Psyllid ID: psy1892

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60----
Protein Sequence
MTIPLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHcccccccEEcc
Coil and Loop (DISEMBL)
mtiplatsTVIGGAVVGLLCAILVVMFIVYRMRkkdegsyaleepkrspasnsymknsnrefya
Flexible Loop (DISEMBL)
mtiplatstviggaVVGLLCAILVVMFIVYRMRKKDegsyaleepkrspasnsymknsnrefya
Low Complexity Region (SEG)
MTIPLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA
Disordered region (IsUnstruct)
****LATSTVIGGAVVGLLCAILVVMFIVYRM********************************
Disordered Region (DISOPRED)
****LATSTVIGGAVVGLLCAILVVMFIVYRMRKKD****************************
Disordered Region (DISEMBL)
MTIPLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEG**************SYMKNSNREFYA
Disordered Region (DISPRO)
**IPLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASN************
Transmembrane Helix (TMHMM)
oooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTIPLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA
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	64	2.2.26 [Sep-21-2011]
P49415	399	Syndecan OS=Drosophila me	no	N/A	0.953	0.152	0.838	1e-23
P50605	288	Probable syndecan OS=Caen	yes	N/A	0.859	0.190	0.578	3e-12
P26260	313	Syndecan-1 OS=Rattus norv	yes	N/A	0.859	0.175	0.509	7e-10
Q6GR51	190	Syndecan-2-B OS=Xenopus l	N/A	N/A	0.828	0.278	0.527	1e-09
P49414	191	Syndecan-2-A OS=Xenopus l	N/A	N/A	0.828	0.277	0.527	1e-09
P18828	311	Syndecan-1 OS=Mus musculu	yes	N/A	0.859	0.176	0.509	1e-09
P18827	310	Syndecan-1 OS=Homo sapien	yes	N/A	0.859	0.177	0.509	2e-09
P47951	309	Syndecan-1 OS=Cricetulus	yes	N/A	0.859	0.177	0.509	2e-09
P34740	309	Syndecan-1 OS=Mesocricetu	N/A	N/A	0.859	0.177	0.509	2e-09
Q08DZ5	311	Syndecan-1 OS=Bos taurus	yes	N/A	0.859	0.176	0.509	2e-09

>sp|P49415|SDC_DROME Syndecan OS=Drosophila melanogaster GN=Sdc PE=2 SV=2

 Score =  108 bits (269), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 338 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 397

Query: 63  YA 64
           YA
Sbjct: 398 YA 399

Cell surface proteoglycan that bears heparan sulfate. Required for axonal and myotube guidance, is a necessary component of slit/robo signaling and is required in the slit target cells.
Drosophila melanogaster (taxid: 7227)

>sp|P50605|SDC_CAEEL Probable syndecan OS=Caenorhabditis elegans GN=sdn-1 PE=2 SV=1

 Score = 70.5 bits (171), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/57 (57%), Positives = 44/57 (77%), Gaps = 2/57 (3%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPK--RSPASNSYMKNSNREFYA 64
           + GG +V ++ AIL+V+F+V+R+RKKDEGSYAL+EPK  R  AS  Y K S +EFYA
Sbjct: 232 IAGGVLVAVITAILLVLFVVFRIRKKDEGSYALDEPKQARPYASYGYTKASTKEFYA 288

Cell surface proteoglycan that bears heparan sulfate.

Caenorhabditis elegans (taxid: 6239)

>sp|P26260|SDC1_RAT Syndecan-1 OS=Rattus norvegicus GN=Sdc1 PE=2 SV=2

 Score = 62.4 bits (150), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 28/55 (50%), Positives = 38/55 (69%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
           VI G +VGL+ A+ +V F++YRM+KKDEGSY+LEEPK++            EFYA
Sbjct: 259 VIAGGLVGLIFAVCLVAFMLYRMKKKDEGSYSLEEPKQANGGAYQKPTKQEEFYA 313

Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.

Rattus norvegicus (taxid: 10116)

>sp|Q6GR51|SDC2B_XENLA Syndecan-2-B OS=Xenopus laevis GN=sdc2-b PE=2 SV=1

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 37/55 (67%), Gaps = 2/55 (3%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
           VI G  +G L A+ +++ +VYRMRKKDEGSY L E  R P+S  Y K   +EFYA
Sbjct: 138 VIAGGGIGFLFAVFLILLLVYRMRKKDEGSYDLGE--RKPSSAVYQKAPTKEFYA 190

Cell surface proteoglycan that bears heparan sulfate.

Xenopus laevis (taxid: 8355)

>sp|P49414|SDC2A_XENLA Syndecan-2-A OS=Xenopus laevis GN=sdc2-a PE=2 SV=2

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 37/55 (67%), Gaps = 2/55 (3%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
           VI G  +G L A+ +++ +VYRMRKKDEGSY L E  R P+S  Y K   +EFYA
Sbjct: 139 VIAGGGIGFLFAVFLILLLVYRMRKKDEGSYDLGE--RKPSSAVYQKAPTKEFYA 191

Cell surface proteoglycan that bears heparan sulfate.

Xenopus laevis (taxid: 8355)

>sp|P18828|SDC1_MOUSE Syndecan-1 OS=Mus musculus GN=Sdc1 PE=1 SV=1

 Score = 61.6 bits (148), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/55 (50%), Positives = 38/55 (69%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
           VI G +VGL+ A+ +V F++YRM+KKDEGSY+LEEPK++            EFYA
Sbjct: 257 VIAGGLVGLIFAVCLVAFMLYRMKKKDEGSYSLEEPKQANGGAYQKPTKQEEFYA 311

Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.

Mus musculus (taxid: 10090)

>sp|P18827|SDC1_HUMAN Syndecan-1 OS=Homo sapiens GN=SDC1 PE=1 SV=3

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/55 (50%), Positives = 38/55 (69%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
           VI G +VGL+ A+ +V F++YRM+KKDEGSY+LEEPK++            EFYA
Sbjct: 256 VIAGGLVGLIFAVCLVGFMLYRMKKKDEGSYSLEEPKQANGGAYQKPTKQEEFYA 310

Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.

Homo sapiens (taxid: 9606)

>sp|P47951|SDC1_CRIGR Syndecan-1 OS=Cricetulus griseus GN=SDC1 PE=2 SV=1

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/55 (50%), Positives = 38/55 (69%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
           VI G +VGL+ A+ +V F++YRM+KKDEGSY+LEEPK++            EFYA
Sbjct: 255 VIAGGLVGLIFAVCLVGFMLYRMKKKDEGSYSLEEPKQANGGAYQKPTKQEEFYA 309

Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.

Cricetulus griseus (taxid: 10029)

>sp|P34740|SDC1_MESAU Syndecan-1 OS=Mesocricetus auratus GN=SDC1 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/55 (50%), Positives = 38/55 (69%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
           VI G +VGL+ A+ +V F++YRM+KKDEGSY+LEEPK++            EFYA
Sbjct: 255 VIAGGLVGLIFAVCLVGFMLYRMKKKDEGSYSLEEPKQANGGAYQKPTKQEEFYA 309

Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.

Mesocricetus auratus (taxid: 10036)

>sp|Q08DZ5|SDC1_BOVIN Syndecan-1 OS=Bos taurus GN=SDC1 PE=2 SV=1

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/55 (50%), Positives = 38/55 (69%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
           VI G +VGL+ A+ +V F++YRM+KKDEGSY+LEEPK++            EFYA
Sbjct: 257 VIAGGLVGLIFAVCLVGFMLYRMKKKDEGSYSLEEPKQANGGAYQKPTKQEEFYA 311

Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.

Bos taurus (taxid: 9913)

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	64
437283	395	syndecan [Drosophila melanogaster]	0.953	0.154	0.838	5e-22
24657011	226	syndecan, isoform B [Drosophila melanoga	0.953	0.269	0.838	5e-22
221330491	468	syndecan, isoform E [Drosophila melanoga	0.953	0.130	0.838	5e-22
221330489	398	syndecan, isoform D [Drosophila melanoga	0.953	0.153	0.838	5e-22
198460390	468	GA10355 [Drosophila pseudoobscura pseudo	0.953	0.130	0.838	5e-22
195585432	398	GD25198 [Drosophila simulans] gi|1941944	0.953	0.153	0.838	5e-22
195486490	499	GE13713 [Drosophila yakuba] gi|194177635	0.953	0.122	0.838	5e-22
195426602	570	GK20743 [Drosophila willistoni] gi|19415	0.953	0.107	0.838	5e-22
195346435	388	GM15720 [Drosophila sechellia] gi|194135	0.953	0.157	0.838	5e-22
195121846	426	GI20467 [Drosophila mojavensis] gi|19391	0.953	0.143	0.838	5e-22

>gi|437283|gb|AAC34307.1| syndecan [Drosophila melanogaster]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 334 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 393

Query: 63  YA 64
           YA
Sbjct: 394 YA 395

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24657011|ref|NP_726071.1| syndecan, isoform B [Drosophila melanogaster] gi|24657016|ref|NP_726072.1| syndecan, isoform C [Drosophila melanogaster] gi|19528467|gb|AAL90348.1| RE22862p [Drosophila melanogaster] gi|21645266|gb|AAM70897.1| syndecan, isoform B [Drosophila melanogaster] gi|21645267|gb|AAM70898.1| syndecan, isoform C [Drosophila melanogaster] gi|220948164|gb|ACL86625.1| Sdc-PB [synthetic construct] gi|220957478|gb|ACL91282.1| Sdc-PB [synthetic construct]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 165 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 224

Query: 63  YA 64
           YA
Sbjct: 225 YA 226

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|221330491|ref|NP_001137729.1| syndecan, isoform E [Drosophila melanogaster] gi|220902320|gb|ACL83183.1| syndecan, isoform E [Drosophila melanogaster]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 407 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 466

Query: 63  YA 64
           YA
Sbjct: 467 YA 468

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|221330489|ref|NP_001137728.1| syndecan, isoform D [Drosophila melanogaster] gi|220902319|gb|ACL83182.1| syndecan, isoform D [Drosophila melanogaster] gi|314122273|gb|ADR83711.1| LP21789p [Drosophila melanogaster]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 337 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 396

Query: 63  YA 64
           YA
Sbjct: 397 YA 398

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198460390|ref|XP_001361704.2| GA10355 [Drosophila pseudoobscura pseudoobscura] gi|198137001|gb|EAL26283.2| GA10355 [Drosophila pseudoobscura pseudoobscura]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 407 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 466

Query: 63  YA 64
           YA
Sbjct: 467 YA 468

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195585432|ref|XP_002082485.1| GD25198 [Drosophila simulans] gi|194194494|gb|EDX08070.1| GD25198 [Drosophila simulans]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 337 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 396

Query: 63  YA 64
           YA
Sbjct: 397 YA 398

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195486490|ref|XP_002091534.1| GE13713 [Drosophila yakuba] gi|194177635|gb|EDW91246.1| GE13713 [Drosophila yakuba]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 438 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 497

Query: 63  YA 64
           YA
Sbjct: 498 YA 499

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195426602|ref|XP_002061404.1| GK20743 [Drosophila willistoni] gi|194157489|gb|EDW72390.1| GK20743 [Drosophila willistoni]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 509 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 568

Query: 63  YA 64
           YA
Sbjct: 569 YA 570

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195346435|ref|XP_002039763.1| GM15720 [Drosophila sechellia] gi|194135112|gb|EDW56628.1| GM15720 [Drosophila sechellia]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 327 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 386

Query: 63  YA 64
           YA
Sbjct: 387 YA 388

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195121846|ref|XP_002005429.1| GI20467 [Drosophila mojavensis] gi|193910497|gb|EDW09364.1| GI20467 [Drosophila mojavensis]

 Score =  108 bits (269), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/62 (83%), Positives = 56/62 (90%), Gaps = 1/62 (1%)

Query: 4   PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNS-NREF 62
           P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+ NREF
Sbjct: 365 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 424

Query: 63  YA 64
           YA
Sbjct: 425 YA 426

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	64
FB|FBgn0010415	399	Sdc "Syndecan" [Drosophila mel	0.953	0.152	0.838	8.4e-22
WB|WBGene00004749	288	sdn-1 [Caenorhabditis elegans	0.890	0.197	0.559	2.7e-12
UNIPROTKB|F1NV24	313	SDC1 "Syndecan" [Gallus gallus	0.828	0.169	0.535	3e-11
UNIPROTKB|F1NEY0	200	SDC2 "Syndecan" [Gallus gallus	0.859	0.275	0.543	4.5e-11
UNIPROTKB|F1P3L6	181	SDC2 "Syndecan" [Gallus gallus	0.859	0.303	0.543	4.5e-11
UNIPROTKB|Q58DD4	202	SDC2 "Syndecan-2" [Bos taurus	0.859	0.272	0.543	4.5e-11
UNIPROTKB|E7ESK6	165	SDC2 "Syndecan" [Homo sapiens	0.859	0.333	0.543	4.5e-11
UNIPROTKB|E9PBI9	172	SDC2 "Syndecan" [Homo sapiens	0.859	0.319	0.543	4.5e-11
UNIPROTKB|P34741	201	SDC2 "Syndecan-2" [Homo sapien	0.859	0.273	0.543	4.5e-11
UNIPROTKB|F1S0L5	191	SDC2 "Syndecan" [Sus scrofa (t	0.859	0.287	0.543	4.5e-11

FB|FBgn0010415 Sdc "Syndecan" [Drosophila melanogaster (taxid:7227)]

 Score = 256 (95.2 bits), Expect = 8.4e-22, P = 8.4e-22
 Identities = 52/62 (83%), Positives = 56/62 (90%)

Query:     4 PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSN-REF 62
             P   + VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYAL+EPKRSPA+NSY KN+N REF
Sbjct:   338 PGILAAVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALDEPKRSPANNSYAKNANNREF 397

Query:    63 YA 64
             YA
Sbjct:   398 YA 399

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

GO:0005576 "extracellular region" evidence=NAS

GO:0005925 "focal adhesion" evidence=ISS

GO:0004888 "transmembrane signaling receptor activity" evidence=ISS

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0007411 "axon guidance" evidence=IMP

GO:0050908 "detection of light stimulus involved in visual perception" evidence=IMP

GO:0008045 "motor neuron axon guidance" evidence=IMP

GO:0031594 "neuromuscular junction" evidence=IMP;IDA

GO:0045202 "synapse" evidence=IDA

GO:0045887 "positive regulation of synaptic growth at neuromuscular junction" evidence=IMP

GO:0097009 "energy homeostasis" evidence=IMP

GO:0044246 "regulation of multicellular organismal metabolic process" evidence=IMP

GO:0007427 "epithelial cell migration, open tracheal system" evidence=IMP

GO:2000637 "positive regulation of gene silencing by miRNA" evidence=IMP

WB|WBGene00004749 sdn-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 167 (63.8 bits), Expect = 2.7e-12, P = 2.7e-12
 Identities = 33/59 (55%), Positives = 47/59 (79%)

