Citrus Sinensis ID: 047723

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------8
Protein Sequence
ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDELEVELGLRD
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccHHHEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHcccc
Coil and Loop (DISEMBL)
isndssstkkgkqsaahhtsrsntgaKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDELEVELGLRD
Flexible Loop (DISEMBL)
isndssstkkgkqsaahhtsrsntgaKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLklfeeddelevelglrd
Low Complexity Region (SEG)
ISNDSSSTKKGKQSAAHHTSRSNTGAKvgiillglvavglFSFFLFKLWQKKKREEQYARllklfeeddelevelglrd
Disordered region (IsUnstruct)
*************************AKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFE*************
Disordered Region (DISOPRED)
**************************KVGIILLGLVAVGLFSFFLFKLWQ*********RLLKLFEEDDELEVELGL**
Disordered Region (DISEMBL)
**********************NTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDE*********
Disordered Region (DISPRO)
***********************TGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDELEVELGLR*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDELEVELGLRD
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

No hits with e-value below 0.001 by BLAST

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	79
356526441	105	PREDICTED: uncharacterized protein LOC10	1.0	0.752	0.620	8e-21
359493474	111	PREDICTED: uncharacterized protein LOC10	1.0	0.711	0.607	4e-19
296089426	110	unnamed protein product [Vitis vinifera]	1.0	0.718	0.607	4e-19
357470405	106	hypothetical protein MTR_4g032200 [Medic	0.974	0.726	0.584	2e-18
449447605	107	PREDICTED: uncharacterized protein LOC10	1.0	0.738	0.6	1e-17
297604523	107	Os05g0419600 [Oryza sativa Japonica Grou	0.949	0.700	0.607	1e-17
53982668	106	unknown protein [Oryza sativa Japonica G	0.949	0.707	0.607	2e-17
224145111	104	predicted protein [Populus trichocarpa]	0.974	0.740	0.556	2e-16
224129730	105	predicted protein [Populus trichocarpa]	1.0	0.752	0.645	4e-16
297843764	105	hypothetical protein ARALYDRAFT_888210 [	0.987	0.742	0.721	5e-16

>gi|356526441|ref|XP_003531826.1| PREDICTED: uncharacterized protein LOC100803193 [Glycine max]

 Score =  104 bits (259), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 49/79 (62%), Positives = 59/79 (74%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYAR 60
           + N+ S  K   +   HH SRS+ G K+ II LG+V V  F  FLFKLWQ+KKREEQ+AR
Sbjct: 27  LDNNPSGAKNENKDVNHHASRSSVGLKIIIIFLGVVTVIAFCVFLFKLWQRKKREEQHAR 86

Query: 61  LLKLFEEDDELEVELGLRD 79
           LLKLFE+DDELEVELG+RD
Sbjct: 87  LLKLFEDDDELEVELGMRD 105

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493474|ref|XP_003634607.1| PREDICTED: uncharacterized protein LOC100854818 isoform 1 [Vitis vinifera] gi|359493476|ref|XP_003634608.1| PREDICTED: uncharacterized protein LOC100854818 isoform 2 [Vitis vinifera]

 Score = 98.6 bits (244), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 62/79 (78%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYAR 60
           +++D S++K  K++  H T  +  G ++ II LGLVA   FS FLFK+WQKKKREEQ+AR
Sbjct: 33  LADDPSNSKDVKKAERHDTHGNMIGIRIVIICLGLVAGAAFSVFLFKIWQKKKREEQHAR 92

Query: 61  LLKLFEEDDELEVELGLRD 79
           LLKLFE+DDELEVELG+RD
Sbjct: 93  LLKLFEDDDELEVELGIRD 111

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089426|emb|CBI39245.3| unnamed protein product [Vitis vinifera]

 Score = 98.6 bits (244), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 62/79 (78%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYAR 60
           +++D S++K  K++  H T  +  G ++ II LGLVA   FS FLFK+WQKKKREEQ+AR
Sbjct: 32  LADDPSNSKDVKKAERHDTHGNMIGIRIVIICLGLVAGAAFSVFLFKIWQKKKREEQHAR 91

Query: 61  LLKLFEEDDELEVELGLRD 79
           LLKLFE+DDELEVELG+RD
Sbjct: 92  LLKLFEDDDELEVELGIRD 110

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357470405|ref|XP_003605487.1| hypothetical protein MTR_4g032200 [Medicago truncatula] gi|355506542|gb|AES87684.1| hypothetical protein MTR_4g032200 [Medicago truncatula] gi|388501530|gb|AFK38831.1| unknown [Medicago truncatula]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/77 (58%), Positives = 60/77 (77%)

Query: 3   NDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLL 62
           N++S +KK  +  + H S  + G K+ I+ +G++AV  F  FLFKLWQ+KKREEQ+ARLL
Sbjct: 30  NNTSDSKKENKDVSAHVSSGSAGLKILIVFVGVLAVIAFGVFLFKLWQRKKREEQHARLL 89

Query: 63  KLFEEDDELEVELGLRD 79
           KLFE+DDELEVELG+RD
Sbjct: 90  KLFEDDDELEVELGMRD 106

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447605|ref|XP_004141558.1| PREDICTED: uncharacterized protein LOC101207831 [Cucumis sativus]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 48/80 (60%), Positives = 61/80 (76%), Gaps = 1/80 (1%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNT-GAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYA 59
           ++ ++SS K G ++      RS + G K+ II LG+V V +FS  LFK+WQKKKREEQ+A
Sbjct: 28  LAKENSSAKDGGKTKKDDARRSPSMGIKILIICLGVVTVIIFSVILFKIWQKKKREEQHA 87

Query: 60  RLLKLFEEDDELEVELGLRD 79
           RLLKLFE+DDELEVELGLRD
Sbjct: 88  RLLKLFEDDDELEVELGLRD 107

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297604523|ref|NP_001055573.2| Os05g0419600 [Oryza sativa Japonica Group] gi|255676376|dbj|BAF17487.2| Os05g0419600 [Oryza sativa Japonica Group]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 62/79 (78%), Gaps = 4/79 (5%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYAR 60
           ++ D+ ++K  K++     S+ +TG  V I+LLG+ AV L SFFLFK WQKKKREEQ+AR
Sbjct: 33  LAGDTQTSKDDKKA----QSKGHTGRTVLIVLLGIGAVVLLSFFLFKYWQKKKREEQHAR 88

Query: 61  LLKLFEEDDELEVELGLRD 79
           LLKLFEEDD++EVELGLRD
Sbjct: 89  LLKLFEEDDDIEVELGLRD 107

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|53982668|gb|AAV25647.1| unknown protein [Oryza sativa Japonica Group] gi|125552373|gb|EAY98082.1| hypothetical protein OsI_20000 [Oryza sativa Indica Group] gi|215769439|dbj|BAH01668.1| unnamed protein product [Oryza sativa Japonica Group] gi|222631628|gb|EEE63760.1| hypothetical protein OsJ_18579 [Oryza sativa Japonica Group]

 Score = 93.2 bits (230), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 48/79 (60%), Positives = 62/79 (78%), Gaps = 4/79 (5%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYAR 60
           ++ D+ ++K  K++     S+ +TG  V I+LLG+ AV L SFFLFK WQKKKREEQ+AR
Sbjct: 32  LAGDTQTSKDDKKAQ----SKGHTGRTVLIVLLGIGAVVLLSFFLFKYWQKKKREEQHAR 87

Query: 61  LLKLFEEDDELEVELGLRD 79
           LLKLFEEDD++EVELGLRD
Sbjct: 88  LLKLFEEDDDIEVELGLRD 106

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224145111|ref|XP_002325530.1| predicted protein [Populus trichocarpa] gi|222862405|gb|EEE99911.1| predicted protein [Populus trichocarpa]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 44/79 (55%), Positives = 60/79 (75%), Gaps = 2/79 (2%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYAR 60
           +++D ++ K   + A+H  S+S+ G KV I  L +VA+  F+  L K+WQKKKREEQ+AR
Sbjct: 28  LASDPANPKDTNKPASH--SKSSVGIKVVIACLSVVAIIGFTMLLIKIWQKKKREEQHAR 85

Query: 61  LLKLFEEDDELEVELGLRD 79
           LLKLFE+DDELEVELG+RD
Sbjct: 86  LLKLFEDDDELEVELGIRD 104

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224129730|ref|XP_002328788.1| predicted protein [Populus trichocarpa] gi|222839086|gb|EEE77437.1| predicted protein [Populus trichocarpa]

 Score = 89.0 bits (219), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 51/79 (64%), Positives = 63/79 (79%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYAR 60
           IS+DSS  K G ++  H  S++N G ++ I+ + +VA+G F+ FLFK WQKKKREEQYAR
Sbjct: 27  ISDDSSGAKNGTKADPHAASKNNDGPEIAIVFVFVVAIGFFALFLFKFWQKKKREEQYAR 86

Query: 61  LLKLFEEDDELEVELGLRD 79
           LLKLFEEDDELEVELGLRD
Sbjct: 87  LLKLFEEDDELEVELGLRD 105

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843764|ref|XP_002889763.1| hypothetical protein ARALYDRAFT_888210 [Arabidopsis lyrata subsp. lyrata] gi|297335605|gb|EFH66022.1| hypothetical protein ARALYDRAFT_888210 [Arabidopsis lyrata subsp. lyrata]

 Score = 88.2 bits (217), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 57/79 (72%), Positives = 65/79 (82%), Gaps = 1/79 (1%)

Query: 1   ISNDSSSTKKGKQSAAHHTSRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYAR 60
           +S DS +T  G + A  HTS S TG KV +IL+G VAV +FSFFL+KLWQKKKR+EQYAR
Sbjct: 28  LSGDSKNTNAGVK-AESHTSSSKTGTKVILILVGFVAVAVFSFFLYKLWQKKKRDEQYAR 86

Query: 61  LLKLFEEDDELEVELGLRD 79
           LLKLFEEDDELEVELGLRD
Sbjct: 87  LLKLFEEDDELEVELGLRD 105

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

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	79
TAIR|locus:504956278	106	AT1G09645 "AT1G09645" [Arabido	0.746	0.556	0.5	3.2e-10

TAIR|locus:504956278 AT1G09645 "AT1G09645" [Arabidopsis thaliana (taxid:3702)]

 Score = 145 (56.1 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 30/60 (50%), Positives = 37/60 (61%)

