Query psy16323
Match_columns 448
No_of_seqs 398 out of 1522
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 18:27:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16323.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16323hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3546|consensus 100.0 2E-25 4.4E-30 234.9 32.6 15 357-371 984-998 (1167)
2 KOG3546|consensus 99.9 1.4E-23 3E-28 221.1 30.3 28 276-303 808-835 (1167)
3 smart00038 COLFI Fibrillar col 99.9 5.1E-23 1.1E-27 200.0 3.8 133 298-446 8-169 (232)
4 PF01410 COLFI: Fibrillar coll 99.8 3E-21 6.4E-26 185.5 5.0 123 308-446 1-152 (214)
5 cd01477 vWA_F09G8-8_type VWA F 75.4 2.3 5E-05 40.4 2.7 49 313-361 14-74 (193)
6 cd01475 vWA_Matrilin VWA_Matri 73.0 2.9 6.2E-05 40.1 2.8 47 317-363 1-53 (224)
7 cd01481 vWA_collagen_alpha3-VI 67.0 4.3 9.3E-05 37.3 2.5 43 320-362 2-50 (165)
8 cd01469 vWA_integrins_alpha_su 53.8 9.5 0.00021 35.1 2.3 43 320-362 2-50 (177)
9 cd01473 vWA_CTRP CTRP for CS 37.5 22 0.00048 33.5 2.1 42 321-362 3-51 (192)
10 cd01480 vWA_collagen_alpha_1-V 34.4 24 0.00053 32.6 1.8 44 318-361 2-57 (186)
11 cd01482 vWA_collagen_alphaI-XI 31.2 49 0.0011 29.7 3.2 43 320-362 2-50 (164)
12 PF00092 VWA: von Willebrand f 29.6 45 0.00097 29.4 2.6 43 321-363 2-50 (178)
13 cd01471 vWA_micronemal_protein 29.0 43 0.00094 30.6 2.5 44 320-363 2-52 (186)
14 PRK11901 hypothetical protein; 26.8 78 0.0017 33.0 4.0 34 329-362 254-288 (327)
15 cd01474 vWA_ATR ATR (Anthrax T 25.3 53 0.0012 30.2 2.4 44 317-361 3-50 (185)
16 PF06453 LT-IIB: Type II heat- 24.6 51 0.0011 29.0 1.9 44 330-373 21-64 (122)
17 PF04811 Sec23_trunk: Sec23/Se 21.7 58 0.0013 31.6 1.9 44 316-359 1-50 (243)
18 cd01470 vWA_complement_factors 20.5 68 0.0015 29.8 2.1 42 321-362 3-50 (198)
19 KOG1924|consensus 20.1 7.3E+02 0.016 29.4 10.1 86 16-106 514-602 (1102)
No 1
>KOG3546|consensus
Probab=99.95 E-value=2e-25 Score=234.92 Aligned_cols=15 Identities=20% Similarity=0.239 Sum_probs=7.8
Q ss_pred eeeeEeccCCceeeh
Q psy16323 357 LYILTVEDDTVILLF 371 (448)
Q Consensus 357 ~~~~~vrkDqk~~WF 371 (448)
+-.++.+|+|.-+.|
T Consensus 984 ypmllaek~~pllhl 998 (1167)
T KOG3546|consen 984 YPMLLAEKPQPLLHL 998 (1167)
T ss_pred ccccCCCCcchhhhh
Confidence 344455555555554
No 2
>KOG3546|consensus
Probab=99.93 E-value=1.4e-23 Score=221.15 Aligned_cols=28 Identities=18% Similarity=0.155 Sum_probs=14.3
Q ss_pred CCCCCCCCCCCCCCCCCCCccccccccC
Q psy16323 276 SSAPDLPGPSSAPDLPGPSSTVLGSYLG 303 (448)
Q Consensus 276 ~~~~g~p~~~~~~~~p~~~~~~l~sl~g 303 (448)
|++-|.-++.+|.|.+|.-+-..+++++
T Consensus 808 kg~~gd~g~kge~ge~g~g~f~~s~~pg 835 (1167)
T KOG3546|consen 808 KGDRGDAGQKGERGEPGGGGFFGSSLPG 835 (1167)
T ss_pred cccccccccccccCCCCCCceecCCCCC
Confidence 4445555555555566544444555543
No 3
>smart00038 COLFI Fibrillar collagens C-terminal domain. Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc.