Query:     8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRS-P-ASNSYMKNSNREFYA 64
             + + GG +V ++ AIL+V+F+V+R+RKKDEGSYAL+EPK++ P AS  Y K S +EFYA
Sbjct:   230 AAIAGGVLVAVITAILLVLFVVFRIRKKDEGSYALDEPKQARPYASYGYTKASTKEFYA 288

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0040039 "inductive cell migration" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0009986 "cell surface" evidence=IDA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IGI

GO:0048730 "epidermis morphogenesis" evidence=IGI;IMP

GO:0002119 "nematode larval development" evidence=IGI

UNIPROTKB|F1NV24 SDC1 "Syndecan" [Gallus gallus (taxid:9031)]

 Score = 149 (57.5 bits), Expect = 3.0e-11, Sum P(2) = 3.0e-11
 Identities = 30/56 (53%), Positives = 42/56 (75%)

Query:    10 VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMK-NSNREFYA 64
             VI G +VGL+ A+ +V F++YRM+KKDEGSY+L+EPK+S  +  Y K +   EFYA
Sbjct:   260 VIAGGLVGLVFAVFLVAFMLYRMKKKDEGSYSLDEPKQS--NGGYQKPHKQEEFYA 313

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0001948 "glycoprotein binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

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

GO:0009897 "external side of plasma membrane" evidence=IEA

GO:0048627 "myoblast development" evidence=IEA

GO:0055002 "striated muscle cell development" evidence=IEA

GO:0060070 "canonical Wnt receptor signaling pathway" evidence=IEA

UNIPROTKB|F1NEY0 SDC2 "Syndecan" [Gallus gallus (taxid:9031)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query:     8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
             + VI G V+G L AI +++ +VYRMRKKDEGSY L E  R P+S +Y K   +EFYA
Sbjct:   146 AAVIAGGVIGFLFAIFLILLLVYRMRKKDEGSYDLGE--RKPSSAAYQKAPTKEFYA 200

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0030165 "PDZ domain binding" evidence=IEA

UNIPROTKB|F1P3L6 SDC2 "Syndecan" [Gallus gallus (taxid:9031)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query:     8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
             + VI G V+G L AI +++ +VYRMRKKDEGSY L E  R P+S +Y K   +EFYA
Sbjct:   127 AAVIAGGVIGFLFAIFLILLLVYRMRKKDEGSYDLGE--RKPSSAAYQKAPTKEFYA 181

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0030165 "PDZ domain binding" evidence=IEA

UNIPROTKB|Q58DD4 SDC2 "Syndecan-2" [Bos taurus (taxid:9913)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query:     8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
             + VI G V+G L AI +++ +VYRMRKKDEGSY L E  R P+S +Y K   +EFYA
Sbjct:   148 AAVIAGGVIGFLFAIFLILLLVYRMRKKDEGSYDLGE--RKPSSAAYQKAPTKEFYA 202

GO:0048814 "regulation of dendrite morphogenesis" evidence=ISS

GO:0030165 "PDZ domain binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008092 "cytoskeletal protein binding" evidence=IEA

UNIPROTKB|E7ESK6 SDC2 "Syndecan" [Homo sapiens (taxid:9606)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query:     8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
             + VI G V+G L AI +++ +VYRMRKKDEGSY L E  R P+S +Y K   +EFYA
Sbjct:   111 AAVIAGGVIGFLFAIFLILLLVYRMRKKDEGSYDLGE--RKPSSAAYQKAPTKEFYA 165

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

UNIPROTKB|E9PBI9 SDC2 "Syndecan" [Homo sapiens (taxid:9606)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query:     8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
             + VI G V+G L AI +++ +VYRMRKKDEGSY L E  R P+S +Y K   +EFYA
Sbjct:   118 AAVIAGGVIGFLFAIFLILLLVYRMRKKDEGSYDLGE--RKPSSAAYQKAPTKEFYA 172

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

GO:0031000 "response to caffeine" evidence=IEA

GO:0042060 "wound healing" evidence=IEA

GO:0043025 "neuronal cell body" evidence=IEA

GO:0048813 "dendrite morphogenesis" evidence=IEA

UNIPROTKB|P34741 SDC2 "Syndecan-2" [Homo sapiens (taxid:9606)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query:     8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
             + VI G V+G L AI +++ +VYRMRKKDEGSY L E  R P+S +Y K   +EFYA
Sbjct:   147 AAVIAGGVIGFLFAIFLILLLVYRMRKKDEGSYDLGE--RKPSSAAYQKAPTKEFYA 201

GO:0008092 "cytoskeletal protein binding" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

GO:0031000 "response to caffeine" evidence=IEA

GO:0042060 "wound healing" evidence=IEA

GO:0043025 "neuronal cell body" evidence=IEA

GO:0048813 "dendrite morphogenesis" evidence=IEA

GO:0005887 "integral to plasma membrane" evidence=NAS

GO:0008150 "biological_process" evidence=ND

GO:0048814 "regulation of dendrite morphogenesis" evidence=ISS

GO:0005796 "Golgi lumen" evidence=TAS

GO:0005886 "plasma membrane" evidence=TAS

GO:0005975 "carbohydrate metabolic process" evidence=TAS

GO:0006024 "glycosaminoglycan biosynthetic process" evidence=TAS

GO:0006027 "glycosaminoglycan catabolic process" evidence=TAS

GO:0030203 "glycosaminoglycan metabolic process" evidence=TAS

GO:0030204 "chondroitin sulfate metabolic process" evidence=TAS

GO:0043202 "lysosomal lumen" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0030165 "PDZ domain binding" evidence=IPI

UNIPROTKB|F1S0L5 SDC2 "Syndecan" [Sus scrofa (taxid:9823)]

 Score = 153 (58.9 bits), Expect = 4.5e-11, P = 4.5e-11
 Identities = 31/57 (54%), Positives = 40/57 (70%)

Query:     8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA 64
             + VI G V+G L AI +++ +VYRMRKKDEGSY L E  R P+S +Y K   +EFYA
Sbjct:   137 AAVIAGGVIGFLFAIFLILLLVYRMRKKDEGSYDLGE--RKPSSAAYQKAPTKEFYA 191

GO:0030165 "PDZ domain binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008092 "cytoskeletal protein binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P18828	SDC1_MOUSE	No assigned EC number	0.5090	0.8593	0.1768	yes	N/A
P26260	SDC1_RAT	No assigned EC number	0.5090	0.8593	0.1757	yes	N/A
P18827	SDC1_HUMAN	No assigned EC number	0.5090	0.8593	0.1774	yes	N/A
Q08DZ5	SDC1_BOVIN	No assigned EC number	0.5090	0.8593	0.1768	yes	N/A
P50605	SDC_CAEEL	No assigned EC number	0.5789	0.8593	0.1909	yes	N/A
P47951	SDC1_CRIGR	No assigned EC number	0.5090	0.8593	0.1779	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	64
pfam01034	207	pfam01034, Syndecan, Syndecan domain	8e-30
smart00294	19	smart00294, 4	2e-04

>gnl|CDD|216257 pfam01034, Syndecan, Syndecan domain

 Score =  103 bits (258), Expect = 8e-30
 Identities = 34/54 (62%), Positives = 39/54 (72%), Gaps = 3/54 (5%)

Query: 10  VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKN-SNREF 62
           VI G VVGLL A+ +VMF+VYRM+KKDEGSYALEEPK   A+  Y K     EF
Sbjct: 156 VIAGGVVGLLFAVFLVMFLVYRMKKKDEGSYALEEPK--QANAGYQKPAKQEEF 207

Syndecans are transmembrane heparin sulfate proteoglycans which are implicated in the binding of extracellular matrix components and growth factors. Length = 207

>gnl|CDD|128590 smart00294, 4

 Score = 34.0 bits (79), Expect = 2e-04
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 30 YRMRKKDEGSYALEEPK 46
          YR + +DEGSY   EPK
Sbjct: 2  YRYKHRDEGSYHTHEPK 18

1m, putative band 4.1 homologues' binding motif. Length = 19

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	64
PF01034	64	Syndecan: Syndecan domain; InterPro: IPR001050 The	99.97
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	98.46
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	97.92
smart00294	26	4.1m putative band 4.1 homologues' binding motif.	97.89
KOG3514|consensus	1591		97.68
PTZ00382	96	Variant-specific surface protein (VSP); Provisiona	96.77
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	96.66
PF03302	397	VSP: Giardia variant-specific surface protein; Int	96.11
PF02009	299	Rifin_STEVOR: Rifin/stevor family; InterPro: IPR00	95.97
PF02480	439	Herpes_gE: Alphaherpesvirus glycoprotein E; InterP	95.85
PF01299	306	Lamp: Lysosome-associated membrane glycoprotein (L	95.57
PF08693	40	SKG6: Transmembrane alpha-helix domain; InterPro:	95.26
PF08374	221	Protocadherin: Protocadherin; InterPro: IPR013585	95.18
PF05808	162	Podoplanin: Podoplanin; InterPro: IPR008783 This f	94.82
PF05808	162	Podoplanin: Podoplanin; InterPro: IPR008783 This f	94.25
PF14575	75	EphA2_TM: Ephrin type-A receptor 2 transmembrane d	94.21
PTZ00046	358	rifin; Provisional	93.78
TIGR01477	353	RIFIN variant surface antigen, rifin family. This	93.66
PF10873	155	DUF2668: Protein of unknown function (DUF2668); In	93.55
PF04478	154	Mid2: Mid2 like cell wall stress sensor; InterPro:	93.48
PF15179	197	Myc_target_1: Myc target protein 1	92.98
PF12732	74	YtxH: YtxH-like protein; InterPro: IPR024623 This	92.94
PF09472	64	MtrF: Tetrahydromethanopterin S-methyltransferase,	92.26
TIGR01478	295	STEVOR variant surface antigen, stevor family. Thi	92.16
PF12732	74	YtxH: YtxH-like protein; InterPro: IPR024623 This	91.95
PTZ00370	296	STEVOR; Provisional	91.88
PF06295	128	DUF1043: Protein of unknown function (DUF1043); In	91.75
PF10031	51	DUF2273: Small integral membrane protein (DUF2273)	90.91
PF07213	79	DAP10: DAP10 membrane protein; InterPro: IPR009861	90.72
KOG3817|consensus	452		90.51
PRK14748	29	kdpF potassium-transporting ATPase subunit F; Prov	90.39
PF04478	154	Mid2: Mid2 like cell wall stress sensor; InterPro:	90.02
PF13908	179	Shisa: Wnt and FGF inhibitory regulator	89.6
PRK09459	76	pspG phage shock protein G; Reviewed	89.35
PF05283	186	MGC-24: Multi-glycosylated core protein 24 (MGC-24	89.03
PF15069	143	FAM163: FAM163 family	88.39
PF05356	83	Phage_Coat_B: Phage Coat protein B ; InterPro: IPR	88.21
PRK06287	107	cobalt transport protein CbiN; Validated	88.21
PF12191	129	stn_TNFRSF12A: Tumour necrosis factor receptor stn	88.12
PF06295	128	DUF1043: Protein of unknown function (DUF1043); In	88.11
PF05545	49	FixQ: Cbb3-type cytochrome oxidase component FixQ;	87.95
COG4218	73	MtrF Tetrahydromethanopterin S-methyltransferase,	87.82
PF12669	58	P12: Virus attachment protein p12 family	87.69
PF12877	684	DUF3827: Domain of unknown function (DUF3827); Int	87.52
PF01034	64	Syndecan: Syndecan domain; InterPro: IPR001050 The	87.3
PF06305	68	DUF1049: Protein of unknown function (DUF1049); In	87.28
TIGR02205	284	septum_zipA cell division protein ZipA. This model	86.89
KOG0196|consensus	996		86.54
PTZ00382	96	Variant-specific surface protein (VSP); Provisiona	86.3
PF12768	281	Rax2: Cortical protein marker for cell polarity	86.05
PF05393	94	Hum_adeno_E3A: Human adenovirus early E3A glycopro	85.83
PRK11677	134	hypothetical protein; Provisional	85.62
PF07213	79	DAP10: DAP10 membrane protein; InterPro: IPR009861	85.57
PF01299	306	Lamp: Lysosome-associated membrane glycoprotein (L	85.57
PF13908	179	Shisa: Wnt and FGF inhibitory regulator	85.44
COG5547	62	Small integral membrane protein [Function unknown]	85.43
PF15102	146	TMEM154: TMEM154 protein family	85.22
PF15330	107	SIT: SHP2-interacting transmembrane adaptor protei	84.76
COG4980	115	GvpP Gas vesicle protein [General function predict	84.73
PRK12659	117	putative monovalent cation/H+ antiporter subunit C	84.15
PF05454	290	DAG1: Dystroglycan (Dystrophin-associated glycopro	84.08
PRK13275	67	mtrF tetrahydromethanopterin S-methyltransferase s	83.96
PF04971	68	Lysis_S: Lysis protein S ; InterPro: IPR007054 The	83.74
PRK11677	134	hypothetical protein; Provisional	83.73
PF12301	169	CD99L2: CD99 antigen like protein 2; InterPro: IPR	83.42
PF13937	81	DUF4212: Domain of unknown function (DUF4212)	82.95
COG4980	115	GvpP Gas vesicle protein [General function predict	82.86
PF10225	249	DUF2215: Uncharacterized conserved protein (DUF221	82.63
TIGR01167	34	LPXTG_anchor LPXTG-motif cell wall anchor domain.	82.54
PF11021	56	DUF2613: Protein of unknown function (DUF2613); In	82.32
PRK12660	114	putative monovalent cation/H+ antiporter subunit C	81.74
PF04277	79	OAD_gamma: Oxaloacetate decarboxylase, gamma chain	81.46
PRK14750	29	kdpF potassium-transporting ATPase subunit F; Prov	80.99
KOG3637|consensus	1030		80.92
PF09835	154	DUF2062: Uncharacterized protein conserved in bact	80.92
COG3944	226	Capsular polysaccharide biosynthesis protein [Cell	80.82
PF13807	82	GNVR: G-rich domain on putative tyrosine kinase	80.51
PRK15083	639	PTS system mannitol-specific transporter subunit I	80.51
COG5336	116	Uncharacterized protein conserved in bacteria [Fun	80.43
PHA03265	402	envelope glycoprotein D; Provisional	80.26

>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]

Probab=99.97  E-value=4.6e-32  Score=165.89  Aligned_cols=60  Identities=53%  Similarity=0.896  Sum_probs=7.8

Q ss_pred             CCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccCCCCCCCCCccccCCcccc
Q psy1892           1 MTIPLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREF   62 (64)
Q Consensus         1 ~~~~~~~ag~IaG~VvGlv~ailLIlfli~r~rKKdegsY~leE~K~~~~~~~y~k~~~~ef   62 (64)
                      |.||++++|+|||+|+|++|+++||+|++|||||||||||++||+|+++  ++|||+||+||
T Consensus         5 ~~~~~vlaavIaG~Vvgll~ailLIlf~iyR~rkkdEGSY~l~e~K~s~--~~Y~k~~~~ef   64 (64)
T PF01034_consen    5 FERSEVLAAVIAGGVVGLLFAILLILFLIYRMRKKDEGSYDLDEPKPSN--YAYQKAPTKEF   64 (64)
T ss_dssp             --------------------------------S------SS--S-------------SSS-E
T ss_pred             cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccCCCCCccc--cccccCCcCCC
Confidence            6899999999999999999999999999999999999999999999885  56999999998

Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.

