Query 027300
Match_columns 225
No_of_seqs 17 out of 19
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 07:53:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027300.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027300hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03423 CBM_25: Carbohydrate 97.6 6.5E-05 1.4E-09 55.5 4.1 76 106-186 1-77 (87)
2 PLN02316 synthase/transferase 96.7 0.0049 1.1E-07 63.3 7.2 93 99-195 321-418 (1036)
3 PLN02316 synthase/transferase 96.3 0.0085 1.8E-07 61.6 6.5 90 99-194 483-577 (1036)
4 PF14125 DUF4292: Domain of un 60.6 12 0.00026 30.6 3.6 38 160-198 169-208 (210)
5 PF06200 tify: tify domain; I 55.4 9.5 0.00021 25.4 1.8 14 102-115 1-14 (36)
6 PF06830 Root_cap: Root cap; 52.9 6.6 0.00014 29.0 0.8 22 126-148 23-44 (57)
7 PF14524 Wzt_C: Wzt C-terminal 47.2 29 0.00064 24.9 3.5 77 93-172 18-97 (142)
8 smart00809 Alpha_adaptinC2 Ada 41.5 70 0.0015 22.8 4.7 35 164-198 13-48 (104)
9 PF05773 RWD: RWD domain; Int 39.6 83 0.0018 22.0 4.7 48 151-199 23-78 (113)
10 PRK11385 putativi pili assembl 39.6 28 0.0006 30.3 2.7 37 89-125 110-156 (236)
11 cd01514 Elongation_Factor_C El 39.1 9.7 0.00021 26.4 -0.1 39 157-195 1-48 (79)
12 PF02883 Alpha_adaptinC2: Adap 38.7 84 0.0018 22.9 4.8 32 167-198 22-54 (115)
13 PF10102 DUF2341: Domain of un 31.7 60 0.0013 24.5 3.1 41 80-121 16-59 (89)
14 PRK10150 beta-D-glucuronidase; 31.5 37 0.00079 32.2 2.4 46 162-208 43-90 (604)
15 PHA02739 hypothetical protein; 30.6 46 0.00099 27.3 2.5 26 188-213 2-27 (116)
16 PRK15195 fimbrial chaperone pr 29.0 52 0.0011 28.4 2.7 35 90-124 103-151 (229)
17 PF01630 Glyco_hydro_56: Hyalu 28.9 33 0.00072 32.0 1.6 32 104-136 44-76 (337)
18 PRK15188 fimbrial chaperone pr 27.1 61 0.0013 28.2 2.8 37 89-125 104-153 (228)
19 PF05725 FNIP: FNIP Repeat; I 26.8 52 0.0011 21.2 1.8 22 121-142 10-31 (44)
20 PF05393 Hum_adeno_E3A: Human 26.3 40 0.00087 27.1 1.4 30 149-178 55-93 (94)
21 PF11619 P53_C: Transcription 26.0 46 0.001 25.6 1.7 13 184-196 14-26 (71)
22 PF08648 DUF1777: Protein of u 24.2 32 0.0007 27.7 0.6 7 132-138 170-176 (180)
23 TIGR01943 rnfA electron transp 24.2 43 0.00094 28.9 1.4 18 192-209 161-178 (190)
24 smart00216 VWD von Willebrand 23.8 94 0.002 23.6 3.0 20 181-200 122-141 (162)
25 cd03713 EFG_mtEFG_C EFG_mtEFG_ 23.7 28 0.00061 24.1 0.2 36 157-195 1-47 (78)
26 PRK15285 putative fimbrial cha 23.4 75 0.0016 28.0 2.7 36 89-124 105-150 (250)
27 PF00094 VWD: von Willebrand f 23.0 1.5E+02 0.0032 21.7 3.8 32 169-200 104-137 (159)
28 PF06572 DUF1131: Protein of u 22.8 36 0.00078 29.4 0.6 25 163-189 128-152 (171)
29 PF14545 DBB: Dof, BCAP, and B 22.5 82 0.0018 26.4 2.7 27 170-196 28-60 (142)
30 PF12158 DUF3592: Protein of u 21.9 58 0.0013 24.1 1.5 13 105-117 94-106 (148)
31 PRK15192 fimbrial chaperone Bc 21.4 84 0.0018 27.5 2.6 36 89-124 105-150 (234)
32 cd01450 vWFA_subfamily_ECM Von 21.0 53 0.0012 23.5 1.1 44 171-216 104-154 (161)
33 PF14508 GH97_N: Glycosyl-hydr 20.8 59 0.0013 28.1 1.5 69 118-193 28-100 (259)
34 PRK09926 putative chaperone pr 20.6 98 0.0021 26.8 2.8 35 89-123 107-156 (246)
35 PF11763 DIPSY: Cell-wall adhe 20.5 1.3E+02 0.0029 25.2 3.4 28 157-190 47-75 (123)
36 PRK15253 putative fimbrial ass 20.2 82 0.0018 27.6 2.3 36 89-124 114-162 (242)
37 smart00838 EFG_C Elongation fa 20.1 38 0.00083 23.9 0.2 37 156-195 2-49 (85)
No 1
>PF03423 CBM_25: Carbohydrate binding domain (family 25); InterPro: IPR005085 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM25 from CAZY which has a starch-binding function as has been demonstrated in one case.; PDB: 2LAB_A 2C3X_B 2C3V_A 2C3W_C 2LAA_A.