Probab=99.87 E-value=5.1e-23 Score=199.95 Aligned_cols=133 Identities=27% Similarity=0.287 Sum_probs=112.5
Q ss_pred cccccCCCCCCCCCCCCCCCCCceeeee-------------------------ccchhHHHhhhhhhccceeeeecceeE
Q psy16323 298 LGSYLGEAGHQKSPKGLEPKPAQISFVL-------------------------NIFANFHQTLRFLHFSCTSLVVTRATV 352 (448)
Q Consensus 298 l~sl~g~~g~~~sp~g~~~~P~~~~~vi-------------------------~~~~n~~~~~rfv~~~c~~i~~~r~tv 352 (448)
|+++..+++.++.|.|++.+|+++|.+| .+||||+.. ++| |+.....+
T Consensus 8 l~~l~~~i~~i~~P~Gt~~~PartC~dl~~~~p~~~~G~YwIdPn~G~~~Da~~V~C~~~~g-----~Tc--v~p~~~~~ 80 (232)
T smart00038 8 LKSLNNQIEQLKSPTGTKDNPARTCKDLKLCHPEFKDGEYWVDPNQGCIRDAIKVFCNFETG-----ETC--VSPSPSSI 80 (232)
T ss_pred HHHHHhHHhcccCCCCCCCCCcchhhHHHhcCCCCCCCCEEECCCCCCCCCCeEEEEEeecC-----CeE--Eccccccc
Confidence 6788889999999999999999999883 455666553 777 66666677
Q ss_pred eeceeeeeEeccCCceeehhhhhCCCCceeccCCCCCCCCCCCCchhHHHHHHHhhcCCCccee---ecccccCccCCCC
Q psy16323 353 VKLPLYILTVEDDTVILLFIETFIQLPQQAYTTNSFAPMDPSKDDTVILLFIKTCIQLPQQAYT---TNSFAPMDRWTHP 429 (448)
Q Consensus 353 ~~~~~~~~~vrkDqk~~WF~Et~~~g~qf~Y~~~~~~~~~~~~d~~vQL~FLrLlS~~A~Q~iT---~nS~a~~d~~~~~ 429 (448)
...+||.. +.+++||+|.|+.+++|.|.+....+ +.+|||+||||||++|+|+|| +||++|+|..+.+
T Consensus 81 ~~~~~~~~----~~~~~wf~e~~~~g~~f~Y~~~~~~~-----~~~vQltfLrllS~~A~Q~iTy~C~ns~a~~d~~~~~ 151 (232)
T smart00038 81 PRKTWYSG----KSKHVWFGETMNGGFQFSYGDSEGPP-----VGVVQLTFLRLLSTSAHQNITYHCKNSVAYMDEATGN 151 (232)
T ss_pred cccccccC----CCCCceeeeeccCCeEEEEecCCCCc-----cchHHHHHHHHhcccceeEEEEEEEcceeEEeccccc
Confidence 88888852 35899999999999999997765422 468999999999999999999 5999999998865
Q ss_pred -CCceEEeccCccccccc
Q psy16323 430 -SKAATFLGLLDEDTDEE 446 (448)
Q Consensus 430 -~ka~~l~g~nd~e~~~~ 446 (448)
+++|+|+++||+||+|+
T Consensus 152 ~~~al~l~g~n~~el~~~ 169 (232)
T smart00038 152 LKKALRLRGSNDVELSAE 169 (232)
T ss_pred ccccEEEEecCCCeEecC
Confidence 89999999999999987
No 4
>PF01410 COLFI: Fibrillar collagen C-terminal domain; InterPro: IPR000885 Collagens contain a large number of globular domains in between the regions of triple helical repeats IPR008160 from INTERPRO. These domains are involved in binding diverse substrates. One of these domains is found at the C terminus of fibrillar collagens. The exact function of this domain is unknown.; GO: 0005201 extracellular matrix structural constituent, 0005581 collagen
Probab=99.83 E-value=3e-21 Score=185.51 Aligned_cols=123 Identities=26% Similarity=0.296 Sum_probs=103.3
Q ss_pred CCCCCCCCCCCCceeee-------------------------eccchhHHHhhhhhhccceeeeecceeEeeceeeeeEe
Q psy16323 308 QKSPKGLEPKPAQISFV-------------------------LNIFANFHQTLRFLHFSCTSLVVTRATVVKLPLYILTV 362 (448)
Q Consensus 308 ~~sp~g~~~~P~~~~~v-------------------------i~~~~n~~~~~rfv~~~c~~i~~~r~tv~~~~~~~~~v 362 (448)
|++|.|++.+|+++|.+ |.+||||+.. +|| |+.....+....||.