>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane

Probab=98.46  E-value=2.1e-07  Score=62.24  Aligned_cols=32  Identities=31%  Similarity=0.534  Sum_probs=24.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1892           5 LATSTVIGGAVVGLLCAILVVMFIVYRMRKKD   36 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~ailLIlfli~r~rKKd   36 (64)
                      ++++|+|.|+++|++..||||.|+++|+|||.
T Consensus        64 ~~i~~Ii~gv~aGvIg~Illi~y~irR~~Kk~   95 (122)
T PF01102_consen   64 PAIIGIIFGVMAGVIGIILLISYCIRRLRKKS   95 (122)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHHHHHS---
T ss_pred             cceeehhHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            46788888888888888999999999888874

Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.

>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane

Probab=97.92  E-value=8.2e-06  Score=54.59  Aligned_cols=36  Identities=22%  Similarity=0.427  Sum_probs=27.0

Q ss_pred             chhHHHHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCc
Q psy1892           4 PLATSTVIGGAVVGLLCA-ILVVMFIVYRMRKKDEGS   39 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~a-ilLIlfli~r~rKKdegs   39 (64)
                      -++..++|+|+++|+++| |++|+|+.|+.|++.+.+
T Consensus        59 h~fs~~~i~~Ii~gv~aGvIg~Illi~y~irR~~Kk~   95 (122)
T PF01102_consen   59 HRFSEPAIIGIIFGVMAGVIGIILLISYCIRRLRKKS   95 (122)
T ss_dssp             SSSS-TCHHHHHHHHHHHHHHHHHHHHHHHHHHS---
T ss_pred             cCccccceeehhHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            367789999999999999 566677788899988874

Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.

>smart00294 4

Probab=97.89  E-value=1.5e-06  Score=45.65  Aligned_cols=20  Identities=50%  Similarity=0.951  Sum_probs=17.5

Q ss_pred             HHHHHhcCCCcccccCCCCC
Q psy1892          29 VYRMRKKDEGSYALEEPKRS   48 (64)
Q Consensus        29 i~r~rKKdegsY~leE~K~~   48 (64)
                      ++|+++||||||.++|+|..
T Consensus         1 myry~~R~kGSY~t~E~kg~   20 (26)
T smart00294        1 MYRYKHRDEGSYHTHEPKGX   20 (26)
T ss_pred             CcEEEecccCceEcCCCCCc
Confidence            46899999999999999854

1m putative band 4.1 homologues' binding motif.

>KOG3514|consensus

Probab=97.68  E-value=2.3e-05  Score=68.22  Aligned_cols=43  Identities=30%  Similarity=0.663  Sum_probs=38.0

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccCCC
Q psy1892           4 PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPK   46 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ailLIlfli~r~rKKdegsY~leE~K   46 (64)
                      +.-..|+++|+|+.+.++||++++.+|.+|+||||||..+|+.
T Consensus      1511 sssttGmVvGIvaAaaLcILilL~am~kyRnrdEGSYhvd~sr 1553 (1591)
T KOG3514|consen 1511 SSSTTGMVVGIVAAAALCILILLYAMYKYRNRDEGSYHVDESR 1553 (1591)
T ss_pred             CCCccchhhHHHHHHHHHHHHHHhhcccccccccCccccccch
Confidence            3446788889999888999999999999999999999999965

>PTZ00382 Variant-specific surface protein (VSP); Provisional

Probab=96.77  E-value=6.7e-05  Score=47.80  Aligned_cols=28  Identities=18%  Similarity=0.322  Sum_probs=18.2

Q ss_pred             chhHHHHHHHHHHHHHHHH-HHHHHHHHH
Q psy1892           4 PLATSTVIGGAVVGLLCAI-LVVMFIVYR   31 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ai-lLIlfli~r   31 (64)
                      .++..|+|+|++||++..+ .|+.|++|.
T Consensus        61 ~~ls~gaiagi~vg~~~~v~~lv~~l~w~   89 (96)
T PTZ00382         61 SGLSTGAIAGISVAVVAVVGGLVGFLCWW   89 (96)
T ss_pred             CCcccccEEEEEeehhhHHHHHHHHHhhe
Confidence            4677899999999877554 333344443

>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []

Probab=96.66  E-value=0.0043  Score=34.94  Aligned_cols=31  Identities=26%  Similarity=0.462  Sum_probs=23.7

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1892           4 PLATSTVIGGAVVGLLCAILVVMFIVYRMRK   34 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ailLIlfli~r~rK   34 (64)
                      |+-..|+|+|+++|++.-++.++...-++||
T Consensus         2 p~s~IaIIv~V~vg~~iiii~~~~YaCcykk   32 (38)
T PF02439_consen    2 PSSTIAIIVAVVVGMAIIIICMFYYACCYKK   32 (38)
T ss_pred             CcchhhHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            5667899999999998887777776655554

This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.

>PF03302 VSP: Giardia variant-specific surface protein; InterPro: IPR005127 During infection, the intestinal protozoan parasite Giardia lamblia virus undergoes continuous antigenic variation which is determined by diversification of the parasite's major surface antigen, named VSP (variant surface protein)

Probab=96.11  E-value=0.0012  Score=50.13  Aligned_cols=29  Identities=17%  Similarity=0.281  Sum_probs=21.8

Q ss_pred             cchhHHHHHHHHHHHHHHHHH-HHHHHHHH
Q psy1892           3 IPLATSTVIGGAVVGLLCAIL-VVMFIVYR   31 (64)
Q Consensus         3 ~~~~~ag~IaG~VvGlv~ail-LIlfli~r   31 (64)
                      +.+++.|+||||.|++|+.|- ||-||.|+
T Consensus       361 ~s~LstgaIaGIsvavvvvVgglvGfLcWw  390 (397)
T PF03302_consen  361 KSGLSTGAIAGISVAVVVVVGGLVGFLCWW  390 (397)
T ss_pred             cccccccceeeeeehhHHHHHHHHHHHhhh
Confidence            458899999999998776643 56666665

>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world

Probab=95.97  E-value=0.011  Score=44.28  Aligned_cols=27  Identities=26%  Similarity=0.652  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHH-HHHHHHHHHHHHHhcC
Q psy1892          10 VIGGAVVGLLC-AILVVMFIVYRMRKKD   36 (64)
Q Consensus        10 ~IaG~VvGlv~-ailLIlfli~r~rKKd   36 (64)
                      +|+.+|+-|+. .|.+|+++|||+|||.
T Consensus       258 I~aSiiaIliIVLIMvIIYLILRYRRKK  285 (299)
T PF02009_consen  258 IIASIIAILIIVLIMVIIYLILRYRRKK  285 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            44444433333 3778888999966643

Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].

>PF02480 Herpes_gE: Alphaherpesvirus glycoprotein E; InterPro: IPR003404 Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI), functioning as an immunoglobulin G (IgG) Fc binding protein

Probab=95.85  E-value=0.0022  Score=49.78  Aligned_cols=53  Identities=21%  Similarity=0.192  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccCCCCCCCCCccccCCccccc
Q psy1892           6 ATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKRSPASNSYMKNSNREFY   63 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ailLIlfli~r~rKKdegsY~leE~K~~~~~~~y~k~~~~efy   63 (64)
                      ++.++++|++++++++++++++++.|+|||  ..|+   +...+.++.|..-|++|+|
T Consensus       353 ~~l~vVlgvavlivVv~viv~vc~~~rrrR--~~~~---~~~~~~~~~YtsLPtNE~~  405 (439)
T PF02480_consen  353 ALLGVVLGVAVLIVVVGVIVWVCLRCRRRR--RQRD---KILNPFSPVYTSLPTNEPY  405 (439)
T ss_dssp             ----------------------------------------------------------
T ss_pred             chHHHHHHHHHHHHHHHHHhheeeeehhcc--cccc---cccCcCCCccccCCCCCcc
Confidence            445555555555555555555555443332  2333   3333344568777777753

gE is involved in virus spread but is not essential for propagation [].; GO: 0016020 membrane; PDB: 2GJ7_F 2GIY_B.

>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear

Probab=95.57  E-value=0.0077  Score=43.65  Aligned_cols=32  Identities=19%  Similarity=0.328  Sum_probs=22.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1892           5 LATSTVIGGAVVGLLCAILVVMFIVYRMRKKD   36 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~ailLIlfli~r~rKKd   36 (64)
                      ..+..+|.|++++.|+.|.||.++|+|+|.+.
T Consensus       270 ~~~vPIaVG~~La~lvlivLiaYli~Rrr~~~  301 (306)
T PF01299_consen  270 SDLVPIAVGAALAGLVLIVLIAYLIGRRRSRA  301 (306)
T ss_pred             cchHHHHHHHHHHHHHHHHHHhheeEeccccc
Confidence            45667777777777777777788888655544

Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane

>PF08693 SKG6: Transmembrane alpha-helix domain; InterPro: IPR014805 SKG6 and AXL2 are membrane proteins that show polarised intracellular localisation [, ]

Probab=95.26  E-value=0.0058  Score=34.56  Aligned_cols=20  Identities=30%  Similarity=0.551  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhc
Q psy1892          16 VGLLCAILVVMFIVYRMRKK   35 (64)
Q Consensus        16 vGlv~ailLIlfli~r~rKK   35 (64)
                      ||++.++|+++|++||+|+|
T Consensus        21 V~vI~~vl~~~l~~~~rR~k   40 (40)
T PF08693_consen   21 VGVIIIVLGAFLFFWYRRKK   40 (40)
T ss_pred             hHHHHHHHHHHhheEEeccC
Confidence            45566666666665544443

This entry represents the highly conserved transmembrane alpha-helical domain found in these proteins [, ]. The full-length AXL2 protein has a negative regulatory function in cytokinesis [].

>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains

Probab=95.18  E-value=0.0086  Score=44.07  Aligned_cols=12  Identities=8%  Similarity=0.263  Sum_probs=6.8

Q ss_pred             hhHHHHHHHHHH
Q psy1892           5 LATSTVIGGAVV   16 (64)
Q Consensus         5 ~~~ag~IaG~Vv   16 (64)
                      .++.|+|||+++
T Consensus        38 ~I~iaiVAG~~t   49 (221)
T PF08374_consen   38 KIMIAIVAGIMT   49 (221)
T ss_pred             eeeeeeecchhh
Confidence            355666666544

They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].

>PF05808 Podoplanin: Podoplanin; InterPro: IPR008783 This family consists of several mammalian podoplanin-like proteins which are thought to control specifically the unique shape of podocytes []

Probab=94.82  E-value=0.0077  Score=42.49  Aligned_cols=29  Identities=28%  Similarity=0.448  Sum_probs=0.0

Q ss_pred             chhHHHHHHHHHHHHHHHHHH----HHHHHHHH
Q psy1892           4 PLATSTVIGGAVVGLLCAILV----VMFIVYRM   32 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ailL----Ilfli~r~   32 (64)
                      .|+..+.++|++||+|+||-+    |+++++||
T Consensus       124 ~GL~T~tLVGIIVGVLlaIG~igGIIivvvRKm  156 (162)
T PF05808_consen  124 DGLSTVTLVGIIVGVLLAIGFIGGIIIVVVRKM  156 (162)
T ss_dssp             ---------------------------------
T ss_pred             CCcceeeeeeehhhHHHHHHHHhheeeEEeehh
Confidence            466667777777777777544    44555444

; GO: 0016021 integral to membrane; PDB: 3IET_X.

>PF05808 Podoplanin: Podoplanin; InterPro: IPR008783 This family consists of several mammalian podoplanin-like proteins which are thought to control specifically the unique shape of podocytes []

Probab=94.25  E-value=0.013  Score=41.43  Aligned_cols=16  Identities=19%  Similarity=0.457  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHH
Q psy1892           9 TVIGGAVVGLLCAILV   24 (64)
Q Consensus         9 g~IaG~VvGlv~ailL   24 (64)
                      |+-.+.+||+++++|+
T Consensus       125 GL~T~tLVGIIVGVLl  140 (162)
T PF05808_consen  125 GLSTVTLVGIIVGVLL  140 (162)
T ss_dssp             ----------------
T ss_pred             CcceeeeeeehhhHHH
Confidence            3344445555555444

; GO: 0016021 integral to membrane; PDB: 3IET_X.

>PF14575 EphA2_TM: Ephrin type-A receptor 2 transmembrane domain; PDB: 3KUL_A 2XVD_A 2VX1_A 2VWV_A 2VX0_A 2VWY_A 2VWZ_A 2VWW_A 2VWU_A 2VWX_A

Probab=94.21  E-value=0.021  Score=34.92  Aligned_cols=6  Identities=17%  Similarity=0.861  Sum_probs=2.5

Q ss_pred             HHHHHH
Q psy1892          26 MFIVYR   31 (64)
Q Consensus        26 lfli~r   31 (64)
                      +++++|
T Consensus        20 ~~~~~r   25 (75)
T PF14575_consen   20 VIVCFR   25 (75)
T ss_dssp             HHCCCT
T ss_pred             EEEEEe
Confidence            334444

...

>PTZ00046 rifin; Provisional

Probab=93.78  E-value=0.12  Score=40.22  Aligned_cols=30  Identities=23%  Similarity=0.593  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHHHhcC
Q psy1892           7 TSTVIGGAVVGLLCA-ILVVMFIVYRMRKKD   36 (64)
Q Consensus         7 ~ag~IaG~VvGlv~a-ilLIlfli~r~rKKd   36 (64)
                      ..++||.+|+-|+.. |.+|+++|.|+|||.
T Consensus       314 ~taIiaSiiAIvVIVLIMvIIYLILRYRRKK  344 (358)
T PTZ00046        314 QTAIIASIVAIVVIVLIMVIIYLILRYRRKK  344 (358)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            345566655544443 567778888865553

>TIGR01477 RIFIN variant surface antigen, rifin family

Probab=93.66  E-value=0.13  Score=40.02  Aligned_cols=29  Identities=24%  Similarity=0.641  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHHHHH-HHHHHHHHHHHHhcC
Q psy1892           8 STVIGGAVVGLLCA-ILVVMFIVYRMRKKD   36 (64)
Q Consensus         8 ag~IaG~VvGlv~a-ilLIlfli~r~rKKd   36 (64)
                      .++||.+|+-|+.. |.+|+++|.|+|||.
T Consensus       310 t~IiaSiIAIvvIVLIMvIIYLILRYRRKK  339 (353)
T TIGR01477       310 TPIIASIIAILIIVLIMVIIYLILRYRRKK  339 (353)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            45555555544443 667788888866553

This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits.