Query:     1 ISNDSSSTKKGKQSAAHHTSRSNTGAKXXXXXXXXXXXXXFSFFLFKLWQKKKREEQYAR 60
             +S DS +T  G ++ +H TS S TG K             FSFFL+KLWQKKKR+EQYAR
Sbjct:    29 LSGDSKNTNAGVKTESH-TSSSKTGTKVILVLVGFVAVAMFSFFLYKLWQKKKRDEQYAR 87


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.311   0.119   0.335    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       79        47   0.00091  102 3  10 23  0.47    26
                                                     29  0.47    25


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  519 (55 KB)
  Total size of DFA:  102 KB (2072 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.88u 0.09s 8.97t   Elapsed:  00:00:12
  Total cpu time:  8.88u 0.09s 8.97t   Elapsed:  00:00:13
  Start:  Thu May  9 14:01:15 2013   End:  Thu May  9 14:01:28 2013

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: 4338819 expressed protein (106 aa) (Oryza sativa Japonica)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	79
PF08114	43	PMP1_2: ATPase proteolipid family; InterPro: IPR01	99.21
PF08693	40	SKG6: Transmembrane alpha-helix domain; InterPro:	97.71
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	96.58
PF04689	69	S1FA: DNA binding protein S1FA; InterPro: IPR00677	96.46
PF06679	163	DUF1180: Protein of unknown function (DUF1180); In	95.89
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	95.53
PF14610	189	DUF4448: Protein of unknown function (DUF4448)	95.26
PF02404	273	SCF: Stem cell factor; InterPro: IPR003452 Stem ce	93.96
COG4736	60	CcoQ Cbb3-type cytochrome oxidase, subunit 3 [Post	93.9
PF10883	87	DUF2681: Protein of unknown function (DUF2681); In	93.82
PF06365	202	CD34_antigen: CD34/Podocalyxin family; InterPro: I	93.81
PF00558	81	Vpu: Vpu protein; InterPro: IPR008187 The Human im	93.45
PHA03265	402	envelope glycoprotein D; Provisional	93.07
PF12669	58	P12: Virus attachment protein p12 family	92.67
PF15345	233	TMEM51: Transmembrane protein 51	91.91
PF04478	154	Mid2: Mid2 like cell wall stress sensor; InterPro:	91.71
PF11669	102	WBP-1: WW domain-binding protein 1; InterPro: IPR0	91.53
KOG3839	351	consensus Lectin VIP36, involved in the transport	91.53
PF14981	51	FAM165: FAM165 family	90.75
PF05795	354	Plasmodium_Vir: Plasmodium vivax Vir protein; Inte	90.19
TIGR00739	84	yajC preprotein translocase, YajC subunit. While t	89.87
PRK00888	105	ftsB cell division protein FtsB; Reviewed	89.85
TIGR02797	211	exbB tonB-system energizer ExbB. This model descri	89.38
PF14316	146	DUF4381: Domain of unknown function (DUF4381)	89.27
PF10883	87	DUF2681: Protein of unknown function (DUF2681); In	89.23
PRK10414	244	biopolymer transport protein ExbB; Provisional	88.8
PF12301	169	CD99L2: CD99 antigen like protein 2; InterPro: IPR	88.78
PTZ00382	96	Variant-specific surface protein (VSP); Provisiona	88.78
PF02009	299	Rifin_STEVOR: Rifin/stevor family; InterPro: IPR00	88.57
PF05545	49	FixQ: Cbb3-type cytochrome oxidase component FixQ;	88.47
PF06864	414	PAP_PilO: Pilin accessory protein (PilO); InterPro	88.0
PF14316	146	DUF4381: Domain of unknown function (DUF4381)	87.9
PF05283	186	MGC-24: Multi-glycosylated core protein 24 (MGC-24	87.28
PF06024	101	DUF912: Nucleopolyhedrovirus protein of unknown fu	87.15
PRK05585	106	yajC preprotein translocase subunit YajC; Validate	86.74
PRK10506	162	hypothetical protein; Provisional	86.6
PRK10801	227	colicin uptake protein TolQ; Provisional	85.72
PF06305	68	DUF1049: Protein of unknown function (DUF1049); In	85.66
PRK05886	109	yajC preprotein translocase subunit YajC; Validate	85.57
PRK01844	72	hypothetical protein; Provisional	85.56
PF02480	439	Herpes_gE: Alphaherpesvirus glycoprotein E; InterP	85.42
PF02699	82	YajC: Preprotein translocase subunit; InterPro: IP	84.44
PF07010	259	Endomucin: Endomucin; InterPro: IPR010740 This fam	84.3
PF06295	128	DUF1043: Protein of unknown function (DUF1043); In	84.3
PF01034	64	Syndecan: Syndecan domain; InterPro: IPR001050 The	84.03
PF10855	33	DUF2648: Protein of unknown function (DUF2648); In	83.5
PF12072	201	DUF3552: Domain of unknown function (DUF3552); Int	83.22
KOG3054	299	consensus Uncharacterized conserved protein [Funct	83.14
KOG4550	606	consensus Predicted membrane protein [Function unk	83.05
PLN03150	623	hypothetical protein; Provisional	82.65
PF01299	306	Lamp: Lysosome-associated membrane glycoprotein (L	82.65
KOG3839	351	consensus Lectin VIP36, involved in the transport	82.59
PF05454	290	DAG1: Dystroglycan (Dystrophin-associated glycopro	82.51
PF15102	146	TMEM154: TMEM154 protein family	82.48
PF13908	179	Shisa: Wnt and FGF inhibitory regulator	82.28
COG2165	149	PulG Type II secretory pathway, pseudopilin PulG [	82.04
PF02009	299	Rifin_STEVOR: Rifin/stevor family; InterPro: IPR00	81.96
PRK00523	72	hypothetical protein; Provisional	81.76
PF14283	218	DUF4366: Domain of unknown function (DUF4366)	81.7
PF12877	684	DUF3827: Domain of unknown function (DUF3827); Int	81.53
PF11368	248	DUF3169: Protein of unknown function (DUF3169); In	81.25
PF00558	81	Vpu: Vpu protein; InterPro: IPR008187 The Human im	81.25
PF03229	126	Alpha_GJ: Alphavirus glycoprotein J; InterPro: IPR	80.28

>PF08114 PMP1_2: ATPase proteolipid family; InterPro: IPR012589 This family consists of small proteolipids associated with the plasma membrane H+ ATPase

Probab=99.21  E-value=2.3e-11  Score=72.82  Aligned_cols=36  Identities=33%  Similarity=0.720  Sum_probs=33.9

Q ss_pred             CCCceEehhHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 047723           23 NTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQY   58 (79)
Q Consensus        23 ~tgv~VviIl~vlv~v~l~~~~lYK~WQKKKREeQ~   58 (79)
                      ..||+++++++++++|+++++|+||+||+|||..|+
T Consensus         7 p~GVIlVF~lVglv~i~iva~~iYRKw~aRkr~l~r   42 (43)
T PF08114_consen    7 PGGVILVFCLVGLVGIGIVALFIYRKWQARKRALQR   42 (43)
T ss_pred             CCCeeeehHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            478999999999999999999999999999999885

Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast. No modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear [].

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

Probab=97.71  E-value=7.7e-06  Score=48.14  Aligned_cols=30  Identities=27%  Similarity=0.435  Sum_probs=26.6

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKK   53 (79)
                      ..+.+.+++++.++++++++|+|..|+|+|
T Consensus        11 vaIa~~VvVPV~vI~~vl~~~l~~~~rR~k   40 (40)
T PF08693_consen   11 VAIAVGVVVPVGVIIIVLGAFLFFWYRRKK   40 (40)
T ss_pred             EEEEEEEEechHHHHHHHHHHhheEEeccC
Confidence            668888999999999999999999998876

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 [].

>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=96.58  E-value=0.0023  Score=44.63  Aligned_cols=47  Identities=26%  Similarity=0.385  Sum_probs=21.3

Q ss_pred             cCCCCceEehhHHHHH-HHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcch
Q 047723           21 RSNTGAKVGIILLGLV-AVGLFSFFLFKLWQKKKREEQYARLLKLFEEDD   69 (79)
Q Consensus        21 ~~~tgv~VviIl~vlv-~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedD   69 (79)
                      +...+.+..||+-|++ ++++++++.|-.+|+|||..-...-  +.++||
T Consensus        60 ~fs~~~i~~Ii~gv~aGvIg~Illi~y~irR~~Kk~~~~~~p--~P~~~d  107 (122)
T PF01102_consen   60 RFSEPAIIGIIFGVMAGVIGIILLISYCIRRLRKKSSSDVQP--LPEEDD  107 (122)
T ss_dssp             SSS-TCHHHHHHHHHHHHHHHHHHHHHHHHHHS-----------------
T ss_pred             CccccceeehhHHHHHHHHHHHHHHHHHHHHHhccCCCCCCC--CCCCCC
Confidence            3435555555555555 5666688899999999886332222  677733

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.

>PF04689 S1FA: DNA binding protein S1FA; InterPro: IPR006779 S1FA is an unusual small plant peptide of only 70 amino acids with a basic domain which contains a nuclear localization signal and a putative DNA binding helix

Probab=96.46  E-value=0.0056  Score=39.89  Aligned_cols=33  Identities=24%  Similarity=0.313  Sum_probs=27.1

Q ss_pred             cccCCCCceEehhHHHHH-HHHHHHHHHHHHHHH
Q 047723           19 TSRSNTGAKVGIILLGLV-AVGLFSFFLFKLWQK   51 (79)
Q Consensus        19 ~~~~~tgv~VviIl~vlv-~v~l~~~~lYK~WQK   51 (79)
                      +.+-|-|.+|++++.+++ ++.++.+++|-||||
T Consensus         7 ~KGlnPGlIVLlvV~g~ll~flvGnyvlY~Yaqk   40 (69)
T PF04689_consen    7 AKGLNPGLIVLLVVAGLLLVFLVGNYVLYVYAQK   40 (69)
T ss_pred             ccCCCCCeEEeehHHHHHHHHHHHHHHHHHHHhh
Confidence            367788999988888887 556668999999997

S1FA is highly conserved between dicotyledonous and monocotyledonous plants and may be a DNA-binding protein that specifically recognises the negative promoter element S1F [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins

Probab=95.89  E-value=0.0085  Score=43.56  Aligned_cols=27  Identities=11%  Similarity=0.337  Sum_probs=16.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhHHHH
Q 047723           30 IILLGLVAVGLFSFFLFKLWQKKKREE   56 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQKKKREe   56 (79)
                      +++++.+..++++.|++|.||=|||..
T Consensus        98 ~~Vl~g~s~l~i~yfvir~~R~r~~~r  124 (163)
T PF06679_consen   98 LYVLVGLSALAILYFVIRTFRLRRRNR  124 (163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccccc
Confidence            344444455556667889998777543

Their function is unknown.