T Consensus 1 ~k~P~Gt~~~PArtC~dL~~~~p~~~dG~YwIDPN~G~~~Dai~v~C~~~~g-----~TC--i~p~~~~~~~~~~~~--- 70 (214)
T PF01410_consen 1 IKKPDGTKENPARTCRDLKLCHPELPDGEYWIDPNGGSPRDAIEVFCNFTTG-----ETC--ISPDQSSVPSKSWYK--- 70 (214)
T ss_pred CCCCCCCccchhhhHHHHHhhCcccCCCcEeECCCCCCCCCcEEEEEeeeec-----eEE--EeccCcccccccccC---
Confidence 57899999999999988 4677888873 889 666666666666776
Q ss_pred ccCCceeehhhhhCCCCceeccCCCCCCCCCCCCchhHHHHHHHhhcCCCccee---ecccccCccCCCC-CCceEEecc
Q psy16323 363 EDDTVILLFIETFIQLPQQAYTTNSFAPMDPSKDDTVILLFIKTCIQLPQQAYT---TNSFAPMDRWTHP-SKAATFLGL 438 (448)
Q Consensus 363 rkDqk~~WF~Et~~~g~qf~Y~~~~~~~~~~~~d~~vQL~FLrLlS~~A~Q~iT---~nS~a~~d~~~~~-~ka~~l~g~ 438 (448)
...++.||++.+..+++|.|......+ ..+|||+||||||++|+|+|| +|+++|+|+.+.+ +++|+|+++
T Consensus 71 -~~~~~~w~~~~~~g~~~f~Y~~~~~~~-----~~~vQL~FLrLlS~~A~Q~iTy~C~ns~~~~d~~~~~~~~ai~~~g~ 144 (214)
T PF01410_consen 71 -GSPKGHWFSESMNGGFQFSYSISDGSP-----VGVVQLNFLRLLSSEARQNITYHCKNSVAWYDQSTGSYNKAIRFRGD 144 (214)
T ss_pred -CCCccceeeeecccccceeecCCcCCc-----cchHHHHHHHHHhhhheeeEEEEcCCCccccccccCCcccceEEEcC
Confidence 223899999999999999998775544 458999999999999999999 5899999998855 899999999
Q ss_pred Cccccccc
Q psy16323 439 LDEDTDEE 446 (448)
Q Consensus 439 nd~e~~~~ 446 (448)
||+|++++
T Consensus 145 n~~~~~~~ 152 (214)
T PF01410_consen 145 NDEELSYD 152 (214)
T ss_pred CCCEEecC
Confidence 99999987
No 5
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo
Probab=75.37 E-value=2.3 Score=40.44 Aligned_cols=49 Identities=20% Similarity=0.090 Sum_probs=37.5
Q ss_pred CCCCCCCceeeeeccch-----hHHHhhhhhhccceeeee-------cceeEeeceeeeeE
Q psy16323 313 GLEPKPAQISFVLNIFA-----NFHQTLRFLHFSCTSLVV-------TRATVVKLPLYILT 361 (448)
Q Consensus 313 g~~~~P~~~~~vi~~~~-----n~~~~~rfv~~~c~~i~~-------~r~tv~~~~~~~~~ 361 (448)
-+++..+.++|+||.+. ||+.++.|+..+.....+ ...+|++++.|+..