Probab=97.65 E-value=6.5e-05 Score=55.46 Aligned_cols=76 Identities=25% Similarity=0.528 Sum_probs=39.3
Q ss_pred CCceEEEEccccCCCCCCCceeeeecCCCCCccccCCchhhhhhhhhCCCCCCceEEEeeeccceeeEEEEeecC-CcCC
Q 027300 106 GEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQPFMCGGEPRAMLRKNRGQNDSPFYTIQICVPKHAINLIFSFTNG-VEWD 184 (225)
Q Consensus 106 Ge~L~lfyNp~a~~l~PNe~fGIaFNGgFNQPIMCGGEPR~M~~k~RGkad~PiYtI~I~vPkHA~~LiFSFTnG-~dWD 184 (225)
|+.++|||||..+.|.-.. -|=..+|||. -. ....-.|.+... .....-++..|.||+.|..|.|-|+|| -.||
T Consensus 1 G~~vtVyYn~~~~~l~g~~--~v~~~~G~n~-W~-~~~~~~m~~~~~-~~~~~~~~~tv~vP~~a~~~dfvF~dg~~~wD 75 (87)
T PF03423_consen 1 GETVTVYYNPSLTALSGAP--NVHLHGGFNR-WT-HVPGFGMTKMCV-PDEGGWWKATVDVPEDAYVMDFVFNDGAGNWD 75 (87)
T ss_dssp -SEEEEEE---E-SSS-S---EEEEEETTS--B--SSS-EE-EEESS----TTEEEEEEE--TTTSEEEEEEE-SSS-EE
T ss_pred CCEEEEEEEeCCCCCCCCC--cEEEEecCCC-CC-cCCCCCcceeee-eecCCEEEEEEEEcCCceEEEEEEcCCCCcEe
Confidence 7899999999877775222 2444455542 11 111223333221 111678999999999999999999998 4788
Q ss_pred Cc
Q 027300 185 GP 186 (225)
Q Consensus 185 Gp 186 (225)
--
T Consensus 76 NN 77 (87)
T PF03423_consen 76 NN 77 (87)
T ss_dssp ST
T ss_pred CC
Confidence 53
No 2
>PLN02316 synthase/transferase
Probab=96.65 E-value=0.0049 Score=63.34 Aligned_cols=93 Identities=20% Similarity=0.352 Sum_probs=69.5
Q ss_pred CCCCCCCCCceEEEEccccCCCCCCCceeeeecCCCCCccccCCchhhhhhhhhCCCCCCceEEEeeeccceeeEEEEee
Q 027300 99 NGLPPMSGEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQPFMCGGEPRAMLRKNRGQNDSPFYTIQICVPKHAINLIFSFT 178 (225)
Q Consensus 99 nGlpP~sGe~L~lfyNp~a~~l~PNe~fGIaFNGgFNQPIMCGGEPR~M~~k~RGkad~PiYtI~I~vPkHA~~LiFSFT 178 (225)
....|-+|+.++|||||+-+.|.-.+ -|=+.||||.=..-.+.+-.|.+-+.+.-| .+.-.|.||+-|..|-|-|+
T Consensus 321 ~P~~~~aG~~v~lyYN~~~~~L~~~~--~v~i~gg~N~W~~~~~~~~~~~~~~~~~g~--ww~a~v~vP~~A~~mDfVFs 396 (1036)
T PLN02316 321 EPSEFKAGDTVKLYYNRSSGPLAHST--EIWIHGGYNNWIDGLSIVEKLVKSEEKDGD--WWYAEVVVPERALVLDWVFA 396 (1036)
T ss_pred cCCCcCCCCEEEEEECCCCCCCCCCC--cEEEEEeEcCCCCCCcccceeecccCCCCC--EEEEEEecCCCceEEEEEEe
Confidence 46678999999999999999986443 467788888644333322234444443333 89999999999999999999
Q ss_pred cC-----CcCCCceeEEEecCc
Q 027300 179 NG-----VEWDGPYRIKFLVPR 195 (225)
Q Consensus 179 nG-----~dWDGpY~L~f~VP~ 195 (225)
|| ..||--....|.+|=
T Consensus 397 dg~~~~~~~yDNn~~~Dyh~~v 418 (1036)
T PLN02316 397 DGPPGNARNYDNNGRQDFHAIV 418 (1036)
T ss_pred cCCcccccccccCCCcceeeec
Confidence 99 699988777776654
No 3
>PLN02316 synthase/transferase
Probab=96.29 E-value=0.0085 Score=61.62 Aligned_cols=90 Identities=23% Similarity=0.414 Sum_probs=68.6
Q ss_pred CCCCCCCCCceEEEEccccCCCCCCCceeeeecCCCCCccccCC--chhhhhhhhhCCCCCCceEEEeeeccceeeEEEE
Q 027300 99 NGLPPMSGEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQPFMCGG--EPRAMLRKNRGQNDSPFYTIQICVPKHAINLIFS 176 (225)