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.53  E-value=0.022  Score=43.24  Aligned_cols=34  Identities=32%  Similarity=0.558  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHH------HHHHHHhhh
Q 047723           32 LLGLVAVGLFSFFLFKLWQKKKREE------QYARLLKLF   65 (79)
Q Consensus        32 l~vlv~v~l~~~~lYK~WQKKKREe------Q~AR~lkLF   65 (79)
                      +++.++++++++|.|+|||.++-++      +|+-+++.-
T Consensus        25 li~gviLg~~~lfGW~ywq~~q~~q~~~AS~~Y~~~i~~~   64 (207)
T COG2976          25 LIVGVILGLGGLFGWRYWQSHQVEQAQEASAQYQNAIKAV   64 (207)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445577778899999999999986      455555544

>PF14610 DUF4448: Protein of unknown function (DUF4448)

Probab=95.26  E-value=0.012  Score=41.63  Aligned_cols=31  Identities=29%  Similarity=0.421  Sum_probs=25.6

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhHH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKKR   54 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKKR   54 (79)
                      ....++|.|+++++++++++.++=+|.||+|
T Consensus       156 ~~~~laI~lPvvv~~~~~~~~~~~~~~R~~R  186 (189)
T PF14610_consen  156 GKYALAIALPVVVVVLALIMYGFFFWNRKKR  186 (189)
T ss_pred             cceeEEEEccHHHHHHHHHHHhhheeeccce
Confidence            3458999999999888888888888887776

>PF02404 SCF: Stem cell factor; InterPro: IPR003452 Stem cell factor (SCF) is a homodimer involved in hematopoiesis

Probab=93.96  E-value=0.016  Score=45.70  Aligned_cols=29  Identities=31%  Similarity=0.350  Sum_probs=0.0

Q ss_pred             hhHHHHH-HHHHHHHHHHHHHHHhHHHHHHH
Q 047723           30 IILLGLV-AVGLFSFFLFKLWQKKKREEQYA   59 (79)
Q Consensus        30 iIl~vlv-~v~l~~~~lYK~WQKKKREeQ~A   59 (79)
                      ++++.++ .+++|++++. ||.||+|++.++
T Consensus       218 iAL~sl~SLVIGFvlG~l-~WKkkq~~~~~~  247 (273)
T PF02404_consen  218 IALPSLFSLVIGFVLGAL-YWKKKQRSLTQE  247 (273)
T ss_dssp             -------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHH-HHHhhccccccc
Confidence            3344444 3444444444 999999966554

SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. SCF stimulates the proliferation of mast cells and is able to augment the proliferation of both myeloid and lymphoid hematopoietic progenitors in bone marrow culture. It also mediates cell-cell adhesion and acts synergistically with other cytokines. SCF is a type I membrane protein, but is also found in a secretable, soluble form. The crystal structure of human SCF has been resolved and a potential receptor-binding site identified [].; GO: 0005173 stem cell factor receptor binding, 0007155 cell adhesion, 0016020 membrane; PDB: 1EXZ_A 1SCF_D 2E9W_C 2O26_A 2O27_A.

>COG4736 CcoQ Cbb3-type cytochrome oxidase, subunit 3 [Posttranslational modification, protein turnover, chaperones]

Probab=93.90  E-value=0.094  Score=33.00  Aligned_cols=39  Identities=18%  Similarity=0.162  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcchhhhhhhC
Q 047723           37 AVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDELEVELG   76 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedDdle~ELG   76 (79)
                      .+...+++.|=||.+||.+-++|+-. .|..+||.+++.|
T Consensus        19 ~l~fiavi~~ayr~~~K~~~d~aa~~-~l~l~Dd~q~~~~   57 (60)
T COG4736          19 TLFFIAVIYFAYRPGKKGEFDEAARG-ILPLNDDAQDAAG   57 (60)
T ss_pred             HHHHHHHHHHHhcccchhhHHHHhcc-CCCCCcchhhhhc
Confidence            33444667788899999899998753 3677888888876

>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function

Probab=93.82  E-value=0.22  Score=33.17  Aligned_cols=14  Identities=21%  Similarity=0.563  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHhHH
Q 047723           41 FSFFLFKLWQKKKR   54 (79)
Q Consensus        41 ~~~~lYK~WQKKKR   54 (79)
                      ++.+.||.||.+++
T Consensus        18 ~~y~~~k~~ka~~~   31 (87)
T PF10883_consen   18 LAYLWWKVKKAKKQ   31 (87)
T ss_pred             HHHHHHHHHHHHHH
Confidence            33444444444443

>PF06365 CD34_antigen: CD34/Podocalyxin family; InterPro: IPR013836 This family consists of several mammalian CD34 antigen proteins

Probab=93.81  E-value=0.093  Score=39.40  Aligned_cols=37  Identities=8%  Similarity=0.123  Sum_probs=24.9

Q ss_pred             CCceEehhHHH-HHHHHHHHHHHHHHHHHhHHHHHHHH
Q 047723           24 TGAKVGIILLG-LVAVGLFSFFLFKLWQKKKREEQYAR   60 (79)
Q Consensus        24 tgv~VviIl~v-lv~v~l~~~~lYK~WQKKKREeQ~AR   60 (79)
                      +++.|++++++ ++.+|++++.+|-.||||---..+.|
T Consensus        99 ~~~lI~lv~~g~~lLla~~~~~~Y~~~~Rrs~~~~~~r  136 (202)
T PF06365_consen   99 YPTLIALVTSGSFLLLAILLGAGYCCHQRRSWSKKGQR  136 (202)
T ss_pred             ceEEEehHHhhHHHHHHHHHHHHHHhhhhccCCcchhh
Confidence            56777777777 23566667778999999864333334

The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation [, ]. This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteristic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an anti-adhesin that maintains an open filtration pathway between neighbouring foot processes in the glomerular epithelium by charge repulsion [].

>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells []

Probab=93.45  E-value=0.048  Score=36.13  Aligned_cols=26  Identities=19%  Similarity=0.321  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHHh
Q 047723           38 VGLFSFFLFKLWQKKKREEQYARLLK   63 (79)
Q Consensus        38 v~l~~~~lYK~WQKKKREeQ~AR~lk   63 (79)
                      .+++-++.|+.|+|-||++.--|+++
T Consensus        19 aIvvW~iv~ieYrk~~rqrkId~li~   44 (81)
T PF00558_consen   19 AIVVWTIVYIEYRKIKRQRKIDRLIE   44 (81)
T ss_dssp             HHHHHHHH------------CHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            33445667888888888765555554

; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.

>PHA03265 envelope glycoprotein D; Provisional

Probab=93.07  E-value=0.12  Score=42.73  Aligned_cols=38  Identities=24%  Similarity=0.270  Sum_probs=23.9

Q ss_pred             ccCCCCceEehhHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 047723           20 SRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQ   57 (79)
Q Consensus        20 ~~~~tgv~VviIl~vlv~v~l~~~~lYK~WQKKKREeQ   57 (79)
                      |+||..-+=++|=.+++.+++++.|||-.|++||-...
T Consensus       343 s~~~~~~~g~~ig~~i~glv~vg~il~~~~rr~k~~~k  380 (402)
T PHA03265        343 SKSNSTFVGISVGLGIAGLVLVGVILYVCLRRKKELKK  380 (402)
T ss_pred             CCCCCcccceEEccchhhhhhhhHHHHHHhhhhhhhhh
Confidence            44433333334445555667778889999999985443

>PF12669 P12: Virus attachment protein p12 family

Probab=92.67  E-value=0.16  Score=31.12  Aligned_cols=12  Identities=25%  Similarity=0.307  Sum_probs=9.1

Q ss_pred             HHHHHHHHhHHH
Q 047723           44 FLFKLWQKKKRE   55 (79)
Q Consensus        44 ~lYK~WQKKKRE   55 (79)
                      +++++|+++|+.
T Consensus        16 ~~r~~~k~~K~G   27 (58)
T PF12669_consen   16 AIRKFIKDKKKG   27 (58)
T ss_pred             HHHHHHHHhhcC
Confidence            359999888864

>PF15345 TMEM51: Transmembrane protein 51

Probab=91.91  E-value=0.43  Score=36.90  Aligned_cols=36  Identities=17%  Similarity=0.209  Sum_probs=21.6

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYA   59 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKKREeQ~A   59 (79)
                      ....|+++|+|..+..++.-+.-..=+||||.++.+
T Consensus        56 Kt~SVAyVLVG~Gv~LLLLSICL~IR~KRr~rq~~e   91 (233)
T PF15345_consen   56 KTFSVAYVLVGSGVALLLLSICLSIRDKRRRRQGEE   91 (233)
T ss_pred             eeEEEEEehhhHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            446788888887655555444555666666554433

>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=91.71  E-value=0.032  Score=40.78  Aligned_cols=19  Identities=11%  Similarity=0.139  Sum_probs=11.6

Q ss_pred             HHHHHHHHHHHHHHHhHHH
Q 047723           37 AVGLFSFFLFKLWQKKKRE   55 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKRE   55 (79)
                      ++++++.++|-+|.|+||.
T Consensus        62 ill~il~lvf~~c~r~kkt   80 (154)
T PF04478_consen   62 ILLGILALVFIFCIRRKKT   80 (154)
T ss_pred             HHHHHHHhheeEEEecccC
Confidence            4555566667776666653

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 [].

>PF11669 WBP-1: WW domain-binding protein 1; InterPro: IPR021684 This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein

Probab=91.53  E-value=0.4  Score=32.01  Aligned_cols=24  Identities=17%  Similarity=0.189  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHH
Q 047723           37 AVGLFSFFLFKLWQKKKREEQYAR   60 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKREeQ~AR   60 (79)
                      ++++...-+|++|++|.|-++|-|
T Consensus        31 iill~c~c~~~~~r~r~~~~~q~r   54 (102)
T PF11669_consen   31 IILLSCCCACRHRRRRRRLQQQQR   54 (102)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhhhc
Confidence            333456678999998877766555

This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain [].