T Consensus 14 ~~~~~~~DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~ 74 (193)
T cd01477 14 DIKNLWLDIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSN 74 (193)
T ss_pred ccccceeeEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCc
Confidence 34677889999999984 678888888776544444 45799999999943
No 6
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=72.96 E-value=2.9 Score=40.10 Aligned_cols=47 Identities=34% Similarity=0.404 Sum_probs=39.1
Q ss_pred CCCceeeeeccc-----hhHHHhhhhhhccceeeeec-ceeEeeceeeeeEec
Q psy16323 317 KPAQISFVLNIF-----ANFHQTLRFLHFSCTSLVVT-RATVVKLPLYILTVE 363 (448)
Q Consensus 317 ~P~~~~~vi~~~-----~n~~~~~rfv~~~c~~i~~~-r~tv~~~~~~~~~vr 363 (448)
+|+.+.|+||.+ .||+.++.|+..++..+.+. +.++++++.|+..++
T Consensus 1 ~~~DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~ 53 (224)
T cd01475 1 GPTDLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVK 53 (224)
T ss_pred CCccEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCcee
Confidence 578899999988 38889999999988777766 489999999997653
No 7
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=66.98 E-value=4.3 Score=37.34 Aligned_cols=43 Identities=23% Similarity=0.205 Sum_probs=35.7
Q ss_pred ceeeeeccc-----hhHHHhhhhhhccceeeeec-ceeEeeceeeeeEe
Q psy16323 320 QISFVLNIF-----ANFHQTLRFLHFSCTSLVVT-RATVVKLPLYILTV 362 (448)
Q Consensus 320 ~~~~vi~~~-----~n~~~~~rfv~~~c~~i~~~-r~tv~~~~~~~~~v 362 (448)
.+.|+||.. .||+.++.|+..++....++ +.++++++.|+..+
T Consensus 2 DivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~ 50 (165)
T cd01481 2 DIVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTP 50 (165)
T ss_pred CEEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCe
Confidence 478888887 48999999999998778766 48999999999554
No 8
>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.
Probab=53.82 E-value=9.5 Score=35.12 Aligned_cols=43 Identities=26% Similarity=0.301 Sum_probs=34.6
Q ss_pred ceeeeeccch-----hHHHhhhhhhccceeeeec-ceeEeeceeeeeEe
Q psy16323 320 QISFVLNIFA-----NFHQTLRFLHFSCTSLVVT-RATVVKLPLYILTV 362 (448)
Q Consensus 320 ~~~~vi~~~~-----n~~~~~rfv~~~c~~i~~~-r~tv~~~~~~~~~v 362 (448)
.++|+||.+. +|..+++|+..++...++. +.++++++.|+..+
T Consensus 2 Di~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~ 50 (177)
T cd01469 2 DIVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESF 50 (177)
T ss_pred cEEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCce
Confidence 4789998873 7888999998888777764 48999999999553
No 9
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=37.47 E-value=22 Score=33.47 Aligned_cols=42 Identities=17% Similarity=0.304 Sum_probs=33.3
Q ss_pred eeeeeccch-----hHHH-hhhhhhccceeeeecc-eeEeeceeeeeEe
Q psy16323 321 ISFVLNIFA-----NFHQ-TLRFLHFSCTSLVVTR-ATVVKLPLYILTV 362 (448)
Q Consensus 321 ~~~vi~~~~-----n~~~-~~rfv~~~c~~i~~~r-~tv~~~~~~~~~v 362 (448)
++|+||.+. ||+. .+.|+...+....+.+ .++++++.|+..+
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~ 51 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKN 51 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCc
Confidence 678888874 6764 5779988888887775 9999999999553
No 10
>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=34.42 E-value=24 Score=32.61 Aligned_cols=44 Identities=25% Similarity=0.277 Sum_probs=31.1
Q ss_pred CCceeeeeccch-----hHHHhhhhhhccceee------eec-ceeEeeceeeeeE
Q psy16323 318 PAQISFVLNIFA-----NFHQTLRFLHFSCTSL------VVT-RATVVKLPLYILT 361 (448)
Q Consensus 318 P~~~~~vi~~~~-----n~~~~~rfv~~~c~~i------~~~-r~tv~~~~~~~~~ 361 (448)
|+.++|+||++. +|+..+.|+...+..+ .+. ..++++++.|+..