>PF10873 DUF2668: Protein of unknown function (DUF2668); InterPro: IPR022640 Members in this family of proteins are annotated as cysteine and tyrosine-rich protein 1, however currently no function is known []

Probab=93.55  E-value=0.039  Score=38.90  Aligned_cols=18  Identities=28%  Similarity=0.516  Sum_probs=14.0

Q ss_pred             chhHHHHHHHHHHHHHHH
Q psy1892           4 PLATSTVIGGAVVGLLCA   21 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~a   21 (64)
                      ..+.+++|+|+|+|+||-
T Consensus        56 ~~lsgtAIaGIVfgiVfi   73 (155)
T PF10873_consen   56 DVLSGTAIAGIVFGIVFI   73 (155)
T ss_pred             cccccceeeeeehhhHHH
Confidence            345678889999888876

>PF04478 Mid2: Mid2 like cell wall stress sensor; InterPro: IPR007567 This family represents a region near the C terminus of Mid2, which contains a transmembrane region

Probab=93.48  E-value=0.0026  Score=44.53  Aligned_cols=24  Identities=29%  Similarity=0.368  Sum_probs=10.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           6 ATSTVIGGAVVGLLCAILVVMFIV   29 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ailLIlfli   29 (64)
                      ++.|++.|+-+.+++++++|+|++
T Consensus        50 IVIGvVVGVGg~ill~il~lvf~~   73 (154)
T PF04478_consen   50 IVIGVVVGVGGPILLGILALVFIF   73 (154)
T ss_pred             EEEEEEecccHHHHHHHHHhheeE
Confidence            334444444444454444444433

The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress. The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway [].

>PF15179 Myc_target_1: Myc target protein 1

Probab=92.98  E-value=0.49  Score=34.54  Aligned_cols=33  Identities=12%  Similarity=0.211  Sum_probs=28.1

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1892           4 PLATSTVIGGAVVGLLCAILVVMFIVYRMRKKD   36 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ailLIlfli~r~rKKd   36 (64)
                      ..++.+.-..++||+|+|+++-+++.|..|+|-
T Consensus        19 ~~lIlaF~vSm~iGLviG~li~~LltwlSRRRA   51 (197)
T PF15179_consen   19 EDLILAFCVSMAIGLVIGALIWALLTWLSRRRA   51 (197)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            356777888999999999999999999987774

>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria

Probab=92.94  E-value=0.085  Score=31.30  Aligned_cols=15  Identities=20%  Similarity=0.388  Sum_probs=6.6

Q ss_pred             HHHHHHHHHHHHHHH
Q psy1892           8 STVIGGAVVGLLCAI   22 (64)
Q Consensus         8 ag~IaG~VvGlv~ai   22 (64)
                      .|+++|+++|.+.++
T Consensus         3 ~g~l~Ga~~Ga~~gl   17 (74)
T PF12732_consen    3 LGFLAGAAAGAAAGL   17 (74)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            344444444444443

Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.

>PF09472 MtrF: Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF); InterPro: IPR013347 Many archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes

Probab=92.26  E-value=0.3  Score=29.85  Aligned_cols=26  Identities=27%  Similarity=0.358  Sum_probs=18.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           5 LATSTVIGGAVVGLLCAILVVMFIVY   30 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~ailLIlfli~   30 (64)
                      |+.+.-+.|.++|+++|++|+...++
T Consensus        36 Gv~~~~~~GfaiG~~~AlvLv~ip~~   61 (64)
T PF09472_consen   36 GVMATGIKGFAIGFLFALVLVGIPIL   61 (64)
T ss_pred             HHhhhhhHHHHHHHHHHHHHHHHHHH
Confidence            56667778888888888766665444

This domain is mostly found in MtrF, where it covers the entire length of the protein. This polypeptide is one of eight subunits of the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase complex found in methanogenic archaea. This is a membrane-associated enzyme complex that uses methyl-transfer reactions to drive a sodium-ion pump []. MtrF itself is involved in the transfer of the methyl group from N5-methyltetrahydromethanopterin to coenzyme M. Subsequently, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organisms this domain is found at the C-terminal region of what appears to be a fusion of the MtrA and MtrF proteins [, ]. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016020 membrane

>TIGR01478 STEVOR variant surface antigen, stevor family

Probab=92.16  E-value=0.22  Score=38.05  Aligned_cols=21  Identities=10%  Similarity=0.540  Sum_probs=13.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhc
Q psy1892          15 VVGLLCAILVVMFIVYRMRKK   35 (64)
Q Consensus        15 VvGlv~ailLIlfli~r~rKK   35 (64)
                      +|-++++|+||++.||.+|+|
T Consensus       266 lvllil~vvliiLYiWlyrrR  286 (295)
T TIGR01478       266 LVLIILTVVLIILYIWLYRRR  286 (295)
T ss_pred             HHHHHHHHHHHHHHHHHHHhh
Confidence            444556677777777765443

This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.

>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria

Probab=91.95  E-value=0.2  Score=29.69  Aligned_cols=17  Identities=35%  Similarity=0.339  Sum_probs=12.5

Q ss_pred             hhHHHHHHHHHHHHHHH
Q psy1892           5 LATSTVIGGAVVGLLCA   21 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~a   21 (64)
                      |++.|+++|+++|++++
T Consensus         4 g~l~Ga~~Ga~~glL~a   20 (74)
T PF12732_consen    4 GFLAGAAAGAAAGLLFA   20 (74)
T ss_pred             HHHHHHHHHHHHHHHhC
Confidence            56777777777777776

Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.

>PTZ00370 STEVOR; Provisional

Probab=91.88  E-value=0.25  Score=37.78  Aligned_cols=28  Identities=21%  Similarity=0.551  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCccccc
Q psy1892          15 VVGLLCAILVVMFIVYRMRKKDEGSYALE   43 (64)
Q Consensus        15 VvGlv~ailLIlfli~r~rKKdegsY~le   43 (64)
                      +|-++++|+||++.||.+|+| +.|+.=|
T Consensus       262 lvllil~vvliilYiwlyrrR-K~swkhe  289 (296)
T PTZ00370        262 LVLLILAVVLIILYIWLYRRR-KNSWKHE  289 (296)
T ss_pred             HHHHHHHHHHHHHHHHHHHhh-cchhHHH
Confidence            444556677777777765543 3344433

>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=91.75  E-value=0.034  Score=36.58  Aligned_cols=18  Identities=39%  Similarity=0.551  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q psy1892          10 VIGGAVVGLLCAILVVMF   27 (64)
Q Consensus        10 ~IaG~VvGlv~ailLIlf   27 (64)
                      +|+|.|||+++|.++.-+
T Consensus         2 ~~i~lvvG~iiG~~~~r~   19 (128)
T PF06295_consen    2 AIIGLVVGLIIGFLIGRL   19 (128)
T ss_pred             hHHHHHHHHHHHHHHHHH
Confidence            355666666655554333

>PF10031 DUF2273: Small integral membrane protein (DUF2273); InterPro: IPR018730 Members of this family of hypothetical bacterial proteins have no known function

Probab=90.91  E-value=0.49  Score=27.36  Aligned_cols=23  Identities=30%  Similarity=0.631  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           9 TVIGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus         9 g~IaG~VvGlv~ailLIlfli~r   31 (64)
                      +-+.|+++|+++|++++.+=.|+
T Consensus         9 ~~iiG~~~G~ila~l~l~~GF~~   31 (51)
T PF10031_consen    9 GKIIGGLIGLILALLILTFGFWK   31 (51)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHH
Confidence            34566666666666665555553

>PF07213 DAP10: DAP10 membrane protein; InterPro: IPR009861 This family consists of several mammalian DAP10 membrane proteins

Probab=90.72  E-value=0.52  Score=30.02  Aligned_cols=26  Identities=19%  Similarity=0.418  Sum_probs=15.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           6 ATSTVIGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ailLIlfli~r   31 (64)
                      +..|+.||+|+|=+.--|||...+|.
T Consensus        31 ls~g~LaGiV~~D~vlTLLIv~~vy~   56 (79)
T PF07213_consen   31 LSPGLLAGIVAADAVLTLLIVLVVYY   56 (79)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45666777777655555555555554

In activated mouse natural killer (NK) cells, the NKG2D receptor associates with two intracellular adaptors, DAP10 and DAP12, which trigger phosphatidyl inositol 3 kinase (PI3K) and Syk family protein tyrosine kinases, respectively. It has been suggested that the DAP10-PI3K pathway is sufficient to initiate NKG2D-mediated killing of target cells [].

>KOG3817|consensus

Probab=90.51  E-value=0.2  Score=40.07  Aligned_cols=25  Identities=48%  Similarity=0.887  Sum_probs=21.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHH-HHhcC
Q psy1892          12 GGAVVGLLCAILVVMFIVYR-MRKKD   36 (64)
Q Consensus        12 aG~VvGlv~ailLIlfli~r-~rKKd   36 (64)
                      .|+|+|++..+|+++|+++| +-||.
T Consensus       166 sG~v~GilaSLl~Viflv~rf~PKkt  191 (452)
T KOG3817|consen  166 SGIVIGILASLLVVIFLVARFFPKKT  191 (452)
T ss_pred             cccHHHHHHHHHHHHHHHHHhccccc
Confidence            48999999999999999999 55554

>PRK14748 kdpF potassium-transporting ATPase subunit F; Provisional

Probab=90.39  E-value=0.51  Score=25.29  Aligned_cols=20  Identities=30%  Similarity=0.748  Sum_probs=15.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy1892          12 GGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus        12 aG~VvGlv~ailLIlfli~r   31 (64)
                      +++++|++++++|+.+++|-
T Consensus         3 ~~vi~G~ilv~lLlgYLvyA   22 (29)
T PRK14748          3 AGVITGVLLVFLLLGYLVYA   22 (29)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
Confidence            56777888888888888775

>PF04478 Mid2: Mid2 like cell wall stress sensor; InterPro: IPR007567 This family represents a region near the C terminus of Mid2, which contains a transmembrane region

Probab=90.02  E-value=0.012  Score=41.16  Aligned_cols=30  Identities=23%  Similarity=0.390  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHH-HHHHHHHHHHhcCCC
Q psy1892           9 TVIGGAVVGLLCAIL-VVMFIVYRMRKKDEG   38 (64)
Q Consensus         9 g~IaG~VvGlv~ail-LIlfli~r~rKKdeg   38 (64)
                      .+|.|+|||+-.++| +|+.++|.++.|.+.
T Consensus        49 nIVIGvVVGVGg~ill~il~lvf~~c~r~kk   79 (154)
T PF04478_consen   49 NIVIGVVVGVGGPILLGILALVFIFCIRRKK   79 (154)
T ss_pred             cEEEEEEecccHHHHHHHHHhheeEEEeccc
Confidence            368899999877755 557788889655443

The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress. The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway [].

>PF13908 Shisa: Wnt and FGF inhibitory regulator

Probab=89.60  E-value=0.11  Score=34.93  Aligned_cols=21  Identities=14%  Similarity=0.531  Sum_probs=11.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHH
Q psy1892           6 ATSTVIGGAVVGLLCAILVVM   26 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ailLIl   26 (64)
                      +.+++|.|+++|+++.|++|.
T Consensus        76 ~~~~iivgvi~~Vi~Iv~~Iv   96 (179)
T PF13908_consen   76 FITGIIVGVICGVIAIVVLIV   96 (179)
T ss_pred             ceeeeeeehhhHHHHHHHhHh
Confidence            455666666666665544333

>PRK09459 pspG phage shock protein G; Reviewed

Probab=89.35  E-value=1.8  Score=27.50  Aligned_cols=32  Identities=16%  Similarity=0.225  Sum_probs=19.5

Q ss_pred             hhHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHhcC
Q psy1892           5 LATSTVIGGAVVGLLCA-----------ILVVMFIVYRMRKKD   36 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~a-----------ilLIlfli~r~rKKd   36 (64)
                      |+++++..+.++.++.|           ++++...+|.+|+..
T Consensus        23 gv~aAl~va~~vM~l~Gm~~lviKLLPWLil~~v~vW~~r~~~   65 (76)
T PRK09459         23 GIIAALGVATLVMFLGGMFALMIKLLPWLLLAVVVVWVIRAIK   65 (76)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            45556655555555555           566666778777643

>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor

Probab=89.03  E-value=0.49  Score=33.74  Aligned_cols=24  Identities=38%  Similarity=0.816  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1892           9 TVIGGAVVGLLCAILVVMFIVYRMRK   34 (64)
Q Consensus         9 g~IaG~VvGlv~ailLIlfli~r~rK   34 (64)
                      -.|+|||  |+++++-|+|++||+-|
T Consensus       162 SFiGGIV--L~LGv~aI~ff~~KF~k  185 (186)
T PF05283_consen  162 SFIGGIV--LTLGVLAIIFFLYKFCK  185 (186)
T ss_pred             hhhhHHH--HHHHHHHHHHHHhhhcc
Confidence            3566666  57789999999998654

Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.

>PF15069 FAM163: FAM163 family

Probab=88.39  E-value=0.47  Score=32.99  Aligned_cols=22  Identities=18%  Similarity=0.490  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy1892          10 VIGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus        10 ~IaG~VvGlv~ailLIlfli~r   31 (64)
                      +|+|++...|.-+++|..|.|.
T Consensus         7 VItGgILAtVILLcIIaVLCYC   28 (143)
T PF15069_consen    7 VITGGILATVILLCIIAVLCYC   28 (143)
T ss_pred             EEechHHHHHHHHHHHHHHHHH
Confidence            3555555555555556556655

>PF05356 Phage_Coat_B: Phage Coat protein B ; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide

Probab=88.21  E-value=1.1  Score=28.90  Aligned_cols=25  Identities=36%  Similarity=0.591  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1892          10 VIGGAVVGLLCAILVVMFIVYRMRK   34 (64)
Q Consensus        10 ~IaG~VvGlv~ailLIlfli~r~rK   34 (64)
                      -|+|.+||++|.+++.-+++..-||
T Consensus        58 svgg~IVgvl~~laVaGlI~~l~RK   82 (83)
T PF05356_consen   58 SVGGYIVGVLVILAVAGLIYSLLRK   82 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHhc
Confidence            4789999999887777666554554

Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 1QL1_A 2XKM_A 4IFM_A 1QL2_A 1IFM_A 2KLV_A 1IFN_A 2IFN_A 3IFM_A 2KSJ_A ....

