RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780388|ref|YP_003064801.1| hypothetical protein CLIBASIA_01365 [Candidatus Liberibacter asiaticus str. psy62] (458 letters) >gnl|CDD|29223 cd01450, vWFA_subfamily_ECM, 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 most, if not all A domains . Length = 161 Score = 52.3 bits (125), Expect = 3e-07 Identities = 35/175 (20%), Positives = 72/175 (41%), Gaps = 24/175 (13%) Query: 259 VDSS-SLRHVIKKKHLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVISDPSFS--WG 315 +D S S+ +K V+D + ++ +K+D D R+G ++D V + S + Sbjct: 7 LDGSESVGPENFEK--VKDFIEKLV---EKLDIGPDKTRVGLVQYSDDVRVEFSLNDYKS 61 Query: 316 VHKLIRTIVKTFAIDENEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLT 375 L++ + + G T A+Q A + + S + K I++LT Sbjct: 62 KDDLLKAV---KNLKYLGGGGTNTGKALQYALEQLFSESNA-------RENVPKVIIVLT 111 Query: 376 DGENTQDNEEGIAICNKAKSQGIRIMTIAF-SVNKTQQEKARYFLSNCASPNSFF 429 DG + D + K K +GI++ + ++ + + +++C S F Sbjct: 112 DG-RSDDGGDPKEAAAKLKDEGIKVFVVGVGPADEEELRE----IASCPSERHVF 161 >gnl|CDD|29240 cd01467, vWA_BatA_type, VWA BatA 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 most, if not all A domains. Members of this subgroup are bacterial in origin. They are typified by the presence of a MIDAS motif.. Length = 180 Score = 49.9 bits (119), Expect = 2e-06 Identities = 40/157 (25%), Positives = 66/157 (42%), Gaps = 27/157 (17%) Query: 249 LDPSLSEEHFVDSSSLRHVIKKKHLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVIS 308 + S+ + FV S L K ++ D + ++ D + V GA F + Sbjct: 11 VSGSMLAQDFVKPSRLE---AAKEVLSDFIDR-----RENDRIGLVVFAGAAFTQAPLTL 62 Query: 309 DPSFSWGVHKLIRTIVKTFAIDENEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAK 368 D + ++ +++ I G TAI DA+ A + R+KN+ + Sbjct: 63 D-------RESLKELLEDIKIGLAGQG-TAIGDAIGLA-----------IKRLKNSEAKE 103 Query: 369 KYIVLLTDGENTQDNEEGIAICNKAKSQGIRIMTIAF 405 + IVLLTDGEN + AK++G+RI TI Sbjct: 104 RVIVLLTDGENNAGEIDPATAAELAKNKGVRIYTIGV 140 >gnl|CDD|29222 cd00198, vWFA, 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 most, if not all A domains.. Length = 161 Score = 47.6 bits (112), Expect = 7e-06 Identities = 26/142 (18%), Positives = 50/142 (35%), Gaps = 20/142 (14%) Query: 277 ALASVIRSIKKIDNVNDTVRMGATFFNDRV-----ISDPSFSWGVHKLIRTIVKTFAIDE 331 A ++ + + R+G F ++ + + + I + K Sbjct: 21 AKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPLTTDTDKADLLEAIDALKKGL---- 76 Query: 332 NEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQDNEEGIAICN 391 G T I A++ A + + S+ A++ I+LLTDGE E Sbjct: 77 --GGGTNIGAALRLALELLKSAKRPN---------ARRVIILLTDGEPNDGPELLAEAAR 125 Query: 392 KAKSQGIRIMTIAFSVNKTQQE 413 + + GI + TI + + E Sbjct: 126 ELRKLGITVYTIGIGDDANEDE 147 >gnl|CDD|143873 