T Consensus 2 ~~dvv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~ 57 (186)
T cd01480 2 PVDITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQ 57 (186)
T ss_pred CeeEEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCC
Confidence 567899999883 6777777776665555 222 3689999999843
No 11
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=31.18 E-value=49 Score=29.74 Aligned_cols=43 Identities=21% Similarity=0.237 Sum_probs=31.6
Q ss_pred ceeeeeccc-----hhHHHhhhhhhccceeeeec-ceeEeeceeeeeEe
Q psy16323 320 QISFVLNIF-----ANFHQTLRFLHFSCTSLVVT-RATVVKLPLYILTV 362 (448)
Q Consensus 320 ~~~~vi~~~-----~n~~~~~rfv~~~c~~i~~~-r~tv~~~~~~~~~v 362 (448)
-+.|++|.. .+|..++.|+..++....+. +.++++++.|+.++
T Consensus 2 Dv~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~ 50 (164)
T cd01482 2 DIVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDP 50 (164)
T ss_pred CEEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCe
Confidence 467888777 37777888877776555444 48999999999654
No 12
>PF00092 VWA: von Willebrand factor type A domain; InterPro: IPR002035 The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders []. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. Fold recognition algorithms were used to score sequence compatibility with a library of known structures: the vWF domain fold was predicted to be a doubly-wound, open, twisted beta-sheet flanked by alpha-helices []. 3D structures have been determined for the I-domains of integrins CD11b (with bound magnesium) [] and CD11a (with bound manganese) []. The domain adopts a classic alpha/beta Rossmann fold and contains an unusual metal ion coordination site at its surface. It has been suggested that this site represents a general metal ion-dependent adhesion site (MIDAS) for binding protein ligands []. The residues constituting the MIDAS motif in the CD11b and CD11a I-domains are completely conserved, but the manner in which the metal ion is coordinated differs slightly [].; GO: 0005515 protein binding; PDB: 2XGG_B 3ZQK_B 3GXB_A 3PPV_A 3PPX_A 3PPW_A 3PPY_A 1CQP_B 3TCX_B 2ICA_A ....
Probab=29.57 E-value=45 Score=29.44 Aligned_cols=43 Identities=19% Similarity=0.325 Sum_probs=31.9
Q ss_pred eeeeeccch-----hHHHhhhhhhccceee-eecceeEeeceeeeeEec
Q psy16323 321 ISFVLNIFA-----NFHQTLRFLHFSCTSL-VVTRATVVKLPLYILTVE 363 (448)
Q Consensus 321 ~~~vi~~~~-----n~~~~~rfv~~~c~~i-~~~r~tv~~~~~~~~~vr 363 (448)
++|+||... +|+.+..|+...+..+ .....++++++.|+..++
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~ 50 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSAR 50 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEE
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeecccc
Confidence 688998884 6777888888887766 345699999999995544
No 13
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=28.96 E-value=43 Score=30.59 Aligned_cols=44 Identities=14% Similarity=0.218 Sum_probs=32.4
Q ss_pred ceeeeeccch-----h-HHHhhhhhhccceeeeecc-eeEeeceeeeeEec
Q psy16323 320 QISFVLNIFA-----N-FHQTLRFLHFSCTSLVVTR-ATVVKLPLYILTVE 363 (448)
Q Consensus 320 ~~~~vi~~~~-----n-~~~~~rfv~~~c~~i~~~r-~tv~~~~~~~~~vr 363 (448)
.++|++|++. + +..++.|+...+..+++.+ -++++++.|+..++