Q Consensus 99 nGlpP~sGe~L~lfyNp~a~~l~PNe~fGIaFNGgFNQPIMCGG--EPR~M~~k~RGkad~PiYtI~I~vPkHA~~LiFS 176 (225)
.=+-|.+|+.++|||||.-+.|.-..+ |=|-||||.=.---| .|-.|.+.+-| .-+.-.|.||.-|..+-|-
T Consensus 483 eP~~~~aG~~v~v~Yn~~~t~l~~~~e--v~~~g~~NrWth~~~~~~~~~m~~~~~g----~~~~a~v~vP~da~~mdfv 556 (1036)
T PLN02316 483 EPLEVQAGTTVTVLYNPANTVLNGKPE--VWFRGSFNRWTHRLGPLPPQKMVPADNG----SHLKATVKVPLDAYMMDFV 556 (1036)
T ss_pred cCCCCCCCCEEEEEECCCCCcCCCCce--EEEEccccCcCCCCCCCCceeeeecCCC----ceEEEEEEccccceEEEEE
Confidence 345689999999999999888765444 779999997555555 58888888766 5778999999999999999
Q ss_pred eecCC---cCCCceeEEEecC
Q 027300 177 FTNGV---EWDGPYRIKFLVP 194 (225)
Q Consensus 177 FTnG~---dWDGpY~L~f~VP 194 (225)
|.||- .||--....+.+|
T Consensus 557 Fs~~~~g~~yDn~~~~dyh~~ 577 (1036)
T PLN02316 557 FSEKEEGGIFDNRNGLDYHIP 577 (1036)
T ss_pred EecCCCCCCcCCCCCcCCccc
Confidence 96653 4666555544443
No 4
>PF14125 DUF4292: Domain of unknown function (DUF4292)
Probab=60.59 E-value=12 Score=30.57 Aligned_cols=38 Identities=24% Similarity=0.610 Sum_probs=30.3
Q ss_pred eEEEeeecc--ceeeEEEEeecCCcCCCceeEEEecCcccc
Q 027300 160 YTIQICVPK--HAINLIFSFTNGVEWDGPYRIKFLVPRAWR 198 (225)
Q Consensus 160 YtI~I~vPk--HA~~LiFSFTnG~dWDGpY~L~f~VP~~~~ 198 (225)
..|+|.++. .-+.|...|.+ +++|.|..+.|.||+.++
T Consensus 169 ~~i~i~~~~~~~~~~l~l~y~~-v~~n~~~~f~f~iP~~yk 208 (210)
T PF14125_consen 169 KEIEISAPDGKKKTKLNLEYSK-VEFNEPLSFPFSIPSGYK 208 (210)
T ss_pred cEEEEEEecCCceEEEEEEEee-eEcCCCcceeccCCCCcE
Confidence 467777777 66666666666 888999999999999875
No 5
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=55.44 E-value=9.5 Score=25.43 Aligned_cols=14 Identities=36% Similarity=0.664 Sum_probs=11.1
Q ss_pred CCCCCCceEEEEcc
Q 027300 102 PPMSGEKLKIFYNP 115 (225)
Q Consensus 102 pP~sGe~L~lfyNp 115 (225)
|+....+|+||||=
T Consensus 1 ~~~~~~qLTIfY~G 14 (36)
T PF06200_consen 1 PSPETAQLTIFYGG 14 (36)
T ss_pred CCCCCCcEEEEECC
Confidence 45677899999984
No 6
>PF06830 Root_cap: Root cap; InterPro: IPR009646 The cells at the periphery of the root cap are continuously sloughed off from the root into the mucilage, and are thought to be programmed to die [].This family represents a conserved region approximately 60 residues in length within plant root cap proteins, which may be involved in the process.
Probab=52.90 E-value=6.6 Score=28.96 Aligned_cols=22 Identities=27% Similarity=0.395 Sum_probs=16.9
Q ss_pred eeeeecCCCCCccccCCchhhhh
Q 027300 126 FGIGFNGGFNQPFMCGGEPRAML 148 (225)
Q Consensus 126 fGIaFNGgFNQPIMCGGEPR~M~ 148 (225)
|=--.+.|-+.||| |||++-.+
T Consensus 23 yvn~vk~g~~MPvm-GG~~~y~t 44 (57)
T PF06830_consen 23 YVNPVKVGVAMPVM-GGEDKYRT 44 (57)
T ss_pred cccccccCCCCccc-cCCcccee
Confidence 33446788999999 99997654
No 7
>PF14524 Wzt_C: Wzt C-terminal domain; PDB: 2R5O_B.