>KOG3839 consensus Lectin VIP36, involved in the transport of glycoproteins carrying high mannose-type glycans [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.53  E-value=0.035  Score=45.01  Aligned_cols=26  Identities=27%  Similarity=0.478  Sum_probs=12.0

Q ss_pred             eEehhHHHHH---HHHHHHHHHHHHHHHh
Q 047723           27 KVGIILLGLV---AVGLFSFFLFKLWQKK   52 (79)
Q Consensus        27 ~VviIl~vlv---~v~l~~~~lYK~WQKK   52 (79)
                      ...+++.+++   +++++++..|++||.|
T Consensus       317 ~~~ill~~vv~~v~~ai~s~~i~q~r~er  345 (351)
T KOG3839|consen  317 LFLILLFVVVFLVGGAIFSIVIFQVRQER  345 (351)
T ss_pred             hHHHHHHHHHHHHHhhheEEEEEeehhhh
Confidence            3334444444   4444455555555533

>PF14981 FAM165: FAM165 family

Probab=90.75  E-value=0.6  Score=28.91  Aligned_cols=24  Identities=21%  Similarity=0.364  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHH
Q 047723           37 AVGLFSFFLFKLWQKKKREEQYAR   60 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKREeQ~AR   60 (79)
                      .+.-++|..-|.||+|+-|+++.+
T Consensus        18 lilClaFAgvK~yQ~krlEak~~k   41 (51)
T PF14981_consen   18 LILCLAFAGVKMYQRKRLEAKLKK   41 (51)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHH
Confidence            444458889999999998877654

>PF05795 Plasmodium_Vir: Plasmodium vivax Vir protein; InterPro: IPR008780 This family consists of several Vir proteins specific to the genus Plasmodium and Plasmodium vivax in particular

Probab=90.19  E-value=0.2  Score=36.29  Aligned_cols=36  Identities=22%  Similarity=0.509  Sum_probs=23.7

Q ss_pred             hHHHHHHHHHHHHHHHH--HHHHhHHHHHHHHHHhhhh
Q 047723           31 ILLGLVAVGLFSFFLFK--LWQKKKREEQYARLLKLFE   66 (79)
Q Consensus        31 Il~vlv~v~l~~~~lYK--~WQKKKREeQ~AR~lkLFE   66 (79)
                      ..++++++.+++|++||  -|-+++|..-+.++-..++
T Consensus       287 ~~~~~~G~~~~~f~LYK~g~~~~~~~~r~~~~~~~~~~  324 (354)
T PF05795_consen  287 PVLSVLGIPLIFFLLYKFGSWFNRRRGRRRRIINNNFN  324 (354)
T ss_pred             hhhhhHHHHHHHHHHhccchhhcccccccccccccccc
Confidence            34445577778999999  6777777665555444444

The vir genes are present at about 600-1,000 copies per haploid genome and encode proteins that are immunovariant in natural infections, indicating that they may have a functional role in establishing chronic infection through antigenic variation [].

>TIGR00739 yajC preprotein translocase, YajC subunit

Probab=89.87  E-value=0.54  Score=30.39  Aligned_cols=32  Identities=19%  Similarity=0.501  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcchh
Q 047723           37 AVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDE   70 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedDd   70 (79)
                      +++++-|+++|  ..|||.++++.++.=...||+
T Consensus        12 ~~~i~yf~~~r--pqkK~~k~~~~m~~~L~~Gd~   43 (84)
T TIGR00739        12 IFLIFYFLIIR--PQRKRRKAHKKLIESLKKGDK   43 (84)
T ss_pred             HHHHHHHheec--hHHHHHHHHHHHHHhCCCCCE
Confidence            33344444443  344555666677766666654

While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.

>PRK00888 ftsB cell division protein FtsB; Reviewed

Probab=89.85  E-value=1.3  Score=29.65  Aligned_cols=15  Identities=27%  Similarity=0.873  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHHHH
Q 047723           35 LVAVGLFSFFLFKLW   49 (79)
Q Consensus        35 lv~v~l~~~~lYK~W   49 (79)
                      ++++++++++.|..|
T Consensus         6 ~vll~ll~~l~y~l~   20 (105)
T PRK00888          6 LLLLALLVWLQYSLW   20 (105)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            334444555566655

>TIGR02797 exbB tonB-system energizer ExbB

Probab=89.38  E-value=0.77  Score=33.42  Aligned_cols=44  Identities=23%  Similarity=0.262  Sum_probs=29.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcchhhhh
Q 047723           30 IILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDELEV   73 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedDdle~   73 (79)
                      +.++.++.++..+++++|+|+=++....-.+|++-|....++|.
T Consensus        17 m~~Ll~~Si~s~aiiieR~~~~~~~~~~~~~~~~~~~~~~~~~~   60 (211)
T TIGR02797        17 MIGLALASVVTWTIWIAKSVELAGARRRLKRALKALGEARTLAE   60 (211)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhCCCHHH
Confidence            33344445666788899999887766666778887766555443

This model describes ExbB proteins, part of the MotA/TolQ/ExbB protein family. The paired proteins MotA and MotB, TolQ and TolR, and ExbB and ExbD harness the proton-motive force to drive the flagellar motor, energize the Tol-Pal system, or energize TonB, respectively. Tol-Pal and TonB are both active at the outer membrane. Genomes may have many different TonB-dependent receptors, of which many of those characterized are involved in siderophore transport across the outer membrane.

>PF14316 DUF4381: Domain of unknown function (DUF4381)

Probab=89.27  E-value=1.1  Score=30.54  Aligned_cols=16  Identities=19%  Similarity=0.578  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHHHHHHh
Q 047723           37 AVGLFSFFLFKLWQKK   52 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKK   52 (79)
                      +++++++..|+.||++
T Consensus        33 ~~~~~~~~~~r~~~~~   48 (146)
T PF14316_consen   33 LLILLLWRLWRRWRRN   48 (146)
T ss_pred             HHHHHHHHHHHHHHcc
Confidence            3444455555555554

>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function

Probab=89.23  E-value=1.1  Score=29.84  Aligned_cols=31  Identities=26%  Similarity=0.431  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 047723           32 LLGLVAVGLFSFFLFKLWQKKKREEQYARLL   62 (79)
Q Consensus        32 l~vlv~v~l~~~~lYK~WQKKKREeQ~AR~l   62 (79)
                      +++.++.+++++++|-+||-+|-.++-++|.
T Consensus         6 iv~~~~~v~~~i~~y~~~k~~ka~~~~~kL~   36 (87)
T PF10883_consen    6 IVGGVGAVVALILAYLWWKVKKAKKQNAKLQ   36 (87)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566677999999999999888755543

>PRK10414 biopolymer transport protein ExbB; Provisional

Probab=88.80  E-value=0.88  Score=34.42  Aligned_cols=45  Identities=22%  Similarity=0.217  Sum_probs=30.4

Q ss_pred             ehhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcchhhhh
Q 047723           29 GIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDELEV   73 (79)
Q Consensus        29 viIl~vlv~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedDdle~   73 (79)
                      ++.+++++.++..+++++|+|+=++-.....++++.|..-.+++.
T Consensus        26 Vm~~Ll~~Si~swaiIieR~~~l~~~~~~~~~~~~~~~~~~~l~~   70 (244)
T PRK10414         26 VMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQLLAEARSLDQ   70 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHH
Confidence            344444446666688999999987766665788888766555443

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

Probab=88.78  E-value=0.81  Score=33.44  Aligned_cols=29  Identities=24%  Similarity=0.204  Sum_probs=19.7

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKK   53 (79)
                      +|++. =|++++++.++.++--|--+||||
T Consensus       114 ~g~Ia-GIvsav~valvGAvsSyiaYqkKK  142 (169)
T PF12301_consen  114 AGTIA-GIVSAVVVALVGAVSSYIAYQKKK  142 (169)
T ss_pred             cchhh-hHHHHHHHHHHHHHHHHHHHHhhc
Confidence            44433 444666666667777888889998

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.

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

Probab=88.78  E-value=0.13  Score=34.08  Aligned_cols=34  Identities=29%  Similarity=0.343  Sum_probs=17.7

Q ss_pred             ccCCCCceEehhHHHHH-HHHHHHHHHHHHHHHhH
Q 047723           20 SRSNTGAKVGIILLGLV-AVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        20 ~~~~tgv~VviIl~vlv-~v~l~~~~lYK~WQKKK   53 (79)
                      ++.++|.+..|.+-+++ +.++++|+.|-++.|||
T Consensus        61 ~~ls~gaiagi~vg~~~~v~~lv~~l~w~f~~r~k   95 (96)
T PTZ00382         61 SGLSTGAIAGISVAVVAVVGGLVGFLCWWFVCRGK   95 (96)
T ss_pred             CCcccccEEEEEeehhhHHHHHHHHHhheeEEeec
Confidence            34446776666665444 33444555555554443

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

Probab=88.57  E-value=0.61  Score=36.58  Aligned_cols=26  Identities=27%  Similarity=0.508  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHH-----HhHHHHHHHHHH
Q 047723           37 AVGLFSFFLFKLWQ-----KKKREEQYARLL   62 (79)
Q Consensus        37 ~v~l~~~~lYK~WQ-----KKKREeQ~AR~l   62 (79)
                      +++++.+|+|-.||     |+|+-+||-.||
T Consensus       267 iIVLIMvIIYLILRYRRKKKmkKKlQYiKLL  297 (299)
T PF02009_consen  267 IIVLIMVIIYLILRYRRKKKMKKKLQYIKLL  297 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhHHHHHHHHh
Confidence            44444555555553     223445555444

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 [].

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

Probab=88.47  E-value=0.67  Score=26.78  Aligned_cols=28  Identities=18%  Similarity=0.197  Sum_probs=18.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHH
Q 047723           35 LVAVGLFSFFLFKLWQKKKREEQYARLL   62 (79)
Q Consensus        35 lv~v~l~~~~lYK~WQKKKREeQ~AR~l   62 (79)
                      +..++.++.+.|-+|.++|+.-+.|.-|
T Consensus        17 ~~~~~F~gi~~w~~~~~~k~~~e~aa~l   44 (49)
T PF05545_consen   17 LFFVFFIGIVIWAYRPRNKKRFEEAANL   44 (49)
T ss_pred             HHHHHHHHHHHHHHcccchhhHHHHHcc
Confidence            3344445667888898877666666544

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 [].