T Consensus 2 Dv~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~ 52 (186)
T cd01471 2 DLYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAK 52 (186)
T ss_pred cEEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCce
Confidence 4688888873 4 6677888888887776554 67899999985443
No 14
>PRK11901 hypothetical protein; Reviewed
Probab=26.79 E-value=78 Score=32.99 Aligned_cols=34 Identities=12% Similarity=0.086 Sum_probs=24.9
Q ss_pred hhHHHhhhhhhcc-ceeeeecceeEeeceeeeeEe
Q psy16323 329 ANFHQTLRFLHFS-CTSLVVTRATVVKLPLYILTV 362 (448)
Q Consensus 329 ~n~~~~~rfv~~~-c~~i~~~r~tv~~~~~~~~~v 362 (448)
.+.+....|+..+ ...+|+|+.+|.+..||++.+
T Consensus 254 s~~~~L~~f~~~~~L~~~~VYqT~RnGkpWYVVvy 288 (327)
T PRK11901 254 SRSDTLNAYAKKQNLSHYHVYETKRDGKPWYVLVS 288 (327)
T ss_pred CCHHHHHHHHHHcCcCceEEEEEEECCceEEEEEe
Confidence 4555556666655 355789999999999999763
No 15
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=25.26 E-value=53 Score=30.20 Aligned_cols=44 Identities=9% Similarity=0.101 Sum_probs=29.1
Q ss_pred CCCceeeeeccchh----HHHhhhhhhccceeeeecceeEeeceeeeeE
Q psy16323 317 KPAQISFVLNIFAN----FHQTLRFLHFSCTSLVVTRATVVKLPLYILT 361 (448)
Q Consensus 317 ~P~~~~~vi~~~~n----~~~~~rfv~~~c~~i~~~r~tv~~~~~~~~~ 361 (448)
.++-++|+||++.- +.....|+.+++..+... -++++++.|+..
T Consensus 3 ~~~Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~~~~-~~rvglv~Fs~~ 50 (185)
T cd01474 3 GHFDLYFVLDKSGSVAANWIEIYDFVEQLVDRFNSP-GLRFSFITFSTR 50 (185)
T ss_pred CceeEEEEEeCcCchhhhHHHHHHHHHHHHHHcCCC-CcEEEEEEecCC
Confidence 46678999998853 333446666665444333 489999999854
No 16
>PF06453 LT-IIB: Type II heat-labile enterotoxin , B subunit (LT-IIB); InterPro: IPR010503 These are B subunits from the type II heat-labile enterotoxin. The B subunits form a pentameric ring, which interacts with one A subunit. Thus, the structural arrangement of type I and type II heat-labile enterotoxins are very similar [].; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1TII_F 1QCB_E 1QB5_D.
Probab=24.57 E-value=51 Score=28.99 Aligned_cols=44 Identities=18% Similarity=0.267 Sum_probs=29.4
Q ss_pred hHHHhhhhhhccceeeeecceeEeeceeeeeEeccCCceeehhh
Q psy16323 330 NFHQTLRFLHFSCTSLVVTRATVVKLPLYILTVEDDTVILLFIE 373 (448)
Q Consensus 330 n~~~~~rfv~~~c~~i~~~r~tv~~~~~~~~~vrkDqk~~WF~E 373 (448)
-+-.+..|..++|.+.+..-+.-+.|.-|+++|-+|.+.+|..+
T Consensus 21 ~yAgvS~~Fkd~C~~TTA~iV~~V~L~k~~sDvN~~t~GiYv~s 64 (122)
T PF06453_consen 21 TYAGVSKHFKDNCNSTTAKIVQGVQLVKYISDVNKNTKGIYVVS 64 (122)
T ss_dssp ------HHHHHHHTTSSSEEEEEE-EEEEEEE-STTT-EEEEEE
T ss_pred ccccHHHHHHhhhhhhHHHHHhhhhhhhhhhhccCCCCcEEEEe
Confidence 33445667778887777777888999999999999999888755
No 17
>PF04811 Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: IPR006896 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain, an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the Sec23/24 alpha/beta trunk domain, which is formed from a single, approximately 250-residue segment plugged into the beta-barrel between strands beta-1 and beta-19. The trunk has an alpha/beta fold with a vWA topology, and it forms the dimer interface, primarily involving strand beta-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_A 2NUP_A 3EG9_A 3EFO_A 3EGX_A 2NUT_A 1PD0_A 1PD1_A 1M2V_B 1PCX_A ....