pfam00092, VWA, von Willebrand factor type A domain. Length = 177 Score = 46.6 bits (111), Expect = 2e-05 Identities = 35/187 (18%), Positives = 68/187 (36%), Gaps = 18/187 (9%) Query: 259 VDSS-SLRHVIKKKHLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVISDPSFSWGVH 317 +D S S+ V++ + ++ + +D D R+G ++ V ++ FS + Sbjct: 6 LDGSGSIGE--ANFEKVKEFIKKLV---ENLDIGPDGTRVGLVQYSSDVTTE--FSLNDY 58 Query: 318 KLIRTIVKTFAIDENEM-GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTD 376 K ++ + + G T A++ A + + S A K ++LLTD Sbjct: 59 KSKDDLLSAVLRNIYYLGGGTNTGKALKYALENLFRSAGS-------RPNAPKVVILLTD 111 Query: 377 GENTQDNEEGIAICNKAKSQGIRIMTIAFSVNKTQQEKARYFLSNCASPNSFFEANSTHE 436 G++ A + G I+ V +E+ R S S F Sbjct: 112 GKSNDGGLVPAAAAALRRKVG--IIVFGVGVGDVDEEELRLIASEPCSEGHVFYVTDFDA 169 Query: 437 LNKIFRD 443 L+ I + Sbjct: 170 LSDIQEE 176 >gnl|CDD|34568 COG4961, TadG, Flp pilus assembly protein TadG [Intracellular trafficking and secretion]. Length = 185 Score = 37.8 bits (87), Expect = 0.006 Identities = 20/138 (14%), Positives = 44/138 (31%), Gaps = 6/138 (4%) Query: 12 KKLIKSCTGHFFIITALLMPVMLGVGGMLVDVVRWSYYEHALKQAAQTAIITASVPLIQS 71 ++ + G + AL+ P +L + +V+ A KQ+ Q A A+ + Sbjct: 13 RRFRRDRRGAAAVEFALVAPPLLLLVFGIVEF---GIAFLA-KQSLQNAADAAARAAARG 68 Query: 72 LEEVSSRAKNSFTFPKQKIEEYLIRNFENNLKKNFTDREVRDIVRDTAVEMNPRKSAYQV 131 L ++ + N ++ N R + + A Q Sbjct: 69 LTTDAADLDTIQAAATAFLNAIAPANAFLTVQSNTPSRGTVTVTANVA--DATLFDTSQF 126 Query: 132 VLSSRYDLLLNPLSLFLR 149 ++S + +N + Sbjct: 127 TVTSAVTVSINLARGLVL 144 >gnl|CDD|29238 cd01465, vWA_subgroup, VWA subgroup: 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 most, if not all A domains. Not much is known about the function of the VWA domain in these proteins. The members do have a conserved MIDAS motif. The biochemical function however is not known.. Length = 170 Score = 33.6 bits (77), Expect = 0.11 Identities = 31/147 (21%), Positives = 50/147 (34%), Gaps = 27/147 (18%) Query: 272 HLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRV-ISDPSFSWGVHKLIRTIVKTFAID 330 LV+ AL ++ D + R+ ++ P+ I AID Sbjct: 19 PLVKSALKLLV------DQLRPDDRLAIVTYDGAAETVLPATPVRDKAAILA-----AID 67 Query: 331 E-NEMGSTAINDAMQTAYDTII-SSNEDEVHRMKNNLEAKKYIVLLTDGENT---QDNEE 385 GSTA +Q Y V+R I+L TDG+ D +E Sbjct: 68 RLTAGGSTAGGAGIQLGYQEAQKHFVPGGVNR----------ILLATDGDFNVGETDPDE 117 Query: 386 GIAICNKAKSQGIRIMTIAFSVNKTQQ 412 + + + GI + T+ F N + Sbjct: 118 LARLVAQKRESGITLSTLGFGDNYNED 144 >gnl|CDD|33968 COG4245, TerY, Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]. Length = 207 Score = 31.1 bits (70), Expect = 0.60 Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 6/94 (6%) Query: 335 GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEA--KKYIVLLTDGENTQDNEEGIAICNK 