>PF06864 PAP_PilO: Pilin accessory protein (PilO); InterPro: IPR009663 This family consists of several enterobacterial PilO proteins

Probab=88.00  E-value=0.83  Score=36.00  Aligned_cols=24  Identities=25%  Similarity=0.427  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHH
Q 047723           35 LVAVGLFSFFLFKLWQKKKREEQY   58 (79)
Q Consensus        35 lv~v~l~~~~lYK~WQKKKREeQ~   58 (79)
                      ++++++++...|.+||..++++++
T Consensus       172 ~~~~~~~~~~g~~~~~~~~~~~~~  195 (414)
T PF06864_consen  172 LVVLALAGGYGWWYWQAQQEEARR  195 (414)
T ss_pred             HHHHHHHHHHHHHHhhhhhhHHHH
Confidence            334445567788899876544333

The function of PilO is unknown although it has been suggested that it is a cytoplasmic protein in the absence of other Pil proteins, but PilO protein is translocated to the outer membrane in the presence of other Pil proteins. Alternatively, PilO protein may form a complex with other Pil protein(s). PilO has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body []. This family does not seem to be related to IPR007445 from INTERPRO.

>PF14316 DUF4381: Domain of unknown function (DUF4381)

Probab=87.90  E-value=1.4  Score=29.99  Aligned_cols=36  Identities=22%  Similarity=0.424  Sum_probs=25.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhh
Q 047723           31 ILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFE   66 (79)
Q Consensus        31 Il~vlv~v~l~~~~lYK~WQKKKREeQ~AR~lkLFE   66 (79)
                      -++.+++++++++++|+.|+++||-.-+..-|+.+.
T Consensus        24 wll~~lll~~~~~~~~~~~r~~~~~~yrr~Al~~L~   59 (146)
T PF14316_consen   24 WLLLALLLLLLILLLWRLWRRWRRNRYRREALRELA   59 (146)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHH
Confidence            445556888889999999999998754444444443

>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=87.28  E-value=0.9  Score=33.75  Aligned_cols=20  Identities=35%  Similarity=0.560  Sum_probs=12.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHH
Q 047723           30 IILLGLVAVGLFSFFLFKLWQ   50 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQ   50 (79)
                      =|+++|.++ .++||+||||+
T Consensus       166 GIVL~LGv~-aI~ff~~KF~k  185 (186)
T PF05283_consen  166 GIVLTLGVL-AIIFFLYKFCK  185 (186)
T ss_pred             HHHHHHHHH-HHHHHHhhhcc
Confidence            344445433 34677999986

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.

>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins

Probab=87.15  E-value=0.86  Score=30.12  Aligned_cols=23  Identities=22%  Similarity=0.436  Sum_probs=11.1

Q ss_pred             CCceEehhHHHHHHHHHHHHHHH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLF   46 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lY   46 (79)
                      .+.+++++++++++++++..++|
T Consensus        60 ~~~iili~lls~v~IlVily~Iy   82 (101)
T PF06024_consen   60 NGNIILISLLSFVCILVILYAIY   82 (101)
T ss_pred             cccchHHHHHHHHHHHHHHhhhe
Confidence            34455555555554444444444

>PRK05585 yajC preprotein translocase subunit YajC; Validated

Probab=86.74  E-value=1.4  Score=29.70  Aligned_cols=32  Identities=22%  Similarity=0.536  Sum_probs=15.7

Q ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcchh
Q 047723           37 AVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDE   70 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedDd   70 (79)
                      +++++-|+++|-  .|||+++++.++.=..-+|+
T Consensus        27 i~~i~yf~~~Rp--qkK~~k~~~~~~~~Lk~Gd~   58 (106)
T PRK05585         27 FFAIFYFLIIRP--QQKRQKEHKKMLSSLAKGDE   58 (106)
T ss_pred             HHHHHHHHhccH--HHHHHHHHHHHHHhcCCCCE
Confidence            333444445442  34444555666665555554

>PRK10506 hypothetical protein; Provisional

Probab=86.60  E-value=1.8  Score=30.08  Aligned_cols=42  Identities=21%  Similarity=0.359  Sum_probs=25.3

Q ss_pred             CCceEehhHHHHH---HHHHHHHHHHHHHHHhHHHHHHHHHHhhh
Q 047723           24 TGAKVGIILLGLV---AVGLFSFFLFKLWQKKKREEQYARLLKLF   65 (79)
Q Consensus        24 tgv~VviIl~vlv---~v~l~~~~lYK~WQKKKREeQ~AR~lkLF   65 (79)
                      .|-.++=++++++   +++.+++-.|.-|+.+.|-++.++-+.-|
T Consensus         9 ~GFTLiEllvvl~Ii~il~~~a~p~~~~~~~~~~~~~~~~~l~~~   53 (162)
T PRK10506          9 RGYTLIELLVVMTIVSILSAWGLYGWQRWQQRQRLWQTAQQLLDF   53 (162)
T ss_pred             CCeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4544443333333   44455556667777888888888777654

>PRK10801 colicin uptake protein TolQ; Provisional

Probab=85.72  E-value=1.6  Score=32.51  Aligned_cols=39  Identities=5%  Similarity=0.073  Sum_probs=28.6

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcc
Q 047723           30 IILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEED   68 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEed   68 (79)
                      +.++.++.++..++++.|+|+=++...+..+|++-|.+.
T Consensus        18 m~~Ll~~Si~s~aIiieR~~~l~~~~~~~~~f~~~~~~~   56 (227)
T PRK10801         18 MLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSG   56 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhC
Confidence            334444466667888999999988888888888877553

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

Probab=85.66  E-value=2.8  Score=24.65  Aligned_cols=21  Identities=14%  Similarity=0.037  Sum_probs=11.1

Q ss_pred             HHHHHHHHHHHHHHHhHHHHH
Q 047723           37 AVGLFSFFLFKLWQKKKREEQ   57 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKREeQ   57 (79)
                      ++++..+.+.++|+-|++-..
T Consensus        32 ~llg~l~~~~~~~~~r~~~~~   52 (68)
T PF06305_consen   32 ALLGWLLSLPSRLRLRRRIRR   52 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            455555556666655554333

>PRK05886 yajC preprotein translocase subunit YajC; Validated

Probab=85.57  E-value=1.4  Score=30.30  Aligned_cols=37  Identities=24%  Similarity=0.304  Sum_probs=19.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcchh
Q 047723           32 LLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDE   70 (79)
Q Consensus        32 l~vlv~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedDd   70 (79)
                      ++.+++++++.|+++|- | |||..+|+.++.=..-+|+
T Consensus         8 l~lv~i~~i~yF~~iRP-Q-kKr~K~~~~m~~~Lk~GD~   44 (109)
T PRK05886          8 LPFLLIMGGFMYFASRR-Q-RKAMQATIDLHESLQPGDR   44 (109)
T ss_pred             HHHHHHHHHHHHHHccH-H-HHHHHHHHHHHHhcCCCCE
Confidence            33344455556655543 3 4445566667665555553

>PRK01844 hypothetical protein; Provisional

Probab=85.56  E-value=0.66  Score=30.33  Aligned_cols=30  Identities=17%  Similarity=0.162  Sum_probs=18.6

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKK   53 (79)
                      +++.++++++++++.++++||+-|+|=+|.
T Consensus         3 ~~~~I~l~I~~li~G~~~Gff~ark~~~k~   32 (72)
T PRK01844          3 IWLGILVGVVALVAGVALGFFIARKYMMNY   32 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444455555566666667777777776654

>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=85.42  E-value=0.26  Score=40.13  Aligned_cols=19  Identities=11%  Similarity=0.044  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHhHHH
Q 047723           37 AVGLFSFFLFKLWQKKKRE   55 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKRE   55 (79)
                      +++++.+.+++..+|++|+
T Consensus       368 v~viv~vc~~~rrrR~~~~  386 (439)
T PF02480_consen  368 VGVIVWVCLRCRRRRRQRD  386 (439)
T ss_dssp             -------------------
T ss_pred             HHHHhheeeeehhcccccc
Confidence            3344445555555555555

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

>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway

Probab=84.44  E-value=1.9  Score=27.54  Aligned_cols=33  Identities=21%  Similarity=0.503  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcchh
Q 047723           36 VAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDE   70 (79)
Q Consensus        36 v~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedDd   70 (79)
                      +.++++-|++++  ..|||+++++.++.=..-+|+
T Consensus        10 ~~~~i~yf~~~r--pqkk~~k~~~~m~~~Lk~Gd~   42 (82)
T PF02699_consen   10 IIFVIFYFLMIR--PQKKQQKEHQEMLASLKPGDE   42 (82)
T ss_dssp             HHHHHHHHHTHH--HHHHHHHHHTTGGG-------
T ss_pred             HHHHHHhhheec--HHHHHHHHHHHHHHcCCCCCE
Confidence            344444444443  445555666666655554443

Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.

>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins

Probab=84.30  E-value=1.5  Score=34.53  Aligned_cols=26  Identities=19%  Similarity=0.134  Sum_probs=17.8

Q ss_pred             eEehhHHHHHHHHHHHHHHHHHHHHh
Q 047723           27 KVGIILLGLVAVGLFSFFLFKLWQKK   52 (79)
Q Consensus        27 ~VviIl~vlv~v~l~~~~lYK~WQKK   52 (79)
                      .|+|+++|+.++++..+.+||.-+|+
T Consensus       192 pvvIaliVitl~vf~LvgLyr~C~k~  217 (259)
T PF07010_consen  192 PVVIALIVITLSVFTLVGLYRMCWKT  217 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence            44455555556777788899987765

Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.

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

Probab=84.30  E-value=1.8  Score=29.53  Aligned_cols=23  Identities=22%  Similarity=0.404  Sum_probs=13.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhH
Q 047723           31 ILLGLVAVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        31 Il~vlv~v~l~~~~lYK~WQKKK   53 (79)
                      +++++++.+++++++.++-+++.
T Consensus         2 ~~i~lvvG~iiG~~~~r~~~~~~   24 (128)
T PF06295_consen    2 AIIGLVVGLIIGFLIGRLTSSNQ   24 (128)
T ss_pred             hHHHHHHHHHHHHHHHHHhccch
Confidence            34555555566666777766553

>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=84.03  E-value=0.29  Score=31.34  Aligned_cols=24  Identities=21%  Similarity=0.380  Sum_probs=0.0

Q ss_pred             CceEehhHHHHHHHHHHHHHHHHH
Q 047723           25 GAKVGIILLGLVAVGLFSFFLFKL   48 (79)
Q Consensus        25 gv~VviIl~vlv~v~l~~~~lYK~   48 (79)
                      +++..+++-.+++++++.|++||+
T Consensus        13 avIaG~Vvgll~ailLIlf~iyR~   36 (64)
T PF01034_consen   13 AVIAGGVVGLLFAILLILFLIYRM   36 (64)
T ss_dssp             ------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            333333333344555556666655

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.