Probab=47.21 E-value=29 Score=24.95 Aligned_cols=77 Identities=18% Similarity=0.207 Sum_probs=47.4
Q ss_pred eEEEecCCCCC---CCCCceEEEEccccCCCCCCCceeeeecCCCCCccccCCchhhhhhhhhCCCCCCceEEEeeeccc
Q 027300 93 VYWKTMNGLPP---MSGEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQPFMCGGEPRAMLRKNRGQNDSPFYTIQICVPKH 169 (225)
Q Consensus 93 VyWkT~nGlpP---~sGe~L~lfyNp~a~~l~PNe~fGIaFNGgFNQPIMCGGEPR~M~~k~RGkad~PiYtI~I~vPkH 169 (225)
|.....+|.+- .+||.++|-+.=.+.+-.++-.+|+.+-.-..|+|+.-.. ..+. ..=.....=.|++.+.+|++
T Consensus 18 v~i~~~~g~~~~~~~~ge~~~i~i~~~~~~~i~~~~~~~~i~~~~g~~v~~~~t-~~~~-~~~~~~~~g~~~~~~~i~~~ 95 (142)
T PF14524_consen 18 VRILDSDGEPTSSFESGEPIRIRIDYEVNEDIDDPVFGFAIRDSDGQRVFGTNT-YDSG-FPIPLSEGGTYEVTFTIPKP 95 (142)
T ss_dssp EEEEETTEES-SSEETTSEEEEEEEEEESS-EEEEEEEEEEEETT--EEEEEEH-HHHT---EEE-TT-EEEEEEEEE--
T ss_pred EEEEeCCCCEeeEEeCCCEEEEEEEEEECCCCCccEEEEEEEcCCCCEEEEECc-cccC-ccccccCCCEEEEEEEEcCc
Confidence 55666677666 3799999999888888888999999999888888875222 2221 11111115578888888888
Q ss_pred eee
Q 027300 170 AIN 172 (225)
Q Consensus 170 A~~ 172 (225)
++
T Consensus 96 -L~ 97 (142)
T PF14524_consen 96 -LN 97 (142)
T ss_dssp -B-
T ss_pred -cC
Confidence 53
No 8
>smart00809 Alpha_adaptinC2 Adaptin C-terminal domain. Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology PUBMED:10430869, PUBMED:12176391. The adaptor appendage contains an additional N-terminal strand.
Probab=41.51 E-value=70 Score=22.78 Aligned_cols=35 Identities=17% Similarity=0.239 Sum_probs=26.9
Q ss_pred eeeccceeeEEEEeecCCcCCCc-eeEEEecCcccc
Q 027300 164 ICVPKHAINLIFSFTNGVEWDGP-YRIKFLVPRAWR 198 (225)
Q Consensus 164 I~vPkHA~~LiFSFTnG~dWDGp-Y~L~f~VP~~~~ 198 (225)
|.-..+.+.+...|+|-.+|+=- +.+++.||+.|+
T Consensus 13 ~~~~~~~~~i~~~~~N~s~~~it~f~~~~avpk~~~ 48 (104)
T smart00809 13 FERRPGLIRITLTFTNKSPSPITNFSFQAAVPKSLK 48 (104)
T ss_pred EEcCCCeEEEEEEEEeCCCCeeeeEEEEEEcccceE
Confidence 33345778899999998888743 889999999775
No 9
>PF05773 RWD: RWD domain; InterPro: IPR006575 The RWD eukaryotic domain is found in RING finger (IPR001841 from INTERPRO) and WD repeat (IPR001680 from INTERPRO) containing proteins and DEXDc-like helicase (IPR001410 from INTERPRO) subfamily related to the ubiquitin-conjugating enzymes domain (IPR000608 from INTERPRO). ; GO: 0005515 protein binding; PDB: 2EBM_A 2EBK_A 2DAX_A 2DAW_A 2DAY_A 2DMF_A 1UKX_A 2YZ0_A.
Probab=39.56 E-value=83 Score=22.05 Aligned_cols=48 Identities=19% Similarity=0.389 Sum_probs=35.3
Q ss_pred hhCCCCCCceEEEe--------eeccceeeEEEEeecCCcCCCceeEEEecCccccc
Q 027300 151 NRGQNDSPFYTIQI--------CVPKHAINLIFSFTNGVEWDGPYRIKFLVPRAWRN 199 (225)
Q Consensus 151 ~RGkad~PiYtI~I--------~vPkHA~~LiFSFTnG~dWDGpY~L~f~VP~~~~n 199 (225)
...+.+++.|+|+| .-..+.+.|.|.|+.+-- +.|=.+.+..++.+.+
T Consensus 23 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~p~~YP-~~~P~i~l~~~~~~~~ 78 (113)
T PF05773_consen 23 EIESKSPPSLEVKLDESSSSFESSSFPSVTLHFTLPPGYP-ESPPKISLESPKNSRN 78 (113)
T ss_dssp SSTSSSSEEEEEEE--CEECCTTTTSEEEEEEEEE-SSTT-SS--EEEEEEESSSHC
T ss_pred ccccCCCCceeeeecccccccccccceeEEEEEeCCCcCC-CcCCEEEEEcCCCCCH
Confidence 44566778899988 356778899999999888 8887888888877773
No 10
>PRK11385 putativi pili assembly chaperone; Provisional
Probab=39.56 E-value=28 Score=30.35 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=28.6
Q ss_pred CCCceEEEecCCCCCCCCC----------ceEEEEccccCCCCCCCc
Q 027300 89 GKAPVYWKTMNGLPPMSGE----------KLKIFYNPYAKKLLPNED 125 (225)
Q Consensus 89 G~apVyWkT~nGlpP~sGe----------~L~lfyNp~a~~l~PNe~ 125 (225)
-|-.+||=.-.++||...+ ++||||.|..-+..|++.