392 G T + A+ A D I E+ + N + + ++ L+TDGE T D + G A+ + Sbjct: 77 GGTPLGAALTLALDMI----EERKRKYDANGKGDYRPWVFLITDGEPTDDWQAGAALVFQ 132 Query: 393 AKSQGIRIMTIAFSVNKTQQEKARYFLSNCASPN 426 + + + + V + Sbjct: 133 GERRAKSVAAFSVGVQGADNKTLNQITEKVRQFL 166 >gnl|CDD|29229 cd01456, vWA_ywmD_type, VWA ywmD 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 most, if not all A domains. Not much is known about the function of the members of this subgroup. All members of this subgroup however have a conserved MIDAS motif. . Length = 206 Score = 31.1 bits (70), Expect = 0.69 Identities = 26/137 (18%), Positives = 52/137 (37%), Gaps = 10/137 (7%) Query: 284 SIKKIDNVNDTVRMGATFFNDRVISDPSFSWGVHK--LIRTIVKTFAIDENEMGSTAIND 341 + + + D R+G F+ + V K L + + + + A+N Sbjct: 51 LDETANALPDGTRLGLWTFSGDGDNPLDVRVLVPKGCLTAPVNGFPSAQRSAL-DAALN- 108 Query: 342 AMQTA-YDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQDNEEGIAICNKAKSQ---- 396 ++QT T +++ E + +VL+TDGE+T + AK + Sbjct: 109 SLQTPTGWTPLAAALAEAAAYVDP-GRVNVVVLITDGEDTCGPDPCEVARELAKRRTPAP 167 Query: 397 GIRIMTIAFSVNKTQQE 413 I++ I F + + E Sbjct: 168 PIKVNVIDFGGDADRAE 184 >gnl|CDD|34274 COG4655, COG4655, Predicted membrane protein [Function unknown]. Length = 565 Score = 30.7 bits (69), Expect = 0.81 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 7/73 (9%) Query: 12 KKLIKSCTGHFFIITALLMPVMLGVGGMLVDVVRWSYYEHALKQAAQTAIITASVPLIQS 71 + +S G ++TAL +P+ L + VD + L++ A A I A+ + Sbjct: 5 PRRQRSMVG---VLTALFVPLALATLLLGVDYGYLYLEQRELQRVADLAAIAAA----SN 57 Query: 72 LEEVSSRAKNSFT 84 L++ + SFT Sbjct: 58 LDDAEQAVQTSFT 70 >gnl|CDD|29253 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.. Length = 186 Score = 30.6 bits (69), Expect = 0.86 Identities = 32/153 (20%), Positives = 64/153 (41%), Gaps = 21/153 (13%) Query: 259 VDSS----SLRHVIKKKHLVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVISDPSFSW 314 +DSS I K + R +A + + R+G ++D+ + F Sbjct: 9 LDSSESVGLQNFDITKNFVKR--VAERFLKDYYRKDPAGSWRVGVVQYSDQQEVEAGFLR 66 Query: 315 GVHKLIRTIVKTFAIDENEM--GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIV 372 + T +K A+D E G T + A++ A + ++ + + + K+++ Sbjct: 67 DIRN--YTSLKE-AVDNLEYIGGGTFTDCALKYATEQLLEGS---------HQKENKFLL 114 Query: 373 LLTDGENTQDNEEGI-AICNKAKSQGIRIMTIA 404 ++TDG + + GI N+A GI+I +A Sbjct: 115 VITDGHSDGSPDGGIEKAVNEADHLGIKIFFVA 147 >gnl|CDD|29245 cd01472, vWA_collagen, von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.. Length = 164 Score = 30.2 bits (68), Expect = 1.4 Identities = 28/134 (20%), Positives = 54/134 (40%), Gaps = 18/134 (13%) Query: 273 LVRDALASVIRSIKKIDNVNDTVRMGATFFNDRVISDPSFSWGVHKLIRTIVKTFAIDEN 332 LV+D + V+ + D D VR+G ++D F ++ + A+ Sbjct: 20 LVKDFVKRVVERL---DIGPDGVRVGVVQYSDDPR--TEFYLNTYRSKDDV--LEAVKNL 