>PRK06287 cobalt transport protein CbiN; Validated

Probab=88.21  E-value=1.4  Score=28.64  Aligned_cols=29  Identities=21%  Similarity=0.264  Sum_probs=13.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1892           7 TSTVIGGAVVGLLCAILVVMFIVYRMRKKD   36 (64)
Q Consensus         7 ~ag~IaG~VvGlv~ailLIlfli~r~rKKd   36 (64)
                      ++.+++| |+|++..+++...+-+..|||+
T Consensus        77 ~g~ilsg-iiGv~i~l~l~~~~~~~l~r~~  105 (107)
T PRK06287         77 IGEIIAM-VIGTLLVLALAYGVGKIFKKKS  105 (107)
T ss_pred             hhHHHHH-HHHHHHHHHHHHHHHHHHhccc
Confidence            3444444 6666444444333333344443

>PF12191 stn_TNFRSF12A: Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain; InterPro: IPR022316 The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more than 20 type-I transmembrane proteins

Probab=88.12  E-value=0.11  Score=35.62  Aligned_cols=38  Identities=24%  Similarity=0.392  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHH-HHHHHHHHHHH-HHhcCCCcccccCCC
Q psy1892           9 TVIGGAVVGLLC-AILVVMFIVYR-MRKKDEGSYALEEPK   46 (64)
Q Consensus         9 g~IaG~VvGlv~-ailLIlfli~r-~rKKdegsY~leE~K   46 (64)
                      ..|.|.|.++++ ..+|..|++|| -|+|++=.+-+|||-
T Consensus        79 ~pi~~sal~v~lVl~llsg~lv~rrcrrr~~~ttPIeeTg  118 (129)
T PF12191_consen   79 WPILGSALSVVLVLALLSGFLVWRRCRRREKFTTPIEETG  118 (129)
T ss_dssp             ----------------------------------------
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHhhhhccccCCCcccccC
Confidence            334444444332 34555777777 444444566777763

Family members are defined based on similarity in their extracellular domain - a region that contains many cysteine residues arranged in a specific repetitive pattern []. The cysteines allow formation of an extended rod-like structure, responsible for ligand binding []. Upon receptor activation, different intracellular signalling complexes are assembled for different members of the TNFR superfamily, depending on their intracellular domains and sequences []. Activation of TNFRs can therefore induce a range of disparate effects, including cell proliferation, differentiation, survival, or apoptotic cell death, depending upon the receptor involved []. TNFRs are widely distributed and play important roles in many crucial biological processes, such as lymphoid and neuronal development, innate and adaptive immunity, and maintenance of cellular homeostasis []. Drugs that manipulate their signalling have potential roles in the prevention and treatment of many diseases, such as viral infections, coronary heart disease, transplant rejection, and immune disease []. TNF receptor 12 (also known as TWEAK receptor, and fibroblast growth factor-inducible-14 (Fn14)) has been implicated in endothelial cell growth and migration []. The receptor may also play a role in cell-matrix interactions [].; PDB: 2KN0_A 2RPJ_A 2KMZ_A 2EQP_A.

>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=88.11  E-value=0.51  Score=30.98  Aligned_cols=10  Identities=20%  Similarity=0.926  Sum_probs=5.0

Q ss_pred             HHHHHHHHHH
Q psy1892          15 VVGLLCAILV   24 (64)
Q Consensus        15 VvGlv~ailL   24 (64)
                      +||+++|++|
T Consensus         3 ~i~lvvG~ii   12 (128)
T PF06295_consen    3 IIGLVVGLII   12 (128)
T ss_pred             HHHHHHHHHH
Confidence            4555555533

>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ)

Probab=87.95  E-value=0.88  Score=25.25  Aligned_cols=29  Identities=7%  Similarity=0.355  Sum_probs=16.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCccc
Q psy1892          13 GAVVGLLCAILVVMFIVYRMRKKDEGSYA   41 (64)
Q Consensus        13 G~VvGlv~ailLIlfli~r~rKKdegsY~   41 (64)
                      ..+..+++.++++..++|-+++|.+..||
T Consensus        11 ~~~~~v~~~~~F~gi~~w~~~~~~k~~~e   39 (49)
T PF05545_consen   11 RSIGTVLFFVFFIGIVIWAYRPRNKKRFE   39 (49)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcccchhhHH
Confidence            33444555555555566666666666443

FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].

>COG4218 MtrF Tetrahydromethanopterin S-methyltransferase, subunit F [Coenzyme metabolism]

Probab=87.82  E-value=0.88  Score=28.78  Aligned_cols=22  Identities=32%  Similarity=0.330  Sum_probs=17.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHH
Q psy1892           5 LATSTVIGGAVVGLLCAILVVM   26 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~ailLIl   26 (64)
                      |+.+.-|+|..+|+++|++|+.
T Consensus        45 Gl~st~i~GlaiGfvfA~vLv~   66 (73)
T COG4218          45 GLNSTRIAGLAIGFVFAGVLVG   66 (73)
T ss_pred             hhhhhhhHHHHHHHHHHHHHHH
Confidence            6677788999999999966554

>PF12669 P12: Virus attachment protein p12 family

Probab=87.69  E-value=0.63  Score=27.34  Aligned_cols=6  Identities=33%  Similarity=0.817  Sum_probs=2.4

Q ss_pred             HhcCCC
Q psy1892          33 RKKDEG   38 (64)
Q Consensus        33 rKKdeg   38 (64)
                      |++.+|
T Consensus        22 k~~K~G   27 (58)
T PF12669_consen   22 KDKKKG   27 (58)
T ss_pred             HHhhcC
Confidence            333334

>PF12877 DUF3827: Domain of unknown function (DUF3827); InterPro: IPR024606 The function of the proteins in this entry is not currently known, but one of the human proteins (Q9HCM3 from SWISSPROT) has been implicated in pilocytic astrocytomas [, , ]

Probab=87.52  E-value=0.47  Score=39.82  Aligned_cols=35  Identities=17%  Similarity=0.570  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccC
Q psy1892          10 VIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEE   44 (64)
Q Consensus        10 ~IaG~VvGlv~ailLIlfli~r~rKKdegsY~leE   44 (64)
                      +|+|+++-+++.+++|+++.|+..+|++..+.-|-
T Consensus       271 II~gVlvPv~vV~~Iiiil~~~LCRk~K~eFqpDa  305 (684)
T PF12877_consen  271 IIAGVLVPVLVVLLIIIILYWKLCRKNKLEFQPDA  305 (684)
T ss_pred             EEehHhHHHHHHHHHHHHHHHHHhcccccCCCchh
Confidence            46777788877788888888887777777665553

In the majority of cases of pilocytic astrocytomas a tandem duplication produces an in-frame fusion of the gene encoding this protein and the BRAF oncogene. The resulting fusion protein has constitutive BRAF kinase activity and is capable of transforming cells.

>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]

Probab=87.30  E-value=0.18  Score=31.04  Aligned_cols=27  Identities=15%  Similarity=0.429  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-HHh
Q psy1892           8 STVIGGAVVGLLCAILVVMFIVYR-MRK   34 (64)
Q Consensus         8 ag~IaG~VvGlv~ailLIlfli~r-~rK   34 (64)
                      .+++||+|+|.+.++++.++++-. +-+
T Consensus         8 ~~vlaavIaG~Vvgll~ailLIlf~iyR   35 (64)
T PF01034_consen    8 SEVLAAVIAGGVVGLLFAILLILFLIYR   35 (64)
T ss_dssp             ----------------------------
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            357788888888875555555544 444

Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.

>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=87.28  E-value=1.5  Score=24.80  Aligned_cols=22  Identities=18%  Similarity=0.221  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy1892          10 VIGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus        10 ~IaG~VvGlv~ailLIlfli~r   31 (64)
                      +++..++|++++.++.+.-.+|
T Consensus        24 il~~f~~G~llg~l~~~~~~~~   45 (68)
T PF06305_consen   24 ILIAFLLGALLGWLLSLPSRLR   45 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            4556667777777666666665

>TIGR02205 septum_zipA cell division protein ZipA

Probab=86.89  E-value=0.36  Score=36.14  Aligned_cols=21  Identities=24%  Similarity=0.471  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q psy1892          14 AVVGLLCAILVVMFIVYRMRK   34 (64)
Q Consensus        14 ~VvGlv~ailLIlfli~r~rK   34 (64)
                      +|||+++-+.|++.-+|++||
T Consensus         7 IIvGaiaI~aLl~hGlwt~Rk   27 (284)
T TIGR02205         7 IIVGILAIAALLFHGLWTSRK   27 (284)
T ss_pred             HHHHHHHHHHHHHcccccccc
Confidence            678888888888889998766

This model represents the full length of bacterial cell division protein ZipA. The N-terminal hydrophobic stretch is an uncleaved signal-anchor sequence. This is followed by an unconserved, variable length, low complexity region, and then a conserved C-terminal region of about 140 amino acids (see pfam04354) that interacts with the tubulin-like cell division protein FtsZ.

>KOG0196|consensus

Probab=86.54  E-value=0.83  Score=39.71  Aligned_cols=56  Identities=27%  Similarity=0.318  Sum_probs=30.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHH----hcCCCcccccCCC-----CCCCCCccccCCccc
Q psy1892           6 ATSTVIGGAVVGLLCAILVVMFIVYRMR----KKDEGSYALEEPK-----RSPASNSYMKNSNRE   61 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ailLIlfli~r~r----KKdegsY~leE~K-----~~~~~~~y~k~~~~e   61 (64)
                      +++|.|.++|+.+|+++++.++++.+++    .|.+..|+.++..     +.|....|-.+.|-|
T Consensus       549 ~i~g~~~~~v~~lll~~vv~~~~~~~r~~~~~~~~~~~~t~~~~~~~~~~~~pG~k~YiDP~TYE  613 (996)
T KOG0196|consen  549 LIIGSILAGVVFLLLAAVVVVAIVCSRKRCGYSRAEQEYTEKLQHYSNGEQLPGTKTYIDPHTYE  613 (996)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhheeecccccchhcccCCChhHhhhhcCCCCCCceeecCCcccc
Confidence            6677777777777777666666665432    1344445554322     233344566665544

>PTZ00382 Variant-specific surface protein (VSP); Provisional

Probab=86.30  E-value=0.037  Score=35.22  Aligned_cols=29  Identities=14%  Similarity=0.080  Sum_probs=16.4

Q ss_pred             cchhHHHHHHHHHHHHHHHH-HHHHHHHHH
Q psy1892           3 IPLATSTVIGGAVVGLLCAI-LVVMFIVYR   31 (64)
Q Consensus         3 ~~~~~ag~IaG~VvGlv~ai-lLIlfli~r   31 (64)
                      .+|.++|+..|+|+.+...+ +|+.|+++|
T Consensus        64 s~gaiagi~vg~~~~v~~lv~~l~w~f~~r   93 (96)
T PTZ00382         64 STGAIAGISVAVVAVVGGLVGFLCWWFVCR   93 (96)
T ss_pred             ccccEEEEEeehhhHHHHHHHHHhheeEEe
Confidence            46778887777765553332 333444443

>PF12768 Rax2: Cortical protein marker for cell polarity

Probab=86.05  E-value=1.1  Score=33.15  Aligned_cols=27  Identities=15%  Similarity=0.392  Sum_probs=20.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy1892          12 GGAVVGLLCAILVVMFIVYRMRKKDEG   38 (64)
Q Consensus        12 aG~VvGlv~ailLIlfli~r~rKKdeg   38 (64)
                      -++.+|+++-+.|+.+++.|.|||++|
T Consensus       234 lAiALG~v~ll~l~Gii~~~~~r~~~~  260 (281)
T PF12768_consen  234 LAIALGTVFLLVLIGIILAYIRRRRQG  260 (281)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            356677778888888888887777666

>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2

Probab=85.83  E-value=1.2  Score=29.35  Aligned_cols=34  Identities=12%  Similarity=0.254  Sum_probs=18.2

Q ss_pred             CcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy1892           2 TIPLATSTVIGGAVVGLLCAILVVMFIVYRMRKK   35 (64)
Q Consensus         2 ~~~~~~ag~IaG~VvGlv~ailLIlfli~r~rKK   35 (64)
                      .|+.-.-|+--++|+|+...++|+.|..++.|||
T Consensus        27 ~n~~~~Lgm~~lvI~~iFil~VilwfvCC~kRkr   60 (94)
T PF05393_consen   27 VNNWPNLGMWFLVICGIFILLVILWFVCCKKRKR   60 (94)
T ss_pred             cCCCCccchhHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3445555555555666545455555555544444

; GO: 0016021 integral to membrane

>PRK11677 hypothetical protein; Provisional

Probab=85.62  E-value=0.17  Score=34.34  Aligned_cols=18  Identities=28%  Similarity=0.560  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q psy1892          10 VIGGAVVGLLCAILVVMF   27 (64)
Q Consensus        10 ~IaG~VvGlv~ailLIlf   27 (64)
                      +++|.|||+++|.++.-+
T Consensus         6 a~i~livG~iiG~~~~R~   23 (134)
T PRK11677          6 ALIGLVVGIIIGAVAMRF   23 (134)
T ss_pred             HHHHHHHHHHHHHHHHhh
Confidence            345666666666555444

>PF07213 DAP10: DAP10 membrane protein; InterPro: IPR009861 This family consists of several mammalian DAP10 membrane proteins

Probab=85.57  E-value=1.1  Score=28.47  Aligned_cols=33  Identities=21%  Similarity=0.318  Sum_probs=22.2

Q ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1892           3 IPLATSTVIGGAVVGLLCAILVVMFIVYRMRKKD   36 (64)
Q Consensus         3 ~~~~~ag~IaG~VvGlv~ailLIlfli~r~rKKd   36 (64)
                      .+++++|+|+|=++--++-++ ..|..-|+|+|.
T Consensus        32 s~g~LaGiV~~D~vlTLLIv~-~vy~car~r~r~   64 (79)
T PF07213_consen   32 SPGLLAGIVAADAVLTLLIVL-VVYYCARPRRRP   64 (79)
T ss_pred             CHHHHHHHHHHHHHHHHHHHH-HHHhhcccccCC
Confidence            479999999998776665444 445555555543

In activated mouse natural killer (NK) cells, the NKG2D receptor associates with two intracellular adaptors, DAP10 and DAP12, which trigger phosphatidyl inositol 3 kinase (PI3K) and Syk family protein tyrosine kinases, respectively. It has been suggested that the DAP10-PI3K pathway is sufficient to initiate NKG2D-mediated killing of target cells [].