T Consensus 110 DRESlf~lnv~~IPp~~~~~n~L~iair~riKLFyRP~~L~~~~~~a 156 (236)
T PRK11385 110 DRETLFELSIASVPSGKVENQSVKVAMRSVFKLFWRPEGLPGDPLEA 156 (236)
T ss_pred CceEEEEEEEEecCCCcCCCceEEEEEEeeEEEEEcccccCCChhhh
Confidence 3457999999999997532 389999999877666653
No 11
>cd01514 Elongation_Factor_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the
Probab=39.08 E-value=9.7 Score=26.39 Aligned_cols=39 Identities=21% Similarity=0.330 Sum_probs=25.1
Q ss_pred CCceEEEeeeccceeeEEEE--------eecCCcCC-CceeEEEecCc
Q 027300 157 SPFYTIQICVPKHAINLIFS--------FTNGVEWD-GPYRIKFLVPR 195 (225)
Q Consensus 157 ~PiYtI~I~vPkHA~~LiFS--------FTnG~dWD-GpY~L~f~VP~ 195 (225)
.|+|.+.|.+|...+.-+++ +.+-...+ +=+.|+..+|-
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rrg~v~~~~~~~~~~~~i~~~iP~ 48 (79)
T cd01514 1 EPIMKVEITVPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPL 48 (79)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHhcCCeeEeeEecCCCeEEEEEECCH
Confidence 48999999999765433322 12222334 56899999994
No 12
>PF02883 Alpha_adaptinC2: Adaptin C-terminal domain; InterPro: IPR008152 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. GGAs (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) are a family of monomeric clathrin adaptor proteins that are conserved from yeasts to humans. GGAs regulate clathrin-mediated the transport of proteins (such as mannose 6-phosphate receptors) from the TGN to endosomes and lysosomes through interactions with TGN-sorting receptors, sometimes in conjunction with AP-1 [, ]. GGAs bind cargo, membranes, clathrin and accessory factors. GGA1, GGA2 and GGA3 all contain a domain homologous to the ear domain of gamma-adaptin. GGAs are composed of a single polypeptide with four domains: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The VHS domain is responsible for endocytosis and signal transduction, recognising transmembrane cargo through the ACLL sequence in the cytoplasmic domains of sorting receptors []. The GAT domain (also found in Tom1 proteins) interacts with ARF (ADP-ribosylation factor) to regulate membrane trafficking [], and with ubiquitin for receptor sorting []. The hinge region contains a clathrin box for recognition and binding to clathrin, similar to that found in AP adaptins. The GAE domain is similar to the AP gamma-adaptin ear domain, and is responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. This entry represents a beta-sandwich structural motif found in the appendage (ear) domain of alpha-, beta- and gamma-adaptin from AP clathrin adaptor complexes, and the GAE (gamma-adaptin ear) domain of GGA adaptor proteins. These domains have an immunoglobulin-like beta-sandwich fold containing 7 or 8 strands in 2 beta-sheets in a Greek key topology [, ]. Although these domains share a similar fold, there is little sequence identity between the alpha/beta-adaptins and gamma-adaptin/GAE. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 3MNM_B 3ZY7_B 1GYU_A 1GYW_B 2A7B_A 1GYV_A 2E9G_A 1E42_B 2G30_A 2IV9_B ....
Probab=38.69 E-value=84 Score=22.93 Aligned_cols=32 Identities=13% Similarity=0.257 Sum_probs=23.9
Q ss_pred ccceeeEEEEeecCCcCCCc-eeEEEecCcccc
Q 027300 167 PKHAINLIFSFTNGVEWDGP-YRIKFLVPRAWR 198 (225)
Q Consensus 167 PkHA~~LiFSFTnG~dWDGp-Y~L~f~VP~~~~ 198 (225)
-.|...+.+.|+|-..++=- +.+++.|||.|+
T Consensus 22 ~~~~~~i~~~f~N~s~~~it~f~~q~avpk~~~ 54 (115)
T PF02883_consen 22 NPNQGRIKLTFGNKSSQPITNFSFQAAVPKSFK 54 (115)
T ss_dssp ETTEEEEEEEEEE-SSS-BEEEEEEEEEBTTSE
T ss_pred CCCEEEEEEEEEECCCCCcceEEEEEEeccccE
Confidence 45778889999998777644 889999998765
No 13
>PF10102 DUF2341: Domain of unknown function (DUF2341); InterPro: IPR018765 This domain of unknown function is found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins.
