_pred             cccCC-CceE-eecccccccCCCCccccceeccCccCCCC------------CCCeeEEEe
Q psy12771        112 EFTKA-DTVI-FRTDLLNFTTGKKEYTFKRTIKYDSKWLD------------SFKSLIAKI  158 (160)
Q Consensus       112 DF~G~-dpvI-~Rs~l~~~~~G~~~~~~LRTe~~dskWLn------------eP~FV~S~~  158 (160)
                      ||.+. .|+| .|++... ..|......+++..++++||+            +++||+||.
T Consensus       159 ~~~~~~~p~Is~R~L~~~-~~~~~~f~~~~~~~~~~~~~~~~~~~l~~~p~~~~~fV~aF~  218 (539)
T 3al9_A          159 DGKQDYFPTLSSRKLPRD-PESSAMLDYELHSDFVSSLIKIPSDTLALVSHFDIFYIYGFA  218 (539)
T ss_dssp             TTCTTTCCSEEEEEECSS-TTCTTTTCBSSBCSSCBSEECCCHHHHHHCTTCCCEEEEEEE
T ss_pred             cCCCCCCcceEEeccCCC-ccccchheeecccccccccccccccccccCCCCCcceEEEEe
Confidence            97653 4677 6887311 111111123456778888876            688899974

>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=98.70  E-value=1.6e-08  Score=94.44  Aligned_cols=111  Identities=11%  Similarity=-0.003  Sum_probs=62.9

Q ss_pred             hhHHHHhhhc-cccc--ceEEeeecCcccccCCCcc----------C---------------C-ccCcccccCCCCCCCC
Q psy12771         38 EEEEEKKKER-GFTK--VFFWKILENNLTHLGRHEH----------V---------------P-GIGSGIAKCPYDPNDN   88 (160)
Q Consensus        38 ~~~~~kk~~~-~~~~--nfirvL~~~N~ThL~~~e~----------v---------------~-~~esG~gkCPydP~~n   88 (160)
                      +|..+.|.+. ..|.  |++++|+++|.+||+.|..          +               . ....+.++|| ||...
T Consensus        79 ~C~~~~k~~~~~~~~n~nkvLl~~~~~~~~L~~CGTafqg~C~~~~l~~~~~~~i~~~~~~~~~~~~~~~~~cp-d~~~s  157 (727)
T 2uzx_B           79 DCSSKANLSGGVWKDNINMALVVDTYYDDQLISCGSVNRGTCQRHVFPHNHTADIQSEVHCIFSPQIEEPSQCP-DCVVS  157 (727)
T ss_dssp             -----------CCCCCCCCEEEEECSSSSEEEEECSSSSSCEEEEECCSCC-----CEECCCCC----CCSCCS-SCCCC
T ss_pred             hccccCCCcccCcCCceEEEEEEcccCCCEEEEEeCCCCCcceeEecCcccccccccccceeeecccCCCCCCC-Ccccc
Confidence            5555544421 2345  5557777889999963211          0               0 0124777999 89988


Q ss_pred             CeeEEe---cCCCCCCCCccceeeccccc-----CCCceEeecccccccCCCCcc-----ccceeccCccCCC--CCCCe
Q psy12771         89 STAIWV---EKGNPGNLPALYSGTNAEFT-----KADTVIFRTDLLNFTTGKKEY-----TFKRTIKYDSKWL--DSFKS  153 (160)
Q Consensus        89 sTal~v---dgg~p~~~~eLYSgT~tDF~-----G~dpvI~Rs~l~~~~~G~~~~-----~~LRTe~~dskWL--neP~F  153 (160)
                      .+++++   +++   .-.+||+||..|+.     |.+++|+|++      +....     ....+...+.+|+  ++|+|
T Consensus       158 ~~g~~v~~~~~~---~~~~Lyvgt~~~~~~~~~~~~~~is~R~L------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f  228 (727)
T 2uzx_B          158 ALGAKVLSSVKD---RFINFFVGNTINSSYFPDHPLHSISVRRL------KETKDGFMFLTDQSYIDVLPEFRDSYPIKY  228 (727)
T ss_dssp             TTCEEEEEEEET---TEEEEEEEECCCSCC----CCCSEEEEEE------CTTCSCEECCSGGGEECCCGGGTTTSCEEE
T ss_pred             cceeeEEccCCC---cceEEEEEEeeccccCCCCCCcceEEccC------CCCcccceeecccceEEeccccccccCCCc
Confidence            877655   432   01269999999853     2358999998      32210     0123344567888  79999