>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear

Probab=85.57  E-value=0.62  Score=33.81  Aligned_cols=31  Identities=16%  Similarity=0.367  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCc
Q psy1892           9 TVIGGAVVGLLCA-ILVVMFIVYRMRKKDEGS   39 (64)
Q Consensus         9 g~IaG~VvGlv~a-ilLIlfli~r~rKKdegs   39 (64)
                      -.++-++||+.++ ++||.++.|.+.+|...+
T Consensus       270 ~~~vPIaVG~~La~lvlivLiaYli~Rrr~~~  301 (306)
T PF01299_consen  270 SDLVPIAVGAALAGLVLIVLIAYLIGRRRSRA  301 (306)
T ss_pred             cchHHHHHHHHHHHHHHHHHHhheeEeccccc
Confidence            3577888998877 667777888898876654

Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane

>PF13908 Shisa: Wnt and FGF inhibitory regulator

Probab=85.44  E-value=0.21  Score=33.61  Aligned_cols=23  Identities=22%  Similarity=0.730  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           8 STVIGGAVVGLLCAILVVMFIVY   30 (64)
Q Consensus         8 ag~IaG~VvGlv~ailLIlfli~   30 (64)
                      .+++++++||++++|++|+.+|-
T Consensus        74 ~~~~~~iivgvi~~Vi~Iv~~Iv   96 (179)
T PF13908_consen   74 IYFITGIIVGVICGVIAIVVLIV   96 (179)
T ss_pred             ccceeeeeeehhhHHHHHHHhHh
Confidence            34567777777776666655553

>COG5547 Small integral membrane protein [Function unknown]

Probab=85.43  E-value=1.7  Score=26.77  Aligned_cols=20  Identities=50%  Similarity=0.778  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q psy1892          11 IGGAVVGLLCAILVVMFIVY   30 (64)
Q Consensus        11 IaG~VvGlv~ailLIlfli~   30 (64)
                      |.|..||++.|+|++-|-.|
T Consensus        11 IIgglvglliAili~t~Gfw   30 (62)
T COG5547          11 IIGGLVGLLIAILILTFGFW   30 (62)
T ss_pred             hHHHHHHHHHHHHHHHHHHH
Confidence            45666777777555544433

>PF15102 TMEM154: TMEM154 protein family

Probab=85.22  E-value=0.28  Score=34.11  Aligned_cols=27  Identities=26%  Similarity=0.332  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy1892          12 GGAVVGLLCAILVVMFIVYRMRKKDEG   38 (64)
Q Consensus        12 aG~VvGlv~ailLIlfli~r~rKKdeg   38 (64)
                      ...|+++++-+++|+++++.+|||.++
T Consensus        63 IP~VLLvlLLl~vV~lv~~~kRkr~K~   89 (146)
T PF15102_consen   63 IPLVLLVLLLLSVVCLVIYYKRKRTKQ   89 (146)
T ss_pred             HHHHHHHHHHHHHHHheeEEeecccCC
Confidence            333444444444444444445555544

>PF15330 SIT: SHP2-interacting transmembrane adaptor protein, SIT

Probab=84.76  E-value=3.9  Score=26.66  Aligned_cols=12  Identities=17%  Similarity=0.711  Sum_probs=6.8

Q ss_pred             HHHHHHHHhcCC
Q psy1892          26 MFIVYRMRKKDE   37 (64)
Q Consensus        26 lfli~r~rKKde   37 (64)
                      -++.|||+||..
T Consensus        18 sl~~wr~~~rq~   29 (107)
T PF15330_consen   18 SLLAWRMKQRQK   29 (107)
T ss_pred             HHHHHHHHhhhc
Confidence            346677655543

>COG4980 GvpP Gas vesicle protein [General function prediction only]

Probab=84.73  E-value=0.77  Score=30.76  Aligned_cols=19  Identities=21%  Similarity=0.301  Sum_probs=11.0

Q ss_pred             hhHHHHHHHHHHHHHHHHH
Q psy1892           5 LATSTVIGGAVVGLLCAIL   23 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~ail   23 (64)
                      .++.|+..|++||.+.|+|
T Consensus         6 ~~l~G~liGgiiGa~aaLL   24 (115)
T COG4980           6 DFLFGILIGGIIGAAAALL   24 (115)
T ss_pred             hHHHHHHHHHHHHHHHHHH
Confidence            4556666666666655544

>PRK12659 putative monovalent cation/H+ antiporter subunit C; Reviewed

Probab=84.15  E-value=2.4  Score=27.78  Aligned_cols=37  Identities=22%  Similarity=0.345  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccCCCC
Q psy1892           9 TVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKR   47 (64)
Q Consensus         9 g~IaG~VvGlv~ailLIlfli~r~rKKdegsY~leE~K~   47 (64)
                      =++.++|+|+....+++.++ +|. +|+-|+-|.+|-+.
T Consensus        76 lvLTaIVIg~Av~a~~lvl~-~r~-~~~~~t~~~~~l~~  112 (117)
T PRK12659         76 LILTAIVIGFGVQAFAIVLI-KRA-YQVVGTDDLDEMKT  112 (117)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HHH-HcccCcccHHHhcc
Confidence            35667777777666555544 433 33455556666443

>PF05454 DAG1: Dystroglycan (Dystrophin-associated glycoprotein 1); InterPro: IPR008465 Dystroglycan is one of the dystrophin-associated glycoproteins, which is encoded by a 5

Probab=84.08  E-value=0.32  Score=36.61  Aligned_cols=34  Identities=32%  Similarity=0.521  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHH-HHHHHHHHHHHHhcCCCcccccC
Q psy1892           9 TVIGGAVVGLLCA-ILVVMFIVYRMRKKDEGSYALEE   44 (64)
Q Consensus         9 g~IaG~VvGlv~a-ilLIlfli~r~rKKdegsY~leE   44 (64)
                      .+|..+||.+++- +.+|..+.|  |||.+|+-.+||
T Consensus       148 T~IpaVVI~~iLLIA~iIa~icy--rrkR~GK~~~ee  182 (290)
T PF05454_consen  148 TFIPAVVIAAILLIAGIIACICY--RRKRKGKMSLEE  182 (290)
T ss_dssp             -------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhh--hhhhccccccch
Confidence            3444444433332 344444555  445555555544

5 kb transcript in Homo sapiens. The protein product is cleaved into two non-covalently associated subunits, [alpha] (N-terminal) and [beta] (C-terminal). In skeletal muscle the dystroglycan complex works as a transmembrane linkage between the extracellular matrix and the cytoskeleton [alpha]-dystroglycan is extracellular and binds to merosin ([alpha]-2 laminin) in the basement membrane, while [beta]-dystroglycan is a transmembrane protein and binds to dystrophin, which is a large rod-like cytoskeletal protein, absent in Duchenne muscular dystrophy patients. Dystrophin binds to intracellular actin cables. In this way, the dystroglycan complex, which links the extracellular matrix to the intracellular actin cables, is thought to provide structural integrity in muscle tissues. The dystroglycan complex is also known to serve as an agrin receptor in muscle, where it may regulate agrin-induced acetylcholine receptor clustering at the neuromuscular junction. There is also evidence which suggests the function of dystroglycan as a part of the signal transduction pathway because it is shown that Grb2, a mediator of the Ras-related signal pathway, can interact with the cytoplasmic domain of dystroglycan. In general, aberrant expression of dystrophin-associated protein complex underlies the pathogenesis of Duchenne muscular dystrophy, Becker muscular dystrophy and severe childhood autosomal recessive muscular dystrophy. Interestingly, no genetic disease has been described for either [alpha]- or [beta]-dystroglycan. Dystroglycan is widely distributed in non-muscle tissues as well as in muscle tissues. During epithelial morphogenesis of kidney, the dystroglycan complex is shown to act as a receptor for the basement membrane. Dystroglycan expression in Mus musculus brain and neural retina has also been reported. However, the physiological role of dystroglycan in non-muscle tissues has remained unclear [].; PDB: 1EG4_P.

>PRK13275 mtrF tetrahydromethanopterin S-methyltransferase subunit F; Provisional

Probab=83.96  E-value=2.6  Score=26.02  Aligned_cols=21  Identities=38%  Similarity=0.444  Sum_probs=15.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHH
Q psy1892           5 LATSTVIGGAVVGLLCAILVV   25 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~ailLI   25 (64)
                      |+.+.-+.|..+|+++|++|+
T Consensus        36 Gv~~~~~~G~aiG~~~AlvLv   56 (67)
T PRK13275         36 GVIATGIIGFAIGFLLALLLV   56 (67)
T ss_pred             HhhhhhHHHHHHHHHHHHHHH
Confidence            566666788888888886554

>PF04971 Lysis_S: Lysis protein S ; InterPro: IPR007054 The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis

Probab=83.74  E-value=2  Score=26.70  Aligned_cols=18  Identities=22%  Similarity=0.569  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q psy1892          13 GAVVGLLCAILVVMFIVY   30 (64)
Q Consensus        13 G~VvGlv~ailLIlfli~   30 (64)
                      |++.|++++++=.+--+|
T Consensus        37 Gvi~gi~~~~lt~ltN~Y   54 (68)
T PF04971_consen   37 GVIGGIFFGLLTYLTNLY   54 (68)
T ss_pred             HHHHHHHHHHHHHHhHhh
Confidence            344444444443333333

The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [].

>PRK11677 hypothetical protein; Provisional

Probab=83.73  E-value=1.1  Score=30.32  Aligned_cols=16  Identities=25%  Similarity=0.563  Sum_probs=7.3

Q ss_pred             HHHHHHHHHHHHHHHH
Q psy1892          14 AVVGLLCAILVVMFIV   29 (64)
Q Consensus        14 ~VvGlv~ailLIlfli   29 (64)
                      +++|+++|+++=+|+.
T Consensus         6 a~i~livG~iiG~~~~   21 (134)
T PRK11677          6 ALIGLVVGIIIGAVAM   21 (134)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            3455555544443333

>PF12301 CD99L2: CD99 antigen like protein 2; InterPro: IPR022078 This family of proteins is found in eukaryotes

Probab=83.42  E-value=1.4  Score=30.93  Aligned_cols=29  Identities=31%  Similarity=0.576  Sum_probs=13.7

Q ss_pred             hHHHHHHHHHHHHHHHHH--HHHHHHHHHHh
Q psy1892           6 ATSTVIGGAVVGLLCAIL--VVMFIVYRMRK   34 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ail--LIlfli~r~rK   34 (64)
                      ..+|+|+|||-.|++|++  +--|+-|..||
T Consensus       112 ~~~g~IaGIvsav~valvGAvsSyiaYqkKK  142 (169)
T PF12301_consen  112 AEAGTIAGIVSAVVVALVGAVSSYIAYQKKK  142 (169)
T ss_pred             cccchhhhHHHHHHHHHHHHHHHHHHHHhhc
Confidence            445555555544444422  23456664333

Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.

>PF13937 DUF4212: Domain of unknown function (DUF4212)

Probab=82.95  E-value=1.1  Score=28.21  Aligned_cols=22  Identities=23%  Similarity=0.702  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHHHhcCCCcccccC
Q psy1892          22 ILVVMFIVYRMRKKDEGSYALEE   44 (64)
Q Consensus        22 ilLIlfli~r~rKKdegsY~leE   44 (64)
                      ++||+...++|.|-|+. |+.||
T Consensus        60 viLi~~Ya~~mnrlD~~-~gv~E   81 (81)
T PF13937_consen   60 VILIFVYAWRMNRLDRK-YGVDE   81 (81)
T ss_pred             HHHHHHHHHHHHHHHHH-HCCCC
Confidence            67777788888887775 77776

>COG4980 GvpP Gas vesicle protein [General function prediction only]

Probab=82.86  E-value=1.9  Score=28.90  Aligned_cols=17  Identities=35%  Similarity=0.122  Sum_probs=10.2

Q ss_pred             hhHHHHHHHHHHHHHHH
Q psy1892           5 LATSTVIGGAVVGLLCA   21 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~a   21 (64)
                      |++.|.|+|++++|++|
T Consensus        10 G~liGgiiGa~aaLL~A   26 (115)
T COG4980          10 GILIGGIIGAAAALLFA   26 (115)
T ss_pred             HHHHHHHHHHHHHHHhC
Confidence            45556666666666665

>PF10225 DUF2215: Uncharacterized conserved protein (DUF2215); InterPro: IPR024233 This entry represents a domain that is found in a number of different proteins, including a family of transmembrane proteins

Probab=82.63  E-value=1.4  Score=31.86  Aligned_cols=24  Identities=25%  Similarity=0.708  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHH-HHhc
Q psy1892          12 GGAVVGLLCAILVVMFIVYR-MRKK   35 (64)
Q Consensus        12 aG~VvGlv~ailLIlfli~r-~rKK   35 (64)
                      +|+.+|+++.+++++|+..| +-||
T Consensus        40 sg~~lGv~~s~li~~~~~~k~lPrk   64 (249)
T PF10225_consen   40 SGISLGVLASLLILLFQLSKLLPRK   64 (249)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHccCc
Confidence            58899999999999999888 4433

>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain

Probab=82.54  E-value=1.8  Score=21.72  Aligned_cols=6  Identities=33%  Similarity=0.479  Sum_probs=2.8

Q ss_pred             HHHHHH
Q psy1892          13 GAVVGL   18 (64)
Q Consensus        13 G~VvGl   18 (64)
                      .+++|+
T Consensus        13 ~~~~G~   18 (34)
T TIGR01167        13 LLLLGL   18 (34)
T ss_pred             HHHHHH
Confidence            344455

A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.

>PF11021 DUF2613: Protein of unknown function (DUF2613); InterPro: IPR022566 This is a family of putative small secreted proteins expressed by Actinobacteria

Probab=82.32  E-value=2.1  Score=25.55  Aligned_cols=27  Identities=22%  Similarity=0.305  Sum_probs=19.2

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           4 PLATSTVIGGAVVGLLCAILVVMFIVY   30 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ailLIlfli~   30 (64)
                      +..+...++.+|+|+++++..++.+-.
T Consensus         2 ~r~l~pa~aSaV~Gi~lG~~av~gvt~   28 (56)
T PF11021_consen    2 PRFLGPAAASAVVGIVLGVAAVFGVTA   28 (56)
T ss_pred             CcchhHHHHHHHHHHHHHHHHHhhhhe
Confidence            345677888888888888776665543

The function is not known.