Probab=31.69 E-value=60 Score=24.52 Aligned_cols=41 Identities=20% Similarity=0.543 Sum_probs=30.8
Q ss_pred CCcchhh-c-cCCCceEEEecCCCCCCCCCceEEEE-ccccCCCC
Q 027300 80 RPSWAMF-E-LGKAPVYWKTMNGLPPMSGEKLKIFY-NPYAKKLL 121 (225)
Q Consensus 80 lPsWa~F-E-lG~apVyWkT~nGlpP~sGe~L~lfy-Np~a~~l~ 121 (225)
||-|-+. . .+.-.+.|--.+-+|+ ....+.|+| ||.|...-
T Consensus 16 L~ywIE~wd~~~~~A~iWVkvp~i~~-~~~~i~lyyGn~~a~~~s 59 (89)
T PF10102_consen 16 LPYWIESWDPTNEQALIWVKVPSIPA-GSTTIYLYYGNPSATSAS 59 (89)
T ss_pred eEEEEEECCCCCCeEEEEEECCCCCC-CCcEEEEEECCCCCccCC
Confidence 7777665 2 3446788888888888 888999999 78776653
No 14
>PRK10150 beta-D-glucuronidase; Provisional
Probab=31.52 E-value=37 Score=32.15 Aligned_cols=46 Identities=17% Similarity=0.331 Sum_probs=27.4
Q ss_pred EEeeeccceeeEEEEeecCCcCCCc--eeEEEecCcccccCChhhhhHH
Q 027300 162 IQICVPKHAINLIFSFTNGVEWDGP--YRIKFLVPRAWRNKPMDFFNKV 208 (225)
Q Consensus 162 I~I~vPkHA~~LiFSFTnG~dWDGp--Y~L~f~VP~~~~nkP~~fFneg 208 (225)
+.|.||-+- +....-.+..++.|. |+-+|.||+.|++|-+..-=||
T Consensus 43 ~~i~vP~~~-~~~~~~~~~~~~~G~~WYrr~f~lp~~~~gk~v~L~Feg 90 (604)
T PRK10150 43 RAMAVPGSF-NDQFADADIRNYVGDVWYQREVFIPKGWAGQRIVLRFGS 90 (604)
T ss_pred cEecCCCch-hhccccccccCCcccEEEEEEEECCcccCCCEEEEEECc
Confidence 567788653 222211112234555 9999999999998765433333
No 15
>PHA02739 hypothetical protein; Provisional
Probab=30.65 E-value=46 Score=27.31 Aligned_cols=26 Identities=19% Similarity=0.551 Sum_probs=22.5
Q ss_pred eEEEecCcccccCChhhhhHHHHHHh
Q 027300 188 RIKFLVPRAWRNKPMDFFNKVITKQM 213 (225)
Q Consensus 188 ~L~f~VP~~~~nkP~~fFnegLa~eL 213 (225)
-|+.-||+.|++.|..+--.-|.+++
T Consensus 2 ~lkiiVP~EW~~~p~~tL~~~L~~~i 27 (116)
T PHA02739 2 SLKLIVPNEWKVLPPATLQTELLRII 27 (116)
T ss_pred cEEEEechhhhhCCHHHHHHHHHHHH
Confidence 37889999999999998888777776
No 16
>PRK15195 fimbrial chaperone protein FimC; Provisional
Probab=28.96 E-value=52 Score=28.36 Aligned_cols=35 Identities=23% Similarity=0.723 Sum_probs=25.9
Q ss_pred CCceEEEecCCCCCCCCC--------------ceEEEEccccCCCCCCC
Q 027300 90 KAPVYWKTMNGLPPMSGE--------------KLKIFYNPYAKKLLPNE 124 (225)
Q Consensus 90 ~apVyWkT~nGlpP~sGe--------------~L~lfyNp~a~~l~PNe 124 (225)
|-.+||=.-.++||...+ .+||||.|..-+-.|++
T Consensus 103 rESlf~Lnv~eIP~~~~~~~~~~n~l~iair~~iKlFyRP~~l~~~~~~ 151 (229)
T PRK15195 103 RESLFWMNVKAIPSVDKNALEGRNVLQLAILSRIKLFVRPINLQELPEE 151 (229)
T ss_pred eeEEEEEEeeecCCCCcccccccceEEEEEEeEEEEEEcccccCCChhh
Confidence 446899999999995321 38999999976554443
No 17
>PF01630 Glyco_hydro_56: Hyaluronidase; InterPro: IPR018155 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 56 GH56 from CAZY comprises enzymes with only one known activity; hyaluronidase 3.2.1.35 from EC. The venom of Apis mellifera (Honeybee) contains several biologically-active peptides and two enzymes, one of which is a hyaluronidase []. The amino acid sequence of bee venom hyaluronidase contains 349 amino acids, and includes four cysteines and a number of potential glycosylation sites []. The sequence shows a high degree of similarity to PH-20, a membrane protein of mammalian sperm involved in sperm-egg adhesion, supporting the view that hyaluronidases play a role in fertilisation []. PH-20 is required for sperm adhesion to the egg zona pellucida; it is located on both the sperm plasma membrane and acrosomal membrane []. The amino acid sequence of the mature protein contains 468 amino acids, and includes six potential N-linked glycosylation sites and twelve cysteines, eight of which are tightly clustered near the C terminus [].; GO: 0004415 hyalurononglucosaminidase activity, 0005975 carbohydrate metabolic process; PDB: 1FCQ_A 1FCV_A 1FCU_A 2J88_A 2PE4_A 2ATM_A.