>PF10855 DUF2648: Protein of unknown function (DUF2648); InterPro: IPR022561 This family of proteins with unknown function appears to be restricted to eubacteia

Probab=83.50  E-value=0.85  Score=26.14  Aligned_cols=18  Identities=28%  Similarity=0.456  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHhHH
Q 047723           37 AVGLFSFFLFKLWQKKKR   54 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKR   54 (79)
                      ++.+.+|+.||++|.+=+
T Consensus         9 ~l~ga~f~~fKKyQ~~vn   26 (33)
T PF10855_consen    9 ILGGAAFYGFKKYQNHVN   26 (33)
T ss_pred             hhhhHHHHHHHHHHHHHh
Confidence            445578999999997644

>PF12072 DUF3552: Domain of unknown function (DUF3552); InterPro: IPR022711 This presumed domain is functionally uncharacterised

Probab=83.22  E-value=2.8  Score=30.22  Aligned_cols=28  Identities=21%  Similarity=0.234  Sum_probs=13.8

Q ss_pred             EehhHHHHHHHHHHHHHHHHHHHHhHHH
Q 047723           28 VGIILLGLVAVGLFSFFLFKLWQKKKRE   55 (79)
Q Consensus        28 VviIl~vlv~v~l~~~~lYK~WQKKKRE   55 (79)
                      |+++++++++.+++++++.+..-+++.+
T Consensus         3 ii~~i~~~~vG~~~G~~~~~~~~~~~~~   30 (201)
T PF12072_consen    3 IIIAIVALIVGIGIGYLVRKKINRKKLE   30 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444445555555555555444443

This domain is found in bacteria, archaea and eukaryotes. This domain is about 200 amino acids in length. This domain is found associated with PF00013 from PFAM, PF01966 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0008663 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity

>KOG3054 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.14  E-value=1.4  Score=35.19  Aligned_cols=25  Identities=24%  Similarity=0.527  Sum_probs=19.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhHH
Q 047723           30 IILLGLVAVGLFSFFLFKLWQKKKR   54 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQKKKR   54 (79)
                      ++++.++++.+++++++++|++++-
T Consensus         4 ~v~vlVaa~llV~~i~l~l~~r~ra   28 (299)
T KOG3054|consen    4 IVAVLVAAALLVAVILLFLWKRRRA   28 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            4555556777788899999998873

>KOG4550 consensus Predicted membrane protein [Function unknown]

Probab=83.05  E-value=1.2  Score=38.31  Aligned_cols=20  Identities=30%  Similarity=0.305  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhH
Q 047723           34 GLVAVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        34 vlv~v~l~~~~lYK~WQKKK   53 (79)
                      +.++|.+++++++-+||.||
T Consensus       569 ~gvC~~il~ii~~Lh~~EKk  588 (606)
T KOG4550|consen  569 IGVCVFILAIIGILHWQEKK  588 (606)
T ss_pred             HHHHHHHHHHHhheehhhhh
Confidence            33466677788899999987

>PLN03150 hypothetical protein; Provisional

Probab=82.65  E-value=1.2  Score=36.74  Aligned_cols=31  Identities=26%  Similarity=0.450  Sum_probs=18.4

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhHH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKKR   54 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKKR   54 (79)
                      ++.++++++.++++++++.++++-+|++||+
T Consensus       543 ~~~~i~~~~~~~~~~l~~~~~~~~~~~~r~~  573 (623)
T PLN03150        543 VGAKIGIAFGVSVAFLFLVICAMCWWKRRQN  573 (623)
T ss_pred             CceEEEEEhHHHHHHHHHHHHHhhheeehhh
Confidence            4555555555555545555566777777764

>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=82.65  E-value=0.43  Score=36.03  Aligned_cols=23  Identities=13%  Similarity=0.316  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhHHH
Q 047723           33 LGLVAVGLFSFFLFKLWQKKKRE   55 (79)
Q Consensus        33 ~vlv~v~l~~~~lYK~WQKKKRE   55 (79)
                      .+|++++++++++|-++|||.|.
T Consensus       279 ~~La~lvlivLiaYli~Rrr~~~  301 (306)
T PF01299_consen  279 AALAGLVLIVLIAYLIGRRRSRA  301 (306)
T ss_pred             HHHHHHHHHHHHhheeEeccccc
Confidence            33457777788899999998865

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

>KOG3839 consensus Lectin VIP36, involved in the transport of glycoproteins carrying high mannose-type glycans [Intracellular trafficking, secretion, and vesicular transport]

Probab=82.59  E-value=0.12  Score=41.92  Aligned_cols=32  Identities=22%  Similarity=0.434  Sum_probs=17.8

Q ss_pred             hhHHHHHHHHHH---HHHHHHHHHHhHHHHHHHHHH
Q 047723           30 IILLGLVAVGLF---SFFLFKLWQKKKREEQYARLL   62 (79)
Q Consensus        30 iIl~vlv~v~l~---~~~lYK~WQKKKREeQ~AR~l   62 (79)
                      ..+.++++++.+   +++.|.+.|+|+ |++|.||+
T Consensus       317 ~~~ill~~vv~~v~~ai~s~~i~q~r~-er~Rkrfy  351 (351)
T KOG3839|consen  317 LFLILLFVVVFLVGGAIFSIVIFQVRQ-ERNRKRFY  351 (351)
T ss_pred             hHHHHHHHHHHHHHhhheEEEEEeehh-hhhhcccC
Confidence            334444444433   334456777665 88888874

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

Probab=82.51  E-value=0.4  Score=37.57  Aligned_cols=29  Identities=17%  Similarity=0.353  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHHHhHHH-HHHHHHHh
Q 047723           35 LVAVGLFSFFLFKLWQKKKRE-EQYARLLK   63 (79)
Q Consensus        35 lv~v~l~~~~lYK~WQKKKRE-eQ~AR~lk   63 (79)
                      |++.++++++.||.=++-|-+ |+|+-|++
T Consensus       159 LLIA~iIa~icyrrkR~GK~~~ee~~~f~~  188 (290)
T PF05454_consen  159 LLIAGIIACICYRRKRKGKMSLEEQKTFIS  188 (290)
T ss_dssp             ------------------------------
T ss_pred             HHHHHHHHHHhhhhhhccccccchhHHHHh
Confidence            334555566677733333444 56777776

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.

>PF15102 TMEM154: TMEM154 protein family

Probab=82.48  E-value=0.12  Score=37.37  Aligned_cols=23  Identities=22%  Similarity=0.138  Sum_probs=9.3

Q ss_pred             eEehhHH-HH-HHHHHHHHHHHHHH
Q 047723           27 KVGIILL-GL-VAVGLFSFFLFKLW   49 (79)
Q Consensus        27 ~VviIl~-vl-v~v~l~~~~lYK~W   49 (79)
                      +++|+++ ++ +++++++++++.+.
T Consensus        58 iLmIlIP~VLLvlLLl~vV~lv~~~   82 (146)
T PF15102_consen   58 ILMILIPLVLLVLLLLSVVCLVIYY   82 (146)
T ss_pred             EEEEeHHHHHHHHHHHHHHHheeEE
Confidence            4444444 33 23333344443333

>PF13908 Shisa: Wnt and FGF inhibitory regulator

Probab=82.28  E-value=0.39  Score=33.57  Aligned_cols=15  Identities=33%  Similarity=0.299  Sum_probs=8.1

Q ss_pred             CCCceEehhHHHHHH
Q 047723           23 NTGAKVGIILLGLVA   37 (79)
Q Consensus        23 ~tgv~VviIl~vlv~   37 (79)
                      .++++|.||+.++++
T Consensus        77 ~~~iivgvi~~Vi~I   91 (179)
T PF13908_consen   77 ITGIIVGVICGVIAI   91 (179)
T ss_pred             eeeeeeehhhHHHHH
Confidence            455666565544443

>COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=82.04  E-value=2.7  Score=26.28  Aligned_cols=16  Identities=25%  Similarity=0.420  Sum_probs=6.4

Q ss_pred             CceEehhHHHHHHHHH
Q 047723           25 GAKVGIILLGLVAVGL   40 (79)
Q Consensus        25 gv~VviIl~vlv~v~l   40 (79)
                      |-.++=+++|++++.+
T Consensus         9 GFTLiElLVvl~Iigi   24 (149)
T COG2165           9 GFTLIELLVVLAIIGI   24 (149)
T ss_pred             CcchHHHHHHHHHHHH
Confidence            4333334444443333

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

Probab=81.96  E-value=1.5  Score=34.46  Aligned_cols=21  Identities=14%  Similarity=0.482  Sum_probs=13.9

Q ss_pred             eEehhHHHHHHHHHHHHHHHH
Q 047723           27 KVGIILLGLVAVGLFSFFLFK   47 (79)
Q Consensus        27 ~VviIl~vlv~v~l~~~~lYK   47 (79)
                      +++|++.||+.+|+-...-||
T Consensus       262 iiaIliIVLIMvIIYLILRYR  282 (299)
T PF02009_consen  262 IIAILIIVLIMVIIYLILRYR  282 (299)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            455666666677777777773

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 [].