Q ss_pred             eEEEe
Q psy12771        154 LIAKI  158 (160)
Q Consensus       154 V~S~~  158 (160)
                      |++|.
T Consensus       229 V~~f~  233 (727)
T 2uzx_B          229 VHAFE  233 (727)
T ss_dssp             EEEEE
T ss_pred             eeeee
Confidence            99975

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

Probab=97.71  E-value=3.4e-05  Score=70.08  Aligned_cols=97  Identities=16%  Similarity=0.097  Sum_probs=72.5

Q ss_pred             ccccceEEeeecCcc-----cccC--------------CCccC----CccCcccccCCCCCCCCCeeEEecCCCCCCCCc
Q psy12771         48 GFTKVFFWKILENNL-----THLG--------------RHEHV----PGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPA  104 (160)
Q Consensus        48 ~~~~nfirvL~~~N~-----ThL~--------------~~e~v----~~~esG~gkCPydP~~nsTal~vdgg~p~~~~e  104 (160)
                      .-|.||+++|..+-.     .-|.              +.+.+    .+.+.+...|  +|..+.+++++.++ |  .+.
T Consensus        66 ~~~~n~nKlLl~~~~~~~~~~~Li~cGs~~q~g~C~~r~l~~l~~~~~~~~~~v~~~--~p~~st~~~v~~~~-~--~~~  140 (476)
T 3nvn_B           66 RPGSSFSKLLLPYREGAAGLGGLLLTGWTFDRGACEVRPLGNLSRNSLRNGTEVVSC--HPQGSTAGVVYRAG-R--NNR  140 (476)
T ss_dssp             SCCCCSEEEEEEESCSSTTSCCEEEEEESHHHHCEEEEESSCTTSCCSCEESSSSCC--STTSCEEEEEEEET-T--TTE
T ss_pred             CCCCCeeEEEEecccccccCCeEEEEeeccCCceeEEEEcCCcceecccCCCceeec--CCCCceEEEEeccC-C--Cce
Confidence            356799999997442     3332              12221    2457788899  99999999998753 2  238


Q ss_pred             cceeecccc---------------cCCCceEeecccccccCCCCccccceeccCccCCCC---CC-CeeEEE
Q psy12771        105 LYSGTNAEF---------------TKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLD---SF-KSLIAK  157 (160)
Q Consensus       105 LYSgT~tDF---------------~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLn---eP-~FV~S~  157 (160)
                      ||.|+.+||               .+.+|+|.|+.      ...  ..|+|+++++.||+   ++ +||.||
T Consensus       141 lfvg~~~~~~~~~~~~~~~~~~~~~~~~~ai~~~~------~~~--r~l~~~~~~~~~~~~~~~~~~fV~af  204 (476)
T 3nvn_B          141 WYLAVAATYVLPEPETASRCNPAASDHDTAIALKD------TEG--RSLATQELGRLKLCEGAGSLHFVDAF  204 (476)
T ss_dssp             EEEEEEECCCCCCCCTTTCCCCCGGGTTEEEEEEE------SSS--GGGCCCTTSEEEBCTTSCCEEECCCE
T ss_pred             eEEEecccccccccccccccCCCccccccceeecc------Ccc--cccchhhhcceeeccCCCCceeeeeh
Confidence            999999999               56689999986      221  46999999999999   88 999993

>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=97.60  E-value=3.9e-05  Score=68.33  Aligned_cols=47  Identities=11%  Similarity=0.130  Sum_probs=32.8

Q ss_pred             cCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeecc
Q psy12771         74 IGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTD  124 (160)
Q Consensus        74 ~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~  124 (160)
                      .+++.+.|+.+|....+++...+ +   .+.||+||..||.|.++++.|+.
T Consensus       129 ~~~~~~~~~~~p~~~~~~~~~~g-~---~~~Lyvgt~~~~~~~~~~~~rsi  175 (527)
T 4fww_A          129 RPDDCPDCVASPLGTRVTVVEQG-Q---ASYFYVASSLDAAVAASFSPRSV  175 (527)
T ss_dssp             BTTBCTTCCCCTTCEEEEEEEET-T---EEEEEEEECCCHHHHSSSCCCSE
T ss_pred             CCCCCceeecCCCCCceEEEecC-C---CceEEEeeecccCCCCCcccccc
Confidence            34566777788765555544433 1   23699999999999998887764

---

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	160
d1olza2	478	b.69.12.1 (A:3-480) Semaphorin 4d {Human (Homo sap	3e-10
d1q47a_	495	b.69.12.1 (A:) Semaphorin 3a {Mouse (Mus musculus)	4e-10
d1shyb1	476	b.69.12.1 (B:40-515) Hepatocyte growth factor rece	3e-05

>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 = 55.5 bits (133), Expect = 3e-10
 Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 17/86 (19%)