Probab=28.95 E-value=33 Score=32.02 Aligned_cols=32 Identities=38% Similarity=0.765 Sum_probs=20.2
Q ss_pred CCCCceEEEEccccCCCCC-CCceeeeecCCCCC
Q 027300 104 MSGEKLKIFYNPYAKKLLP-NEDFGIGFNGGFNQ 136 (225)
Q Consensus 104 ~sGe~L~lfyNp~a~~l~P-Ne~fGIaFNGgFNQ 136 (225)
-.||.++|||.+--- +-| =++-|..+|||.=|
T Consensus 44 f~G~~itIfY~~~lG-~yP~~~~~~~~~NGGlPQ 76 (337)
T PF01630_consen 44 FRGQNITIFYEPRLG-LYPYYDEQGKPVNGGLPQ 76 (337)
T ss_dssp SSSSSEEEEESTSSS-T--EEEETSEEETTSSGG
T ss_pred ccCCeEEEEeCCCCC-CcceECCCCCeecCCCCC
Confidence 369999999998322 122 12234888888765
No 18
>PRK15188 fimbrial chaperone protein BcfB; Provisional
Probab=27.12 E-value=61 Score=28.22 Aligned_cols=37 Identities=16% Similarity=0.421 Sum_probs=28.3
Q ss_pred CCCceEEEecCCCCCCCCC-------------ceEEEEccccCCCCCCCc
Q 027300 89 GKAPVYWKTMNGLPPMSGE-------------KLKIFYNPYAKKLLPNED 125 (225)
Q Consensus 89 G~apVyWkT~nGlpP~sGe-------------~L~lfyNp~a~~l~PNe~ 125 (225)
-|-.+||=...++||..-. .+||||-|..-+..+++.
T Consensus 104 DRESlf~lnv~~IP~~~~~~~~~n~l~ia~r~~IKLFyRP~~l~~~~~~a 153 (228)
T PRK15188 104 DRESVFYLNSKAIPSVDKNKLTGNSLQIATQSVIKLFIRPKNLAEAPAHA 153 (228)
T ss_pred CceEEEEEEEEecCCCCccccccceEEEEEeeeEEEEECCccCCCChhhh
Confidence 3447999999999996431 389999999877666654
No 19
>PF05725 FNIP: FNIP Repeat; InterPro: IPR008615 This repeat is approximately 22 residues long and is only found in Dictyostelium discoideum (Slime mould). It appears to be related to IPR001611 from INTERPRO. The alignment consists of two tandem repeats. It is termed the FNIP repeat after the pattern of conserved residues.
Probab=26.76 E-value=52 Score=21.23 Aligned_cols=22 Identities=32% Similarity=0.533 Sum_probs=16.4
Q ss_pred CCCCceeeeecCCCCCccccCC
Q 027300 121 LPNEDFGIGFNGGFNQPFMCGG 142 (225)
Q Consensus 121 ~PNe~fGIaFNGgFNQPIMCGG 142 (225)
.|+..=-+-|+..|||||..|=
T Consensus 10 iP~~l~~L~~g~~fn~~i~~~~ 31 (44)
T PF05725_consen 10 IPSSLKSLIFGSSFNQPIEPGS 31 (44)
T ss_pred eCCCCeEEEECCccCccCCCCc
Confidence 4555556788999999998663
No 20
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=26.27 E-value=40 Score=27.11 Aligned_cols=30 Identities=37% Similarity=0.602 Sum_probs=21.4
Q ss_pred hhhhCCCCCCceEEEeee-cc--------ceeeEEEEee
Q 027300 149 RKNRGQNDSPFYTIQICV-PK--------HAINLIFSFT 178 (225)
Q Consensus 149 ~k~RGkad~PiYtI~I~v-Pk--------HA~~LiFSFT 178 (225)
-|.|-|+.+|||.=-|-+ |+ -.-++.|||+
T Consensus 55 C~kRkrsRrPIYrPvI~~~P~~~~~~~~~GL~~~~fs~~ 93 (94)
T PF05393_consen 55 CKKRKRSRRPIYRPVIGLEPQNLQIHRDDGLRNLLFSFQ 93 (94)
T ss_pred HHHhhhccCCccccccccCCCcccccccCCcceeEEEee
Confidence 378999999999876663 22 2336778886
No 21
>PF11619 P53_C: Transcription factor P53 - C terminal domain; InterPro: IPR024631 The p53 tumour suppressor [, , , , ] is a protein found in increased amounts in a wide variety of transformed cells. It is also detectable in many proliferating non-transformed cells, but it is undetectable or present at low levels in resting cells. It is frequently mutated or inactivated in many types of cancer. p53 seems to act as a tumour suppressor in some, but probably not all, tumour types. p53 has been implicated in cell cycle regulation, particularly in the monitoring of genomic DNA integrity prior to replication; for this reason it has been dubbed `guardian of the genome'. p53 is a sequence-specific DNA-binding protein and