Probab=21.71 E-value=58 Score=31.57 Aligned_cols=44 Identities=20% Similarity=0.274 Sum_probs=23.2
Q ss_pred CCCCceeeeeccchh-----H-HHhhhhhhccceeeeecceeEeeceeee
Q psy16323 316 PKPAQISFVLNIFAN-----F-HQTLRFLHFSCTSLVVTRATVVKLPLYI 359 (448)
Q Consensus 316 ~~P~~~~~vi~~~~n-----~-~~~~rfv~~~c~~i~~~r~tv~~~~~~~ 359 (448)
+.|+-.+|+||+..+ + +.+++.+....+.+.....++|++..|.
T Consensus 1 P~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd 50 (243)
T PF04811_consen 1 PQPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFD 50 (243)
T ss_dssp -S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEES
T ss_pred CCCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeC
Confidence 357778999998854 2 2223333333322222368899999987
No 18
>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation. They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation of an active protease that cleaves and activates complement C3. Complement C2 is in the classical pathway and complement B is in the alternative pathway. The interaction of C2 with C4 and of factor B with C3b are both dependent on Mg2+ binding sites within the VWA domains and the VWA domain of factor B has been shown to mediate the binding of C3. This is consistent with the common inferred function of VWA domains as magnesium-dependent protein interaction domains.
Probab=20.45 E-value=68 Score=29.77 Aligned_cols=42 Identities=10% Similarity=0.090 Sum_probs=29.6
Q ss_pred eeeeeccch-----hHHHhhhhhhccceeeeecc-eeEeeceeeeeEe
Q psy16323 321 ISFVLNIFA-----NFHQTLRFLHFSCTSLVVTR-ATVVKLPLYILTV 362 (448)
Q Consensus 321 ~~~vi~~~~-----n~~~~~rfv~~~c~~i~~~r-~tv~~~~~~~~~v 362 (448)
++|+||++. +|+.++.|+..++..+...+ -.+++++.|+..+
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~ 50 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDP 50 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCc
Confidence 678888773 66777778887776665443 5678888888543
No 19
>KOG1924|consensus
Probab=20.15 E-value=7.3e+02 Score=29.39 Aligned_cols=86 Identities=28% Similarity=0.534 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy16323 16 LPSTVTERPLEPDLPGPSSAP--DLPGPSSAPDLPGPSSAPD-LPGPSSAPDLPGPSSAPDLPGPSSAPDLPGPSSAPDL 92 (448)
Q Consensus 16 ~~~~~~~~pg~pg~pG~~G~~--G~pG~~G~~G~~G~~G~~G-~pG~~G~~G~pG~~G~~G~pG~~G~pG~pG~~G~pG~ 92 (448)
+++-.+-.+..-+.|.+++.+ |=.|++=+|+.|=.+|-.| +|=+++.+|..|.+..+.++ +|..|++=+|=+
T Consensus 514 l~s~~~~~~~~~~iP~PP~~pp~gG~g~pppPppPPlpggag~PPPPpplPg~aG~PPpPppp-----pg~~gppPPPpp 588 (1102)
T KOG1924|consen 514 LSSPSQLLPIDGGIPPPPPLPPTGGTGPPPPPPPPPLPGGAGPPPPPPPLPGIAGGPPPPPPP-----PGGGGPPPPPPP 588 (1102)
T ss_pred ccCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCcccCCCCccCCC-----CCCCCCCCcCCC
Q ss_pred CCCCCCCCCCCCCC
Q psy16323 93 PGPSSAPDLPGPSS 106 (448)
Q Consensus 93 ~G~~G~~G~pG~~G 106 (448)
.|..|-+=++=++|
T Consensus 589 ~g~~Gg~ppPP~~g 602 (1102)
T KOG1924|consen 589 GGFLGGPPPPPPPG 602 (1102)
T ss_pred CCCCCCCCCCCCCC
Done!