Query: 64  HLGRHEHVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRT 123
           +L   + +     G  +CP+DP  + T++ V+         LYSGT+  F  ++ +I R 
Sbjct: 116 NLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVD-------GELYSGTSYNFLGSEPIISRN 168

Query: 124 DLLNFTTGKKEYTFKRTIKYDSKWLD 149
              +              +Y   WL+
Sbjct: 169 SSHS----------PLRTEYAIPWLN 184

>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 = 55.1 bits (132), Expect = 4e-10
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 15/74 (20%)

Query: 76  SGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEY 135
           +G  K PYDP   + ++ ++         LYSGT A+F   D  IFRT   +        
Sbjct: 139 NGRGKSPYDPKLLTASLLID-------GELYSGTAADFMGRDFAIFRTLGHH-------- 183

Query: 136 TFKRTIKYDSKWLD 149
              RT ++DS+WL+
Sbjct: 184 HPIRTEQHDSRWLN 197

>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 = 40.5 bits (94), Expect = 3e-05
 Identities = 13/101 (12%), Positives = 25/101 (24%), Gaps = 6/101 (5%)

Query: 58  LENNLTHLGRHEHVPGIGSGIAKCPY--DPNDNSTAIWVEKGNPGNLPALYSGTNAEFTK 115
             +N T   + E        I +     D   ++    V           + G     + 
Sbjct: 107 FPHNHTADIQSEVHCIFSPQIEEPSQCPDCVVSALGAKVLSSVKDRFINFFVGNTINSSY 166

Query: 116 ADTVIFRT----DLLNFTTGKKEYTFKRTIKYDSKWLDSFK 152
                  +     L     G    T +  I    ++ DS+ 
Sbjct: 167 FPDHPLHSISVRRLKETKDGFMFLTDQSYIDVLPEFRDSYP 207

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	160
d1q47a_	495	Semaphorin 3a {Mouse (Mus musculus) [TaxId: 10090]	99.82
d1olza2	478	Semaphorin 4d {Human (Homo sapiens) [TaxId: 9606]}	99.79
d1shyb1	476	Hepatocyte growth factor receptor {Human (Homo sap	97.98

>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=99.82  E-value=4.8e-21  Score=168.71  Aligned_cols=131  Identities=28%  Similarity=0.344  Sum_probs=100.7

Q ss_pred             cccCCCCCCCccccccCCCCCccchhhcccccccchhhHHHHhhhcccccceEEeeecCcccccCCCcc-----------
Q psy12771          2 YSFLGLPPLSFENQHNFPAVPPQLATFFGVKKVVEEEEEEEKKKERGFTKVFFWKILENNLTHLGRHEH-----------   70 (160)
Q Consensus         2 ~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~i~~~~~~~kk~~~~~~~nfirvL~~~N~ThL~~~e~-----------   70 (160)
                      |.+. +..++..+.+.||..+.....|           ...-|.+...|.||||+|+.+|.+||..|..           
T Consensus        53 y~L~-~~~~~~~~~~~~~~~~~d~~~C-----------~~~g~~~~~~c~N~iklL~~~~~~~LivCGS~a~qp~C~~~~  120 (495)
T d1q47a_          53 FSFN-LVNIKDFQKIVWPVSYTRRDEC-----------KWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIE  120 (495)
T ss_dssp             EEEE-SSCTTSEEEEECCCCHHHHHHH-----------HHTTCCTTTTSSCBEEEEEECSSSEEEEEECCSSSCEEEEEE
T ss_pred             EEEc-hhhccccceEEccCChhhhhhc-----------cccCCCccccCcceEEEEEEcCCCeEEEecCCCCCccceEEE
Confidence            3443 4455566667777655555444           2222233457899999999999988852211           


Q ss_pred             -------------CCccCcccccCCCCCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeecccccccCCCCcccc
Q psy12771         71 -------------VPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTDLLNFTTGKKEYTF  137 (160)
Q Consensus        71 -------------v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~l~~~~~G~~~~~~  137 (160)
                                   ....++|+++|||+|.+++++++++|       +||+||.+||.|.+++|+|++      +.+  ..
T Consensus       121 l~~~~~~~~~~~~~~~~~~g~~~~p~~P~~~~~~~~~~g-------~LY~gt~~~~~~~~~~i~R~~------~~~--~~  185 (495)
T d1q47a_         121 VGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDG-------ELYSGTAADFMGRDFAIFRTL------GHH--HP  185 (495)
T ss_dssp             CCSCTTSCCCEEEEEEEEECTTTSCSSTTSCCEEEEETT-------EEEEEEECSTTSCCEEEEEEE------SSS--CC
T ss_pred             CCCccccceeecccccccCCceeCCCCCccceeEEecCC-------eEEEEeccCcCCCCceEEecC------CCC--cc
Confidence                         02356899999999999999999997       899999999999999999998      443  68