>PRK12660 putative monovalent cation/H+ antiporter subunit C; Reviewed

Probab=81.74  E-value=4.1  Score=26.51  Aligned_cols=38  Identities=18%  Similarity=0.343  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccCCCC
Q psy1892           8 STVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALEEPKR   47 (64)
Q Consensus         8 ag~IaG~VvGlv~ailLIlfli~r~rKKdegsY~leE~K~   47 (64)
                      +=++.++|+|+....+++.+. +| ..|+-|+-|.+|-+.
T Consensus        72 alvLTaIVIg~av~a~lL~l~-~r-~~~~~~t~~~~~l~~  109 (114)
T PRK12660         72 AIVLTAIVIGFGMTAFLLVLV-YR-TYKVTKEDEIEGLRG  109 (114)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-HH-HHhhcCcchHHHhcc
Confidence            345667777777666665555 43 333556666666554

>PF04277 OAD_gamma: Oxaloacetate decarboxylase, gamma chain ; InterPro: IPR005899 This family comprises distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases

Probab=81.46  E-value=6.9  Score=22.88  Aligned_cols=7  Identities=14%  Similarity=0.662  Sum_probs=2.9

Q ss_pred             HHHHHHH
Q psy1892          16 VGLLCAI   22 (64)
Q Consensus        16 vGlv~ai   22 (64)
                      .|+||.+
T Consensus        12 m~iVF~~   18 (79)
T PF04277_consen   12 MGIVFLV   18 (79)
T ss_pred             HHHHHHH
Confidence            3444443

These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit [].; GO: 0008948 oxaloacetate decarboxylase activity, 0015081 sodium ion transmembrane transporter activity, 0071436 sodium ion export, 0016020 membrane

>PRK14750 kdpF potassium-transporting ATPase subunit F; Provisional

Probab=80.99  E-value=3.2  Score=22.20  Aligned_cols=19  Identities=32%  Similarity=0.639  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q psy1892          13 GAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus        13 G~VvGlv~ailLIlfli~r   31 (64)
                      |++.|.++-++|+.+++|-
T Consensus         4 ~vi~g~llv~lLl~YLvYA   22 (29)
T PRK14750          4 SIVCGALLVLLLLGYLVYA   22 (29)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            4455555556666666664

>KOG3637|consensus

Probab=80.92  E-value=2.1  Score=36.94  Aligned_cols=20  Identities=30%  Similarity=0.539  Sum_probs=10.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q psy1892          11 IGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus        11 IaG~VvGlv~ailLIlfli~r   31 (64)
                      |.+++.|+|+-+||+ +++|+
T Consensus       982 i~svl~GLLlL~llv-~~LwK 1001 (1030)
T KOG3637|consen  982 ILSVLGGLLLLALLV-LLLWK 1001 (1030)
T ss_pred             hHHHHHHHHHHHHHH-HHHHh
Confidence            444555555554444 44555

>PF09835 DUF2062: Uncharacterized protein conserved in bacteria (DUF2062); InterPro: IPR018639 This domain, found in various prokaryotic proteins, has no known function

Probab=80.92  E-value=4.2  Score=26.43  Aligned_cols=30  Identities=33%  Similarity=0.604  Sum_probs=12.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1892           6 ATSTVIGGAVVGLLCAILVVMFIVYRMRKKD   36 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ailLIlfli~r~rKKd   36 (64)
                      +++++|.|++.|+++-.+ +.+++.++|||+
T Consensus       121 ~~G~~i~~~v~~~i~Y~l-~~~~~~~~r~~r  150 (154)
T PF09835_consen  121 LLGSLILGIVLGIISYFL-VYFLVRKYRKRR  150 (154)
T ss_pred             HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence            344444444444443322 333333344443

It is found at the C-terminal of family 2 glycosyltransferase proteins, in addition to proteins of unknown function.

>COG3944 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]

Probab=80.82  E-value=2.1  Score=31.81  Aligned_cols=45  Identities=24%  Similarity=0.311  Sum_probs=34.5

Q ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHH-HHhcCCCcccccCCCCCC
Q psy1892           3 IPLATSTVIGGAVVGLLCAILVVMFIVYR-MRKKDEGSYALEEPKRSP   49 (64)
Q Consensus         3 ~~~~~ag~IaG~VvGlv~ailLIlfli~r-~rKKdegsY~leE~K~~~   49 (64)
                      .|..+--++.|.++|++.++.+++|+-|. .|=|++.  |+||.-+.|
T Consensus       169 sP~~~~Ni~iaf~~Gl~~~igiafl~e~lD~tIKs~e--die~~l~lP  214 (226)
T COG3944         169 SPKVMRNIVIAFLAGLAGAIGIAFLLEYLDKTIKSEE--DIEEVLDLP  214 (226)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCHH--HHHHhhCCc
Confidence            36677788999999999999999999887 5555655  677655544

>PF13807 GNVR: G-rich domain on putative tyrosine kinase

Probab=80.51  E-value=3.9  Score=24.30  Aligned_cols=24  Identities=21%  Similarity=0.337  Sum_probs=15.4

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHH
Q psy1892           4 PLATSTVIGGAVVGLLCAILVVMF   27 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ailLIlf   27 (64)
                      |...-=+..|+++|+++++.++++
T Consensus        56 P~~~lil~l~~~~Gl~lgi~~~~~   79 (82)
T PF13807_consen   56 PKRALILALGLFLGLILGIGLAFL   79 (82)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHH
Confidence            444445667777777777766653

>PRK15083 PTS system mannitol-specific transporter subunit IICBA; Provisional

Probab=80.51  E-value=2.8  Score=33.74  Aligned_cols=31  Identities=13%  Similarity=0.206  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy1892           7 TSTVIGGAVVGLLCAILVVMFIVYRMRKKDE   37 (64)
Q Consensus         7 ~ag~IaG~VvGlv~ailLIlfli~r~rKKde   37 (64)
                      +.+.+.|++++++++.++.+++-++++||+|
T Consensus       313 ~~~~~i~~~v~~~v~~v~t~~~~~~~~~~~~  343 (639)
T PRK15083        313 YFANIASVAAAMAVSFVVSAILLKTSKVKEE  343 (639)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccccch
Confidence            3456668888888888888888888888776

>COG5336 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.43  E-value=2.2  Score=28.95  Aligned_cols=16  Identities=31%  Similarity=0.383  Sum_probs=11.1

Q ss_pred             hHHHHHHHHHHHHHHH
Q psy1892           6 ATSTVIGGAVVGLLCA   21 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~a   21 (64)
                      +++=.|+|++||++++
T Consensus        48 lssefIsGilVGa~iG   63 (116)
T COG5336          48 LSSEFISGILVGAGIG   63 (116)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4455677777777777

>PHA03265 envelope glycoprotein D; Provisional

Probab=80.26  E-value=0.57  Score=37.19  Aligned_cols=31  Identities=19%  Similarity=0.410  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy1892           7 TSTVIGGAVVGLLCAILVVMFIVYRMRKKDEG   38 (64)
Q Consensus         7 ~ag~IaG~VvGlv~ailLIlfli~r~rKKdeg   38 (64)
                      .+.+|+|.++|++..- .|||..||+||-.++
T Consensus       350 ~g~~ig~~i~glv~vg-~il~~~~rr~k~~~k  380 (402)
T PHA03265        350 VGISVGLGIAGLVLVG-VILYVCLRRKKELKK  380 (402)
T ss_pred             cceEEccchhhhhhhh-HHHHHHhhhhhhhhh
Confidence            4455666777766543 455666666654433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	64
1ejp_A	28	Syndecan-4; symmetric-parallel-interwinded dimer,	99.65
2k1k_A	38	Ephrin type-A receptor 1; EPHA1, receptor tyrosine	98.31
2l34_A	33	TYRO protein tyrosine kinase-binding protein; immu	97.66
2jwa_A	44	Receptor tyrosine-protein kinase ERBB-2; transmemb	97.44
2k1k_A	38	Ephrin type-A receptor 1; EPHA1, receptor tyrosine	97.34
1afo_A	40	Glycophorin A; integral membrane protein, transmem	97.31
2l2t_A	44	Receptor tyrosine-protein kinase ERBB-4; transmemb	97.18
2l2t_A	44	Receptor tyrosine-protein kinase ERBB-4; transmemb	97.17
2ks1_B	44	Epidermal growth factor receptor; ERBB1, ERBB2, tr	96.68
2knc_B	79	Integrin beta-3; transmembrane signaling, protein	96.54
2k9y_A	41	Ephrin type-A receptor 2; receptor tyrosine kinase	96.18
2k9j_B	43	Integrin beta-3; transmembrane complex, cell adhes	94.79
2knc_B	79	Integrin beta-3; transmembrane signaling, protein	94.33
2l34_A	33	TYRO protein tyrosine kinase-binding protein; immu	93.6
1s7q_A	348	H-2KB, H-2 class I histocompatibility antigen, K-B	93.58
2knc_A	54	Integrin alpha-IIB; transmembrane signaling, prote	92.2
2l8s_A	54	Integrin alpha-1; transmembrane region, detergent	91.77
1iij_A	35	ERBB-2 receptor protein-tyrosine kinase; alpha-hel	90.12
1cd1_A	315	CD1, MCD1D.1; immunology, MHC, TCR, glycoprotein,	88.21
2klu_A	70	T-cell surface glycoprotein CD4; cell membrane, di	87.58
1q55_A	880	EP-cadherin, C-cadherin; trans interaction, desmos	86.19
1iij_A	35	ERBB-2 receptor protein-tyrosine kinase; alpha-hel	84.96
2l35_A	63	DAP12-NKG2C_TM; immunoreceptor, transmembrane asse	82.88
2l6w_A	39	Beta-type platelet-derived growth factor receptor;	82.32

>1ejp_A Syndecan-4; symmetric-parallel-interwinded dimer, signaling protein; NMR {Synthetic} SCOP: j.80.1.1 PDB: 1ejq_A

Probab=99.65  E-value=1.9e-17  Score=87.32  Aligned_cols=28  Identities=57%  Similarity=0.894  Sum_probs=25.9

Q ss_pred             HHHhcCCCcccccCCCCCCCCCccccCCcccccC
Q psy1892          31 RMRKKDEGSYALEEPKRSPASNSYMKNSNREFYA   64 (64)
Q Consensus        31 r~rKKdegsY~leE~K~~~~~~~y~k~~~~efya   64 (64)
                      ||||||||||+|||+      ++|+|++|+||||
T Consensus         1 RmrKKDEGSY~Lde~------p~Y~k~~~~EfYA   28 (28)
T 1ejp_A            1 RMKKKDEGSYDLGKK------PIYKKAPTNEFYA   28 (28)
T ss_dssp             CCSCCCCCCCCCCSC------CCCCCCCCCCSCC
T ss_pred             CcccccccccccCCC------cccccCCcccccC
Confidence            689999999999996      3799999999998

>2k1k_A Ephrin type-A receptor 1; EPHA1, receptor tyrosine kinase, dimeric transmembrane domain, ATP-binding, glycoprotein, nucleotide-binding; NMR {Homo sapiens} PDB: 2k1l_A

Probab=98.31  E-value=6.4e-07  Score=48.84  Aligned_cols=29  Identities=21%  Similarity=0.122  Sum_probs=22.4

Q ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           3 IPLATSTVIGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus         3 ~~~~~ag~IaG~VvGlv~ailLIlfli~r   31 (64)
                      .+++.+|.|||+|||.+++++|+..++|.
T Consensus         5 ~~~ls~GaIAGiVvG~v~gv~li~~l~~~   33 (38)
T 2k1k_A            5 SRGLTGGEIVAVIFGLLLGAALLLGILVF   33 (38)
T ss_dssp             STTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCceeeeehHHHHHHHHHHHHHHH
Confidence            45788999999999999986666555444

>2l34_A TYRO protein tyrosine kinase-binding protein; immunoreceptor, transmembrane assembly, DAP12, protein bindi; NMR {Homo sapiens} PDB: 2l35_B

Probab=97.66  E-value=3.7e-05  Score=40.87  Aligned_cols=30  Identities=27%  Similarity=0.483  Sum_probs=25.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1892           5 LATSTVIGGAVVGLLCAILVVMFIVYRMRK   34 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~ailLIlfli~r~rK   34 (64)
                      ++..|.|||+|+|-+++++++..++|.++|
T Consensus         3 ~L~~gaIaGIVvgdi~~t~~i~~~vy~~~r   32 (33)
T 2l34_A            3 TVSPGVLAGIVVGDLVLTVLIALAVYFLGR   32 (33)
T ss_dssp             CCCTHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             ccCcceEEeEeHHHHHHHHHHHHHHhheec
Confidence            567899999999999999999988887654

>2jwa_A Receptor tyrosine-protein kinase ERBB-2; transmembrane helix dimer, protein kinase receptor membrane domain, ATP-binding, glycoprotein; NMR {Homo sapiens} PDB: 2ks1_A

Probab=97.44  E-value=0.00026  Score=39.83  Aligned_cols=14  Identities=50%  Similarity=0.489  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHHHH
Q psy1892           8 STVIGGAVVGLLCA   21 (64)
Q Consensus         8 ag~IaG~VvGlv~a   21 (64)
                      ...|||+|||+++.
T Consensus        11 ~~~Ia~~vVGvll~   24 (44)
T 2jwa_A           11 LTSIISAVVGILLV   24 (44)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHH
Confidence            45677778886554

>2k1k_A Ephrin type-A receptor 1; EPHA1, receptor tyrosine kinase, dimeric transmembrane domain, ATP-binding, glycoprotein, nucleotide-binding; NMR {Homo sapiens} PDB: 2k1l_A

Probab=97.34  E-value=0.00012  Score=39.77  Aligned_cols=28  Identities=18%  Similarity=0.142  Sum_probs=22.9

Q ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           3 IPLATSTVIGGAVVGLLCAILVVMFIVY   30 (64)
Q Consensus         3 ~~~~~ag~IaG~VvGlv~ailLIlfli~   30 (64)
                      .+|.++|++.|.|+|+++-+.+++|+++
T Consensus         9 s~GaIAGiVvG~v~gv~li~~l~~~~~r   36 (38)
T 2k1k_A            9 TGGEIVAVIFGLLLGAALLLGILVFRSR   36 (38)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCceeeeehHHHHHHHHHHHHHHHHee
Confidence            3689999999999999987777766554

>1afo_A Glycophorin A; integral membrane protein, transmembrane helix interactions, membrane protein folding; NMR {Homo sapiens} SCOP: j.35.1.1 PDB: 2kpf_A

Probab=97.31  E-value=0.00045  Score=38.57  Aligned_cols=34  Identities=26%  Similarity=0.516  Sum_probs=29.2

Q ss_pred             CCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy1892           1 MTIPLATSTVIGGAVVGLLCAILVVMFIVYRMRKK   35 (64)
Q Consensus         1 ~~~~~~~ag~IaG~VvGlv~ailLIlfli~r~rKK   35 (64)
                      |++| ++..+|-|+.+|++-.+|+|-+.+.|++||
T Consensus         7 fs~p-~i~lII~~vmaGiIG~IllI~y~I~rl~Kk   40 (40)
T 1afo_A            7 FSEP-EITLIIFGVMAGVIGTILLISYGIRRLIKK   40 (40)
T ss_dssp             SSCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCc-hhHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            6778 777888888888888899999999998886

>2l2t_A Receptor tyrosine-protein kinase ERBB-4; transmembrane dimer, membrane domain, membrane protei; NMR {Homo sapiens}

Probab=97.18  E-value=0.00049  Score=38.62  Aligned_cols=9  Identities=33%  Similarity=0.759  Sum_probs=4.7

Q ss_pred             HHHHHHHHH
Q psy1892           9 TVIGGAVVG   17 (64)
Q Consensus         9 g~IaG~VvG   17 (64)
                      +.||+.|||
T Consensus        10 ~aIA~gVVg   18 (44)
T 2l2t_A           10 PLIAAGVIG   18 (44)
T ss_dssp             HHHHHHHHH
T ss_pred             ceEEEeehH
Confidence            445555555

>2l2t_A Receptor tyrosine-protein kinase ERBB-4; transmembrane dimer, membrane domain, membrane protei; NMR {Homo sapiens}

Probab=97.17  E-value=0.00086  Score=37.62  Aligned_cols=33  Identities=12%  Similarity=0.012  Sum_probs=16.3