72 Query: 333 EM--GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQDNEEGIAIC 390 G T A++ + + + E + K +V++TDG+ +QD+ E A+ Sbjct: 73 RYIGGGTNTGKALKYVRENLFT----EASGSREG--VPKVLVVITDGK-SQDDVEEPAVE 125 Query: 391 NKAKSQGIRIMTIA 404 K GI + + Sbjct: 126 --LKQAGIEVFAVG 137 >gnl|CDD|36639 KOG1425, KOG1425, KOG1425, Microfibrillar-associated protein MFAP1 [Cytoskeleton]. Length = 430 Score = 29.7 bits (66), Expect = 1.7 Identities = 28/136 (20%), Positives = 50/136 (36%), Gaps = 15/136 (11%) Query: 330 DENEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQDNEEGIAI 389 DE E + + ++ +T S +D R+K K+ L + E E+ + Sbjct: 156 DEYESDEESEEEESESEEET--DSEDDMEPRLKPVFVRKRDRTTLQEREREAKKEKNLEK 213 Query: 390 CNKAKSQGIRIMT---IAFSVNKTQQEKARYFLSNCA----------SPNSFFEANSTHE 436 K ++ + T + V K + E+ + + + +EA E Sbjct: 214 EAKRDAEERKRETLQIVEEEVIKKELEEKKTKNNEALLNDVDTDDEINEEEEYEAWKLRE 273 Query: 437 LNKIFRDRIGNEIFER 452 L +I RDR E ER Sbjct: 274 LKRIKRDREEREELER 289 >gnl|CDD|39423 KOG4222, KOG4222, KOG4222, Axon guidance receptor Dscam [Signal transduction mechanisms]. Length = 1281 Score = 29.3 bits (65), Expect = 2.2 Identities = 21/96 (21%), Positives = 32/96 (33%), Gaps = 22/96 (22%) Query: 306 VISDPSFSWGVHKLIRTIVKTFAI-------DENEMGSTAINDAMQTAYDTIISSNEDEV 358 V++ P+F GVH+ IV F+I E G T S D + Sbjct: 867 VVNQPAFIAGVHRACLIIVMVFSIIWLYWRRKEPLSGKDL----------TAGLSRLDNL 916 Query: 359 HRMKNNLEAKKYI-----VLLTDGENTQDNEEGIAI 389 N + K Y+ T + Q+ G + Sbjct: 917 FTSLNVNQGKGYLPCYSPGWRTARLDHQNERAGQGL 952 >gnl|CDD|29250 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 most, if not all A domains. The members of this subgroup lack the MIDAS motif. This subgroup is found only in C. elegans and the members identified thus far are always found fused to a C-Lectin type domain. Biochemical function thus far has not be attributed to any of the members of this subgroup.. Length = 193 Score = 28.7 bits (64), Expect = 3.6 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 2/62 (3%) Query: 368 KKYIVLLTDGENTQDNEEGIAICNKAKSQGIRIMTIAFSVNKTQQEKARYFLSNCASPNS 427 KK +++ N + + + I + KS GI I+T+AF+ +++ + L ASP Sbjct: 132 KKVVIVFASDYNDEGSNDPRPIAARLKSTGIAIITVAFTQDESSNLLDK--LGKIASPGM 189 Query: 428 FF 429 F Sbjct: 190 NF 191 >gnl|CDD|29242 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.. Length = 177 Score = 28.7 bits (64), Expect = 3.8 Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 5/52 (9%) Query: 366 EAKKYIVLLTDGENTQDNEEGIAICNKAKSQGIRIMTIA----FSVNKTQQE 413 +A K +V++TDGE+ D+ + +A+ +GI I F +++E Sbjct: 102 DATKVLVVITDGESH-DDPLLKDVIPQAEREGIIRYAIGVGGHFQRENSREE 152 >gnl|CDD|109609 pfam00559, Vif, Retroviral Vif (Viral infectivity) protein. Human