Q ss_pred             ceeccCccCCCCCCCeeEEEec
Q psy12771        138 KRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus       138 LRTe~~dskWLneP~FV~S~~I  159 (160)
                      +||+.++++||++|+||+++.|
T Consensus       186 ~~t~~~~~~~l~~p~Fv~s~~i  207 (495)
T d1q47a_         186 IRTEQHDSRWLNDPRFISAHLI  207 (495)
T ss_dssp             EECCSSCTTTCSSCEEEEEEEE
T ss_pred             ccchhhhhhhcCCccceeeeee
Confidence            9999999999999999999875

>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=99.79  E-value=2.3e-20  Score=164.16  Aligned_cols=97  Identities=25%  Similarity=0.398  Sum_probs=82.2

Q ss_pred             hcccccceEEeeecCcccccCCCc-----------------cCCccCcccccCCCCCCCCCeeEEecCCCCCCCCcccee
Q psy12771         46 ERGFTKVFFWKILENNLTHLGRHE-----------------HVPGIGSGIAKCPYDPNDNSTAIWVEKGNPGNLPALYSG  108 (160)
Q Consensus        46 ~~~~~~nfirvL~~~N~ThL~~~e-----------------~v~~~esG~gkCPydP~~nsTal~vdgg~p~~~~eLYSg  108 (160)
                      +...|.||||+|+.+|.+||..|.                 .+...++|+++|||||.+++++++++|       +||+|
T Consensus        81 ~~~~c~N~ikvL~~~~~~~L~vCGT~a~qp~C~~~~l~~~~~~~~~~~~~~~~p~~p~~~~~~~~~~g-------~lY~g  153 (478)
T d1olza2          81 KQTECLNYIRVLQPLSATSLYVCGTNAFQPACDHLNLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVDG-------ELYSG  153 (478)
T ss_dssp             TTTTSSCBEEEEEECSSSEEEEEECTTTSCEEEEEETTTTEECCCCEECTTTSCSSTTSCEEEEEETT-------EEEEE
T ss_pred             CcccCcceEEEEEEcCCCeEEEecCCCCCCcceEEecccccccccccCCceecCCCcccCeeEEEECC-------eEEEE
Confidence            345789999999999988885221                 135567999999999999999999997       99999


Q ss_pred             ecccccCCCceEeecccccccCCCCccccceeccCccCCCCCCCeeEEEec
Q psy12771        109 TNAEFTKADTVIFRTDLLNFTTGKKEYTFKRTIKYDSKWLDSFKSLIAKII  159 (160)
Q Consensus       109 T~tDF~G~dpvI~Rs~l~~~~~G~~~~~~LRTe~~dskWLneP~FV~S~~I  159 (160)
                      |.+||.|.+|+|+|+.      +.   ..++|+ .+++||++|+||+++.|
T Consensus       154 t~~~~~~~~~~i~r~~------~~---~~~~t~-~~~~~l~~p~fv~~~~i  194 (478)
T d1olza2         154 TSYNFLGSEPIISRNS------SH---SPLRTE-YAIPWLNEPSFVFADVI  194 (478)
T ss_dssp             EESSTTSCSEEEEEEC------SS---CCBCCC-SSTTTCSSCEEEEEEEE
T ss_pred             EecCcCCCCceEEecC------CC---CCccch-hhhhcccCCceEEEeee
Confidence            9999999999999986      33   358887 46899999999999765

>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=97.98  E-value=6.7e-07  Score=77.17  Aligned_cols=41  Identities=7%  Similarity=-0.044  Sum_probs=30.1

Q ss_pred             CCCCCCeeEEecCCCCCCCCccceeecccccCCCceEeecc
Q psy12771         84 DPNDNSTAIWVEKGNPGNLPALYSGTNAEFTKADTVIFRTD  124 (160)
Q Consensus        84 dP~~nsTal~vdgg~p~~~~eLYSgT~tDF~G~dpvI~Rs~  124 (160)
                      |+....+++.+....++....||+|+..+|.+.+..+.|+.
T Consensus       135 ~~~~s~~g~~~~~~~~~~~~~Lyvg~~~~~~~~~~~~~~s~  175 (476)
T d1shyb1         135 DCVVSALGAKVLSSVKDRFINFFVGNTINSSYFPDHPLHSI  175 (476)
T ss_dssp             TBCCCTTCEEEEEEEETTEEEEEEEECCCCCCCTTCCCCSE
T ss_pred             CccccccceeeccccCccceeEEEEEcccccCCCccccCcc
Confidence            55566666666554444555699999999999998887765