Q ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1892           3 IPLATSTVIGGAVVGLLCAILVVMFIVYRMRKKD   36 (64)
Q Consensus         3 ~~~~~ag~IaG~VvGlv~ailLIlfli~r~rKKd   36 (64)
                      +++.+|+-+.|.+++++..+++++| .||+|++.
T Consensus         8 ~~~aIA~gVVgGv~~v~ii~~~~~~-~~RRRr~~   40 (44)
T 2l2t_A            8 RTPLIAAGVIGGLFILVIVGLTFAV-YVRRKSIK   40 (44)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHHHHH-HHHTTCSS
T ss_pred             CcceEEEeehHHHHHHHHHHHHHHH-Hhhhhhhh
Confidence            4455555555555555544444444 44444433

>2ks1_B Epidermal growth factor receptor; ERBB1, ERBB2, transmembrane, heterodimer, complex, tyrosine receptor, bicelles, transferase; NMR {Homo sapiens}

Probab=96.68  E-value=0.0011  Score=37.02  Aligned_cols=30  Identities=23%  Similarity=0.256  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy1892           9 TVIGGAVVGLLCAILVVMFIVYRMRKKDEG   38 (64)
Q Consensus         9 g~IaG~VvGlv~ailLIlfli~r~rKKdeg   38 (64)
                      +.||+.|||-++++++|.+.+|-+.||...
T Consensus        11 ~~IA~gVVgGv~~~~ii~~~~~~~~RRr~~   40 (44)
T 2ks1_B           11 PSIATGMVGALLLLLVVALGIGLFMRRRHI   40 (44)
T ss_dssp             SSSTHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             ceEEeehhHHHHHHHHHHHHHHHHhhhhHh
Confidence            457777777777777888999999998654

>2knc_B Integrin beta-3; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}

Probab=96.54  E-value=0.00068  Score=41.26  Aligned_cols=22  Identities=18%  Similarity=0.144  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy1892           8 STVIGGAVVGLLCAILVVMFIV   29 (64)
Q Consensus         8 ag~IaG~VvGlv~ailLIlfli   29 (64)
                      .+++.|++.|+++..|+++++|
T Consensus        11 ~~Iv~gvi~gilliGllllliw   32 (79)
T 2knc_B           11 LVVLLSVMGAILLIGLAALLIW   32 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHH
Confidence            4555566555555444444444

>2k9y_A Ephrin type-A receptor 2; receptor tyrosine kinase, membrane protein, dimeric transmembrane domain, ephrin receptor, ATP-binding, glycoprotein; NMR {Homo sapiens}

Probab=96.18  E-value=0.0013  Score=34.72  Aligned_cols=16  Identities=38%  Similarity=0.698  Sum_probs=9.3

Q ss_pred             HHHHHHHHHHHHHHHH
Q psy1892           7 TSTVIGGAVVGLLCAI   22 (64)
Q Consensus         7 ~ag~IaG~VvGlv~ai   22 (64)
                      ++++++|+++|+++-+
T Consensus        12 ~~~I~~~vv~Gv~ll~   27 (41)
T 2k9y_A           12 NLAVIGGVAVGVVLLL   27 (41)
T ss_dssp             STHHHHHHHHHHHHHH
T ss_pred             eEEEEeehhHHHHHHH
Confidence            3456666666666533

>2k9j_B Integrin beta-3; transmembrane complex, cell adhesion, cleavage on basic residues, disease mutation, glycoprotein, pyrrolidone carboxylic acid; NMR {Homo sapiens} PDB: 2rmz_A 2rn0_A 2l91_A

Probab=94.79  E-value=0.045  Score=29.94  Aligned_cols=26  Identities=15%  Similarity=0.284  Sum_probs=12.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           6 ATSTVIGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ailLIlfli~r   31 (64)
                      ....+|.|.|+|.++.+=++++++||
T Consensus         7 ~n~~~Iv~gvi~~ivliGl~lLliwk   32 (43)
T 2k9j_B            7 PDILVVLLSVMGAILLIGLAALLIWK   32 (43)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEeehHHHHHHHHHHHHHHHHHHHH
Confidence            34445544444444444444555555

>2knc_B Integrin beta-3; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}

Probab=94.33  E-value=0.011  Score=35.79  Aligned_cols=39  Identities=18%  Similarity=0.283  Sum_probs=20.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccc
Q psy1892           5 LATSTVIGGAVVGLLCAILVVMFIVYRMRKKDEGSYALE   43 (64)
Q Consensus         5 ~~~ag~IaG~VvGlv~ailLIlfli~r~rKKdegsY~le   43 (64)
                      ++..|+|+|+|.--++.+++.-+++.-..||+-.+++-|
T Consensus        12 ~Iv~gvi~gilliGllllliwk~~~~i~DrrE~~kFEkE   50 (79)
T 2knc_B           12 VVLLSVMGAILLIGLAALLIWKLLITIHDRKEFAKFEEE   50 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456677777664444444444444444445555555543

>2l34_A TYRO protein tyrosine kinase-binding protein; immunoreceptor, transmembrane assembly, DAP12, protein bindi; NMR {Homo sapiens} PDB: 2l35_B

Probab=93.60  E-value=0.14  Score=26.87  Aligned_cols=26  Identities=23%  Similarity=0.318  Sum_probs=20.9

Q ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           3 IPLATSTVIGGAVVGLLCAILVVMFI   28 (64)
Q Consensus         3 ~~~~~ag~IaG~VvGlv~ailLIlfl   28 (64)
                      .+|.++|+|.|-+++.++-.+++.|+
T Consensus         5 ~~gaIaGIVvgdi~~t~~i~~~vy~~   30 (33)
T 2l34_A            5 SPGVLAGIVVGDLVLTVLIALAVYFL   30 (33)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcceEEeEeHHHHHHHHHHHHHHhhe
Confidence            57899999999999998666666553

>1s7q_A H-2KB, H-2 class I histocompatibility antigen, K-B alpha chain; LCMV, MHC class I, immune escape, immune system; 1.99A {Mus musculus} SCOP: b.1.1.2 d.19.1.1 PDB: 1s7r_A 1s7s_A 1s7t_A 1bii_A 3qul_A 1s7v_A 1s7w_A 1s7x_A 3quk_A 1s7u_A 1nez_A*

Probab=93.58  E-value=0.013  Score=42.10  Aligned_cols=19  Identities=37%  Similarity=0.623  Sum_probs=0.0

Q ss_pred             HHHHHHH-HHhc--CCCccccc
Q psy1892          25 VMFIVYR-MRKK--DEGSYALE   43 (64)
Q Consensus        25 Ilfli~r-~rKK--degsY~le   43 (64)
                      +.+++|| +|+.  ..|+|..-
T Consensus       303 ~~~~~~~~k~~~~~~~~~~~~~  324 (348)
T 1s7q_A          303 VAFVMKMRRRNTGGKGGDYALA  324 (348)
T ss_dssp             ----------------------
T ss_pred             EEEEEEEEEecCCCCCCCcccC
Confidence            4467787 3332  23566543

>2knc_A Integrin alpha-IIB; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}

Probab=92.20  E-value=0.44  Score=27.41  Aligned_cols=22  Identities=14%  Similarity=0.298  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy1892          10 VIGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus        10 ~IaG~VvGlv~ailLIlfli~r   31 (64)
                      +|.+.|+|-++-..++.+++|+
T Consensus        14 iIi~svl~GLllL~li~~~LwK   35 (54)
T 2knc_A           14 WVLVGVLGGLLLLTILVLAMWK   35 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444444444445555555

>2l8s_A Integrin alpha-1; transmembrane region, detergent micelle, CE adhesion; NMR {Homo sapiens}

Probab=91.77  E-value=0.26  Score=28.55  Aligned_cols=22  Identities=14%  Similarity=0.286  Sum_probs=9.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q psy1892          10 VIGGAVVGLLCAILVVMFIVYR   31 (64)
Q Consensus        10 ~IaG~VvGlv~ailLIlfli~r   31 (64)
                      +|.+.++|-++-..+|.+++|+
T Consensus        11 iIi~svl~GLLLL~Lii~~LwK   32 (54)
T 2l8s_A           11 VILLSAFAGLLLLMLLILALWK   32 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            3344444333344444555555

>1iij_A ERBB-2 receptor protein-tyrosine kinase; alpha-helix-PI-bulge-alpha-helix, signaling protein; NMR {Synthetic} SCOP: j.35.1.1

Probab=90.12  E-value=0.26  Score=26.36  Aligned_cols=12  Identities=42%  Similarity=0.448  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHHH
Q psy1892          10 VIGGAVVGLLCA   21 (64)
Q Consensus        10 ~IaG~VvGlv~a   21 (64)
                      .||..|||+++.
T Consensus         9 sIaagVvglll~   20 (35)
T 1iij_A            9 FIIATVVGVLLF   20 (35)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             EeHHHHHHHHHH
Confidence            466666775444

>1cd1_A CD1, MCD1D.1; immunology, MHC, TCR, glycoprotein, signal, immunoglobulin fold, T-cell; 2.67A {Mus musculus} SCOP: b.1.1.2 d.19.1.1

Probab=88.21  E-value=0.092  Score=36.69  Aligned_cols=18  Identities=11%  Similarity=0.015  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q psy1892           7 TSTVIGGAVVGLLCAILV   24 (64)
Q Consensus         7 ~ag~IaG~VvGlv~ailL   24 (64)
                      +..+|+|+++||++.+++
T Consensus       283 ~~~i~~~vi~~l~ll~~~  300 (315)
T 1cd1_A          283 VGLIVFIVLIMLVVVGAV  300 (315)
T ss_dssp             ------------------
T ss_pred             cceeehhHHHHHHHHHHH
Confidence            344455666555544444

>2klu_A T-cell surface glycoprotein CD4; cell membrane, disulfide bond, HOST- virus interaction, immune response, immunoglobulin domain, lipoprotein; NMR {Homo sapiens}

Probab=87.58  E-value=0.96  Score=27.54  Aligned_cols=55  Identities=31%  Similarity=0.445  Sum_probs=27.4

Q ss_pred             CcchhHHHHHHHHHHHHHHHH-HHHHHHH-HHHHhcCCCcc-----cccCCCCCCCCCccccCC
Q psy1892           2 TIPLATSTVIGGAVVGLLCAI-LVVMFIV-YRMRKKDEGSY-----ALEEPKRSPASNSYMKNS   58 (64)
Q Consensus         2 ~~~~~~ag~IaG~VvGlv~ai-lLIlfli-~r~rKKdegsY-----~leE~K~~~~~~~y~k~~   58 (64)
                      ++|-++  ++-|+++|+++-+ +-|++.+ ||.|+|....-     -|.|.|--.-+..+||+.
T Consensus         6 ~~p~~L--ivlGg~~~lll~~glcI~ccvkcrhRrrqAeRMSQikrlLsEKKTCQC~hr~qk~~   67 (70)
T 2klu_A            6 RGSMAL--IVLGGVAGLLLFIGLGIFFSVRSRHRRRQAERMSQIKRLLSEKKTSQSPHRFQKTH   67 (70)
T ss_dssp             CCSSHH--HHHHHHHHHHHHHHHHHHHHHHSSCCSSSCTTSSHHHHHHHSSSCCCCCCCCCCCC
T ss_pred             hhHHHH--HHHhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhccccccCcHHHhhcc
Confidence            456666  5666666766554 4444466 33333332221     245655332234477763

>1q55_A EP-cadherin, C-cadherin; trans interaction, desmosome, junction, adhesion, structural protein; HET: NAG NDG; 30.00A {Mus musculus} SCOP: i.20.1.1 PDB: 1q5a_A* 1q5b_A* 1q5c_A*

Probab=86.19  E-value=0.14  Score=40.79  Aligned_cols=25  Identities=8%  Similarity=0.101  Sum_probs=0.0

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           4 PLATSTVIGGAVVGLLCAILVVMFI   28 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ailLIlfl   28 (64)
                      .++..++|.++++|+++.+++++++
T Consensus       700 ~~l~~~aii~il~~~~~ll~~~ll~  724 (880)
T 1q55_A          700 GGFDLPIILVILGSVLALLILFLLL  724 (880)
T ss_dssp             -------------------------
T ss_pred             cCccHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666777777766654444443

>1iij_A ERBB-2 receptor protein-tyrosine kinase; alpha-helix-PI-bulge-alpha-helix, signaling protein; NMR {Synthetic} SCOP: j.35.1.1

Probab=84.96  E-value=0.26  Score=26.35  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=14.2

Q ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1892           4 PLATSTVIGGAVVGLLCAILVVMFIVY   30 (64)
Q Consensus         4 ~~~~ag~IaG~VvGlv~ailLIlfli~   30 (64)
                      |.+.+|+++  +..++...+.+.+++.
T Consensus         8 ~sIaagVvg--lll~vii~l~~~~~iR   32 (35)
T 1iij_A            8 TFIIATVVG--VLLFLILVVVVGILIK   32 (35)
T ss_dssp             HHHHHHHHH--HHHHHHHTTTTTHHHH
T ss_pred             cEeHHHHHH--HHHHHHHHHHhheEEe
Confidence            445566665  5555555555555554

>2l35_A DAP12-NKG2C_TM; immunoreceptor, transmembrane assembly, DAP12-NKG2C complex; NMR {Homo sapiens}

Probab=82.88  E-value=0.78  Score=27.39  Aligned_cols=30  Identities=27%  Similarity=0.474  Sum_probs=24.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy1892           6 ATSTVIGGAVVGLLCAILVVMFIVYRMRKK   35 (64)
Q Consensus         6 ~~ag~IaG~VvGlv~ailLIlfli~r~rKK   35 (64)
                      +-.+.++|+++|=+++.+++.+.+|.+-|+
T Consensus         4 Ld~~tvaGIIv~DIi~TllLal~VY~~A~~   33 (63)
T 2l35_A            4 VSPGVLAGIVVGDLVLTVLIALAVYFLGRL   33 (63)
T ss_dssp             SCCSHHHHHHHHHHHHHHHHHHHHHHHCCS
T ss_pred             ccchheehhHHHHHHHHHHHHHHHHhhccc
Confidence            345778999999999999999999986654

>2l6w_A Beta-type platelet-derived growth factor receptor; transmembrane helix, receptor tyrosine kinase, heptad repeat membrane protein; NMR {Homo sapiens}

Probab=82.32  E-value=0.3  Score=26.88  Aligned_cols=26  Identities=15%  Similarity=0.323  Sum_probs=10.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy1892          11 IGGAVVGLLCAILVVMFIVYRMRKKD   36 (64)
Q Consensus        11 IaG~VvGlv~ailLIlfli~r~rKKd   36 (64)
                      ++|+++-++.-++.++.+++.++||.
T Consensus        11 l~avlal~vi~iisLIiLi~~w~qKP   36 (39)
T 2l6w_A           11 ISAILALVVLTIISLIILIMLWQKKP   36 (39)
Confidence            34444444444333333333335554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00