immunodeficiency virus type 1 (HIV-1) Vif is required for productive infection of T lymphocytes and macrophages. Virions produced in the absence of Vif have abnormal core morphology and those produced in primary T cells carry immature core proteins and low levels of mature capsid. Length = 192 Score = 28.1 bits (63), Expect = 4.7 Identities = 19/82 (23%), Positives = 27/82 (32%), Gaps = 14/82 (17%) Query: 154 KSWLIQTKAEAETVSRSYHKEHGVSIQWVIDFSRSMLD---YQRDSEGQPLNCFGQPADR 210 K L T R + + V IQW R+ +D G +CF +R Sbjct: 61 KGKLEVQGYWHLTPERGWLSTYAVGIQWYSRKYRTEVDPDTADSLIHGHYFSCF---TER 117 Query: 211 TVKSYSSQNGKVGIRDEKLSPY 232 ++ IR EKL Sbjct: 118 AIRR--------AIRGEKLLSC 131 >gnl|CDD|153284 cd07600, BAR_Gvp36, The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Golgi vesicle protein of 36 kDa and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Proteomic analysis shows that Golgi vesicle protein of 36 kDa (Gvp36) may be involved in vesicular trafficking and nutritional adaptation. A Saccharomyces cerevisiae strain deficient in Gvp36 shows defects in growth, in actin cytoskeleton polarization, in endocytosis, in vacuolar biogenesis, and in the cell cycle. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. Length = 242 Score = 28.1 bits (63), Expect = 5.1 Identities = 14/51 (27%), Positives = 23/51 (45%) Query: 331 ENEMGSTAINDAMQTAYDTIISSNEDEVHRMKNNLEAKKYIVLLTDGENTQ 381 E A ++TA D +S+ E+ V MK L+ + + LL + Q Sbjct: 174 EPAEKQEAARVEVETAEDEFVSATEEAVELMKEVLDNPEPLQLLKELVKAQ 224 >gnl|CDD|31953 COG1767, CitG, Triphosphoribosyl-dephospho-CoA synthetase [Coenzyme metabolism]. Length = 288 Score = 28.0 bits (62), Expect = 5.5 Identities = 26/157 (16%), Positives = 46/157 (29%), Gaps = 27/157 (17%) Query: 35 GVGGMLVDVVRWSYYEHALKQAAQTAIITASVPLIQSLEEVSSRAK-NSFTFPKQKIEEY 93 +G +L D + E A+ I T PLI + + A ++ Sbjct: 73 DLGALLRDAGLEA--EKAMFGNTNFGINTLLKPLIFAAGLGNLCAAAGRLLARTTPLDAV 130 Query: 94 LIRNFENNLKKNFTDREVRDIVRDTAVEMNPRK-----------------------SAYQ 130 + + RE++ V D + ++ Sbjct: 131 ELCDAIKQACAGLVKRELKADVSDETAGERLFRKYGLLGARGEAASGFPLVRSHALPGFK 190 Query: 131 VVLSSRYDLLLNPLSLFLRSMGIKS-WLIQTKAEAET 166 +L DL L L+ + I S LI ++ AE Sbjct: 191 RLLEGGLDLERALLQTLLKLLAINSDTLIASRGGAEG 227 >gnl|CDD|29237 cd01464, vWA_subfamily, VWA subfamily: 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 most, if not all A domains. Members of this subgroup have no assigned function. This subfamily is typified by the presence of a conserved MIDAS motif.. Length = 176 Score = 27.9 bits (62), Expect = 6.0 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 6/76 (7%) Query: 335 GSTAINDAMQTAYDTIISSNEDEVHRMKNNLEA--KKYIVLLTDGENTQDNEEGIAICNK 392 G T++ A++ A D I + V R + + + + ++ LLTDGE T D I + Sbjct: 77 GGTSMGAALELALDCI----DRRVQRYRADQKGDWRPWVFLLTDGEPTDDLTAAIERIKE 132 Query: 393 AKSQGIRIMTIAFSVN 408 A+ RI+ A Sbjct: 133 ARDSKGRIVACAVGPK 148 >gnl|CDD|80364 cd04821, PA_M28_1_2, PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively little is known about proteins in this subgroup.. Length = 157 Score = 27.9 bits (62), Expect = 6.3 Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%) Query: 45 RWSY-YEHALKQAAQTAII 62 RW+Y YE A +Q A A+I Sbjct: 80 RWTYKYEEAARQGAAGALI 98 >gnl|CDD|32614 COG2721, UxaA, Altronate dehydratase [Carbohydrate transport and metabolism]. Length = 381 Score = 27.9 bits (62), Expect = 6.4 Identities = 9/22 (40%), Positives = 14/22 (63%) Query: 206 QPADRTVKSYSSQNGKVGIRDE 227 A+RT + Y +G+VG R+E Sbjct: 1 PAAERTFQGYRRADGRVGTRNE 22 >gnl|CDD|32386 COG2204, AtoC, Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]. Length = 464 Score = 27.6 bits (61), Expect = 8.5 Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 10/54 (18%) Query: 240 LYYMLYPGPLD-PSLSE---------EHFVDSSSLRHVIKKKHLVRDALASVIR 283 LYY L PL P L E EHF+ + K +ALA+++ Sbjct: 300 LYYRLNVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLA 353 >gnl|CDD|33640 COG3850, NarQ, Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms]. Length = 574 Score = 27.2 bits (60), Expect = 8.9 Identities = 38/228 (16%), Positives = 71/228 (31%), Gaps = 36/228 (15%) Query: 49 YEHALKQAAQTAIITASVPL-----IQSLEEVSSRAKNSFTFPKQKIEEYL--IRNFENN 101 ++ +L A A++ VPL Q L R + Y + +F Sbjct: 72 FQTSLHSPALRALLPWRVPLAVKTQYQQLIA-YWRNMLKPLLLQGDRRPYQADLADFVAQ 130 Query: 102 LKKNFTDREVRDIVRDTAVEMNPRKSAYQVVLSSRYDLLLNPLSLFLRSMGIKSWLIQTK 161 + D+ V + R + +VL +LL L + ++ +++ Sbjct: 131 I-----DQFVLALQRFAE------RKTILLVLVQLAGMLLILLLVVFTIYWLRRRVVRPL 179 Query: 162 AEAETVSRSYHKEHGVSIQWVIDFSRSMLDYQRDSEGQPLNCFGQPADRTVKSYSSQNGK 221 + + ++ F + D R+ G F Q + K Y+ + Sbjct: 180 NQLTSAAQRI--GRR-------QFDQRPTDTGRNELGLLGRAFNQMSGELKKLYADLEQR 230 Query: 222 VGIRDEKLSPYMVSCNKSLYYMLYPGPLDPSLSEEHFVDSSSLRHVIK 269 V + L N+ L LY +D LRHV+ Sbjct: 231 VEEKTRDLE----QKNQRL-SFLYQSSRRLH---TSQIDDERLRHVLN 270 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.319 0.133 0.378 Gapped Lambda K H 0.267 0.0793 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,357,468 Number of extensions: 276656 Number of successful extensions: 735 Number of sequences better than 10.0: 1 Number of HSP's gapped: 733 Number of HSP's successfully gapped: 32 Length of query: 458 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 361 Effective length of database: 4,167,664 Effective search space: 1504526704 Effective search space used: 1504526704 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 59 (26.4 bits)