>PRK00523 hypothetical protein; Provisional

Probab=81.76  E-value=1.2  Score=29.05  Aligned_cols=30  Identities=27%  Similarity=0.428  Sum_probs=18.8

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKK   53 (79)
                      +++.+.++++++++.++++||+-|+|=+|.
T Consensus         4 ~~l~I~l~i~~li~G~~~Gffiark~~~k~   33 (72)
T PRK00523          4 IGLALGLGIPLLIVGGIIGYFVSKKMFKKQ   33 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555556666667777777776664

>PF14283 DUF4366: Domain of unknown function (DUF4366)

Probab=81.70  E-value=0.077  Score=39.80  Aligned_cols=34  Identities=26%  Similarity=0.411  Sum_probs=14.2

Q ss_pred             cCCCCceEehhHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 047723           21 RSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQ   57 (79)
Q Consensus        21 ~~~tgv~VviIl~vlv~v~l~~~~lYK~WQKKKREeQ   57 (79)
                      ++++|.  +++++++++++++++ .|-+-+|+|.+..
T Consensus       157 ks~~g~--ll~lllv~l~gGGa~-yYfK~~K~K~~~~  190 (218)
T PF14283_consen  157 KSGMGS--LLLLLLVALIGGGAY-YYFKFYKPKQEEK  190 (218)
T ss_pred             ccchHH--HHHHHHHHHhhcceE-EEEEEeccccccc
Confidence            344554  333333333333344 4444444444433

>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=81.53  E-value=1.4  Score=38.64  Aligned_cols=35  Identities=26%  Similarity=0.327  Sum_probs=27.6

Q ss_pred             cCCCCceEehhHHHHHHHHHHHHHHHHHHHHhHHH
Q 047723           21 RSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKRE   55 (79)
Q Consensus        21 ~~~tgv~VviIl~vlv~v~l~~~~lYK~WQKKKRE   55 (79)
                      .+|.=+++.++++++++++++.++.||+++++|=|
T Consensus       266 ~~NlWII~gVlvPv~vV~~Iiiil~~~LCRk~K~e  300 (684)
T PF12877_consen  266 PNNLWIIAGVLVPVLVVLLIIIILYWKLCRKNKLE  300 (684)
T ss_pred             CCCeEEEehHhHHHHHHHHHHHHHHHHHhcccccC
Confidence            34455677788888888888888899999988855

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.

>PF11368 DUF3169: Protein of unknown function (DUF3169); InterPro: IPR021509 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed

Probab=81.25  E-value=3.1  Score=30.52  Aligned_cols=10  Identities=40%  Similarity=0.571  Sum_probs=5.2

Q ss_pred             hcchhhhhhh
Q 047723           66 EEDDELEVEL   75 (79)
Q Consensus        66 EedDdle~EL   75 (79)
                      ++|||.++|+
T Consensus        82 ~~deD~~~~~   91 (248)
T PF11368_consen   82 EEDEDENEEY   91 (248)
T ss_pred             cccchHHHHH
Confidence            3455555543

Currently there is no known function.

>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells []

Probab=81.25  E-value=2.2  Score=28.28  Aligned_cols=36  Identities=14%  Similarity=0.236  Sum_probs=15.2

Q ss_pred             hHHHH-HHHHHHHHHHHHHHHHhHHHHHHHHHHhhhh
Q 047723           31 ILLGL-VAVGLFSFFLFKLWQKKKREEQYARLLKLFE   66 (79)
Q Consensus        31 Il~vl-v~v~l~~~~lYK~WQKKKREeQ~AR~lkLFE   66 (79)
                      .++++ +++++..++-...|+.=|+-..|.|+.+|++
T Consensus         8 ~iialiv~~iiaIvvW~iv~ieYrk~~rqrkId~li~   44 (81)
T PF00558_consen    8 AIIALIVALIIAIVVWTIVYIEYRKIKRQRKIDRLIE   44 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHHH------------CHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            33344 4555555656666999999999999999999

; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.

>PF03229 Alpha_GJ: Alphavirus glycoprotein J; InterPro: IPR004913 The exact function of the herpesvirus glycoprotein J is unknown, but it appears to play a role in the inhibition of apotosis of the host cell []

Probab=80.28  E-value=9.8  Score=27.30  Aligned_cols=35  Identities=17%  Similarity=0.126  Sum_probs=23.9

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQY   58 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKKREeQ~   58 (79)
                      ++.++-.++=+|+++.+.++.+.-+-||..|.--+
T Consensus        82 ~d~aLp~VIGGLcaL~LaamGA~~LLrR~cRr~ar  116 (126)
T PF03229_consen   82 VDFALPLVIGGLCALTLAAMGAGALLRRCCRRAAR  116 (126)
T ss_pred             cccchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55566666666777777777777777777776433

; GO: 0019050 suppression by virus of host apoptosis

---

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	79
2l2t_A	44	Receptor tyrosine-protein kinase ERBB-4; transmemb	96.09
2ks1_B	44	Epidermal growth factor receptor; ERBB1, ERBB2, tr	95.37
2k1k_A	38	Ephrin type-A receptor 1; EPHA1, receptor tyrosine	93.06
2knc_B	79	Integrin beta-3; transmembrane signaling, protein	92.91
2jwa_A	44	Receptor tyrosine-protein kinase ERBB-2; transmemb	87.71
2lx0_A	32	Membrane fusion protein P14; membrane fusion prote	87.0
2k9y_A	41	Ephrin type-A receptor 2; receptor tyrosine kinase	86.03
1oqw_A	144	Fimbrial protein; type IV pilin, fiber-forming pro	84.97
2l6w_A	39	Beta-type platelet-derived growth factor receptor;	85.21
2rdd_B	37	UPF0092 membrane protein YAJC; drug resistance, mu	84.6
3qf7_D	50	MRE11; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	84.47
1s7q_A	348	H-2KB, H-2 class I histocompatibility antigen, K-B	84.01
2j5l_A	581	Apical membrane antigen 1; malaria vaccine candida	83.01
1v54_I	73	STA, cytochrome C oxidase polypeptide VIC; oxidore	81.94
1cd1_A	315	CD1, MCD1D.1; immunology, MHC, TCR, glycoprotein,	81.74
2hi2_A	158	Fimbrial protein; type IV pilin, fiber-forming pro	80.73
3sok_A	151	Fimbrial protein; pilus subunit, extracellular, ce	80.19

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

Probab=96.09  E-value=0.00036  Score=40.77  Aligned_cols=36  Identities=11%  Similarity=0.100  Sum_probs=24.4

Q ss_pred             ccCCCCceEehhHHHHHHHHHHHHHHHHHHHHhHHH
Q 047723           20 SRSNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKRE   55 (79)
Q Consensus        20 ~~~~tgv~VviIl~vlv~v~l~~~~lYK~WQKKKRE   55 (79)
                      .+||++.+.+-++.+++++++++...|=||++|++.
T Consensus         5 ~~s~~~aIA~gVVgGv~~v~ii~~~~~~~~RRRr~~   40 (44)
T 2l2t_A            5 QHARTPLIAAGVIGGLFILVIVGLTFAVYVRRKSIK   40 (44)
T ss_dssp             SSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSS
T ss_pred             CCCCcceEEEeehHHHHHHHHHHHHHHHHhhhhhhh
Confidence            356666655556666666666777778888887754

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

Probab=95.37  E-value=0.013  Score=33.95  Aligned_cols=33  Identities=3%  Similarity=-0.035  Sum_probs=23.3

Q ss_pred             CCCCceEehhHHHHHHHHHHHHHHHHHHHHhHH
Q 047723           22 SNTGAKVGIILLGLVAVGLFSFFLFKLWQKKKR   54 (79)
Q Consensus        22 ~~tgv~VviIl~vlv~v~l~~~~lYK~WQKKKR   54 (79)
                      ||++.+.+-++.++++++++++..|=||++|++
T Consensus         8 s~~~~IA~gVVgGv~~~~ii~~~~~~~~RRr~~   40 (44)
T 2ks1_B            8 PKIPSIATGMVGALLLLLVVALGIGLFMRRRHI   40 (44)
T ss_dssp             SCSSSSTHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCcceEEeehhHHHHHHHHHHHHHHHHhhhhHh
Confidence            666666666666677777777777888888764

>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=93.06  E-value=0.021  Score=31.95  Aligned_cols=29  Identities=21%  Similarity=0.155  Sum_probs=17.1

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHh
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKK   52 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKK   52 (79)
                      .|.+..|++-+++.+++++.++|-+|+||
T Consensus        10 ~GaIAGiVvG~v~gv~li~~l~~~~~rrr   38 (38)
T 2k1k_A           10 GGEIVAVIFGLLLGAALLLGILVFRSRRA   38 (38)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CCceeeeehHHHHHHHHHHHHHHHHeecC
Confidence            45454455555555666666677777654

>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=92.91  E-value=0.13  Score=32.35  Aligned_cols=21  Identities=19%  Similarity=0.494  Sum_probs=10.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHH
Q 047723           30 IILLGLVAVGLFSFFLFKLWQ   50 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQ   50 (79)
                      -++.+++++.++.+++||++.
T Consensus        16 gvi~gilliGllllliwk~~~   36 (79)
T 2knc_B           16 SVMGAILLIGLAALLIWKLLI   36 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            333333444555566666443

>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=87.71  E-value=0.31  Score=28.21  Aligned_cols=26  Identities=12%  Similarity=0.250  Sum_probs=13.3

Q ss_pred             EehhHHHHHHHHHHHHHHHHHHHHhH
Q 047723           28 VGIILLGLVAVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        28 VviIl~vlv~v~l~~~~lYK~WQKKK   53 (79)
                      ++..+++++++++++...+=||+||+
T Consensus        14 Ia~~vVGvll~vi~~l~~~~~~RRR~   39 (44)
T 2jwa_A           14 IISAVVGILLVVVLGVVFGILIKRRQ   39 (44)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hHHHHHHHHHHHHHHHHHHhheehhh
Confidence            44444554444445555555566554

>2lx0_A Membrane fusion protein P14; membrane fusion protein transmembrane domain, P14 fast prote ARCH, micelle-peptide complex, membrane protein; NMR {Synthetic}

Probab=87.00  E-value=0.25  Score=27.16  Aligned_cols=21  Identities=48%  Similarity=0.759  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHh
Q 047723           32 LLGLVAVGLFSFFLFKLWQKK   52 (79)
Q Consensus        32 l~vlv~v~l~~~~lYK~WQKK   52 (79)
                      ++.+.....++|-+|||-|||
T Consensus        12 lvalltflafgfwlfkylqkk   32 (32)
T 2lx0_A           12 LVALLTFLAFGFWLFKYLQKK   32 (32)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHhcC
Confidence            333445556677888888765

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

Probab=86.03  E-value=0.076  Score=28.80  Aligned_cols=31  Identities=19%  Similarity=0.223  Sum_probs=11.7

Q ss_pred             cCCCCceEehhHHHHHHHHHHHHHHHHHHHH
Q 047723           21 RSNTGAKVGIILLGLVAVGLFSFFLFKLWQK   51 (79)
Q Consensus        21 ~~~tgv~VviIl~vlv~v~l~~~~lYK~WQK   51 (79)
                      +++...+++-++.+++.++++.++.+=+|+|
T Consensus         9 ~~~~~~I~~~vv~Gv~ll~~iv~~~~~~~rR   39 (41)
T 2k9y_A            9 GSGNLAVIGGVAVGVVLLLVLAGVGFFIHRR   39 (41)
T ss_dssp             CCSSTHHHHHHHHHHHHHHHHHHHHHSSSSS
T ss_pred             CCceEEEEeehhHHHHHHHHHHHHheeEeee
Confidence            3434443333334443333233333334444

>1oqw_A Fimbrial protein; type IV pilin, fiber-forming protein, adhesion, pseudomonas aerugionosa, PAK pilin, cell adhesion; 2.00A {Pseudomonas aeruginosa} SCOP: d.24.1.1

Probab=84.97  E-value=1.5  Score=28.26  Aligned_cols=34  Identities=3%  Similarity=0.057  Sum_probs=19.5

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q 047723           30 IILLGLVAVGLFSFFLFKLWQKKKREEQYARLLK   63 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQKKKREeQ~AR~lk   63 (79)
                      |++..+++++.+++-.|.-|++|.|..+..+.+.
T Consensus         8 ivi~Ii~il~~ia~p~~~~~~~~~~~~~~~~~~~   41 (144)
T 1oqw_A            8 IVVAIIGILAAIAIPQYQNYVARSEGASALASVN   41 (144)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3334444555556667777777766665555543

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

Probab=85.21  E-value=0.18  Score=28.96  Aligned_cols=19  Identities=37%  Similarity=0.466  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHhHHH
Q 047723           37 AVGLFSFFLFKLWQKKKRE   55 (79)
Q Consensus        37 ~v~l~~~~lYK~WQKKKRE   55 (79)
                      ++++...+++-+||||-|-
T Consensus        20 i~iisLIiLi~~w~qKPrY   38 (39)
T 2l6w_A           20 LTIISLIILIMLWQKKPRY   38 (39)
Confidence            4455566788899999874

>2rdd_B UPF0092 membrane protein YAJC; drug resistance, multidrug efflux, transporter, antiporter, novel transmembrane helix, ACRB, inner membrane; HET: AIC; 3.50A {Escherichia coli}

Probab=84.60  E-value=1.3  Score=23.92  Aligned_cols=26  Identities=31%  Similarity=0.462  Sum_probs=13.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhHHHH
Q 047723           31 ILLGLVAVGLFSFFLFKLWQKKKREE   56 (79)
Q Consensus        31 Il~vlv~v~l~~~~lYK~WQKKKREe   56 (79)
                      +++.+++++++-|+++|==|||++|.
T Consensus         6 ~l~~v~~~~ifYFl~iRPQ~Kr~K~~   31 (37)
T 2rdd_B            6 ILMLVVFGLIFYFMILRPQQKRTKEH   31 (37)
T ss_dssp             HHHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            33444455566677776655544443

>3qf7_D MRE11; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima}

Probab=84.47  E-value=0.42  Score=28.52  Aligned_cols=24  Identities=54%  Similarity=0.816  Sum_probs=19.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHhhhhc
Q 047723           43 FFLFKLWQKKKREEQYARLLKLFEE   67 (79)
Q Consensus        43 ~~lYK~WQKKKREeQ~AR~lkLFEe   67 (79)
                      |=+||-+- |+|++.+..+||+|||
T Consensus        10 felfkey~-k~r~~~he~l~k~~~e   33 (50)
T 3qf7_D           10 FELFKEYL-KKREENHEKLLKILDE   33 (50)
T ss_dssp             HHHHHHHH-HHHCTTHHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHhhHHHHHHHHHH
Confidence            45677776 4679999999999986

>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=84.01  E-value=0.2  Score=37.26  Aligned_cols=13  Identities=8%  Similarity=0.123  Sum_probs=0.0

Q ss_pred             HHHHHHHHHH-HhH
Q 047723           41 FSFFLFKLWQ-KKK   53 (79)
Q Consensus        41 ~~~~lYK~WQ-KKK   53 (79)
                      ++++.+-.|+ ||+
T Consensus       300 ~~~~~~~~~~~k~~  313 (348)
T 1s7q_A          300 GAVVAFVMKMRRRN  313 (348)
T ss_dssp             --------------
T ss_pred             eeEEEEEEEEEEec
Confidence            3445566788 544

>2j5l_A Apical membrane antigen 1; malaria vaccine candidate, apical membrane antigen 1, hypothetical protein, immunoglobulin domain; 2.9A {Plasmodium falciparum} SCOP: g.61.1.1 PDB: 1hn6_A

Probab=83.01  E-value=0.24  Score=41.38  Aligned_cols=45  Identities=16%  Similarity=0.160  Sum_probs=0.0

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcc
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEED   68 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEed   68 (79)
                      .-..++||++..++++++...+|++|++++....+.|++.-.+=|
T Consensus       510 ~~~~~ii~~~~~~~~~~a~~~~~~~~k~~~~~~~ydk~~~~~~y~  554 (581)
T 2j5l_A          510 YDNMKIIIASSAAVAVLATILMVYLYKRKGNAEKYDKMDQPQHYG  554 (581)
T ss_dssp             ---------------------------------------------
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCccchhhhcchhccC
Confidence            334555555555566666666777998888888899988765543

>1v54_I STA, cytochrome C oxidase polypeptide VIC; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: f.23.3.1 PDB: 1oco_I* 1occ_I* 1ocz_I* 1ocr_I* 1v55_I* 2dyr_I* 2dys_I* 2eij_I* 2eik_I* 2eil_I* 2eim_I* 2ein_I* 2occ_I* 2ybb_T* 2zxw_I* 3abk_I* 3abl_I* 3abm_I* 3ag1_I* 3ag2_I* ...

Probab=81.94  E-value=2.9  Score=26.14  Aligned_cols=40  Identities=23%  Similarity=0.349  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhcchhhhh
Q 047723           34 GLVAVGLFSFFLFKLWQKKKREEQYARLLKLFEEDDELEV   73 (79)
Q Consensus        34 vlv~v~l~~~~lYK~WQKKKREeQ~AR~lkLFEedDdle~   73 (79)
                      +.+++.+++.++||+---..|-..||.|.|=+.-.+|.|.
T Consensus        23 ~a~~lsl~~~~~~k~~v~~pRK~aYadFYknYD~~k~fer   62 (73)
T 1v54_I           23 GAFMVSLGFATFYKFAVAEKRKKAYADFYRNYDSMKDFEE   62 (73)
T ss_dssp             HHHHHHHHHHHHHHHHTHHHHHHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhcCcHHHHHH
Confidence            3334444555567764444555689999998888777764

>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=81.74  E-value=0.28  Score=35.58  Aligned_cols=28  Identities=29%  Similarity=0.381  Sum_probs=0.0

Q ss_pred             CCceEehhHHHHHHHHHHHHHHHHHHHHhH
Q 047723           24 TGAKVGIILLGLVAVGLFSFFLFKLWQKKK   53 (79)
Q Consensus        24 tgv~VviIl~vlv~v~l~~~~lYK~WQKKK   53 (79)
                      ++.+++.|+++|+++++++  +|=+|++++
T Consensus       283 ~~~i~~~vi~~l~ll~~~~--~~~~~~~~~  310 (315)
T 1cd1_A          283 VGLIVFIVLIMLVVVGAVV--YYIWRRRSA  310 (315)
T ss_dssp             ------------------------------
T ss_pred             cceeehhHHHHHHHHHHHH--HhheehhcC
Confidence            4444333334444443333  333355443

>2hi2_A Fimbrial protein; type IV pilin, fiber-forming protein, membrane protein, DNA protein, contractIle protein, cell adhesion; HET: MEA GLA DT6 HTO; 2.30A {Neisseria gonorrhoeae} PDB: 2hil_A* 1ay2_A* 2pil_A*

Probab=80.73  E-value=1.3  Score=28.80  Aligned_cols=29  Identities=3%  Similarity=0.070  Sum_probs=16.3

Q ss_pred             HHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q 047723           35 LVAVGLFSFFLFKLWQKKKREEQYARLLK   63 (79)
Q Consensus        35 lv~v~l~~~~lYK~WQKKKREeQ~AR~lk   63 (79)
                      +++++.+++-.|.-|++|.|..+..+.++
T Consensus        13 i~il~~~~~p~~~~~~~~~~~~~~~~~~~   41 (158)
T 2hi2_A           13 VGILAAVALPAYQDYTARAQVSEAILLAE   41 (158)
T ss_dssp             HHHHHHHHTTTHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhHHHHH
Confidence            33444445556666666666655555544

>3sok_A Fimbrial protein; pilus subunit, extracellular, cell adhesion; 2.30A {Dichelobacter nodosus}

Probab=80.19  E-value=3.3  Score=27.17  Aligned_cols=34  Identities=9%  Similarity=0.146  Sum_probs=17.8

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q 047723           30 IILLGLVAVGLFSFFLFKLWQKKKREEQYARLLK   63 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQKKKREeQ~AR~lk   63 (79)
                      |++..+++++.+++-.|.-|++|.|..+....++
T Consensus         8 vviaIigiLaaia~p~~~~~~~~~~~~~~~~~~~   41 (151)
T 3sok_A            8 IVVAIIGILAAFAIPAYNDYIARSQAAEGLTLAD   41 (151)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333344555556666666666665554444443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	79
d2pila_	158	Pilin Gc {Neisseria gonorrhoeae [TaxId: 485]}	89.15

>d2pila_ d.24.1.1 (A:) Pilin Gc {Neisseria gonorrhoeae [TaxId: 485]}

class: Alpha and beta proteins (a+b)
fold: Pili subunits
superfamily: Pili subunits
family: Pilin
domain: Pilin Gc
species: Neisseria gonorrhoeae [TaxId: 485]

Probab=89.15  E-value=0.36  Score=27.82  Aligned_cols=31  Identities=3%  Similarity=0.068  Sum_probs=18.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 047723           30 IILLGLVAVGLFSFFLFKLWQKKKREEQYAR   60 (79)
Q Consensus        30 iIl~vlv~v~l~~~~lYK~WQKKKREeQ~AR   60 (79)
                      |++.++++++.+++-.|.-|+++-|..+...
T Consensus         8 VViaIIgILaaia~P~~~~~~~~a~~~~~~~   38 (158)
T d2pila_           8 IVIAIVGILAAVALPAYQDYTARAQVSEAIL   38 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4444444666667777777777755544433