transcription factor. The structure of p53 comprises 4 domains: an N-terminal transactivation domain; a central DNA-binding domain; an oligomerisation domain; and a C-terminal, basic, regulatory domain [, ]. The structure of the oligomerisation domain consists of a dimer of dimers, each dimer consisting of 2 anti-parallel alpha-helices and an anti-parallel beta-sheet. The sheets lie on opposite sides of the tetramer and the helices form an unusual 4-helix bundle [, ]. While the majority of p53 mutations found in human cancers are located in the DNA-binding domain, some are also found in the oligomerisation domain. This entry represents the C-terminal domain of Drosophila transcription factor p53. While the rest of the protein is quite conserved between the different transcription factors such as p53 and p73, the C-terminal domain is highly divergent. The Drosophila p53 structure is characterised by an additional N-terminal beta-strand and a C-terminal helix [].; PDB: 2RP4_B.
Probab=26.01 E-value=46 Score=25.65 Aligned_cols=13 Identities=38% Similarity=0.866 Sum_probs=12.1
Q ss_pred CCceeEEEecCcc
Q 027300 184 DGPYRIKFLVPRA 196 (225)
Q Consensus 184 DGpY~L~f~VP~~ 196 (225)
||.|+|.+.+|++
T Consensus 14 dGdYrL~itcp~K 26 (71)
T PF11619_consen 14 DGDYRLVITCPKK 26 (71)
T ss_dssp TTCEEEEEEESSH
T ss_pred CCceEEEEecCcH
Confidence 8999999999986
No 22
>PF08648 DUF1777: Protein of unknown function (DUF1777); InterPro: IPR013957 This entry shows eukaryotic proteins of unknown function. Some of the proteins are putative nucleic acid binding proteins.
Probab=24.20 E-value=32 Score=27.67 Aligned_cols=7 Identities=71% Similarity=1.668 Sum_probs=6.4
Q ss_pred CCCCCcc
Q 027300 132 GGFNQPF 138 (225)
Q Consensus 132 GgFNQPI 138 (225)
||||-|+
T Consensus 170 GGFNRpL 176 (180)
T PF08648_consen 170 GGFNRPL 176 (180)
T ss_pred cccCCCC
Confidence 9999996
No 23
>TIGR01943 rnfA electron transport complex, RnfABCDGE type, A subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit.
Probab=24.19 E-value=43 Score=28.87 Aligned_cols=18 Identities=28% Similarity=0.617 Sum_probs=16.2
Q ss_pred ecCcccccCChhhhhHHH
Q 027300 192 LVPRAWRNKPMDFFNKVI 209 (225)
Q Consensus 192 ~VP~~~~nkP~~fFnegL 209 (225)
+||+.||+.|+.+.--|+
T Consensus 161 ~vP~~~~G~pI~li~agl 178 (190)
T TIGR01943 161 DVPKAFRGSPIALITAGL 178 (190)
T ss_pred CCCccccCcCHHHHHHHH
Confidence 699999999999988776
No 24
>smart00216 VWD von Willebrand factor (vWF) type D domain. Von Willebrand factor contains several type D domains: D1 and D2 are present within the N-terminal propeptide whereas the remaining D domains are required for multimerisation.
Probab=23.77 E-value=94 Score=23.63 Aligned_cols=20 Identities=30% Similarity=0.571 Sum_probs=16.7
Q ss_pred CcCCCceeEEEecCcccccC
Q 027300 181 VEWDGPYRIKFLVPRAWRNK 200 (225)
Q Consensus 181 ~dWDGpY~L~f~VP~~~~nk 200 (225)
+.|||--.++++||..++|+
T Consensus 122 v~~dg~~~~~V~~~~~~~g~ 141 (162)
T smart00216 122 VTFDGLTLLSVQLPSRYRGK 141 (162)
T ss_pred EEECCCcEEEEEECHHHCCC
Confidence 35899777999999988887
No 25
>cd03713 EFG_mtEFG_C EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide
Probab=23.73 E-value=28 Score=24.07 Aligned_cols=36 Identities=25% Similarity=0.369 Sum_probs=23.5
Q ss_pred CCceEEEeeeccceee-----------EEEEeecCCcCCCceeEEEecCc
Q 027300 157 SPFYTIQICVPKHAIN-----------LIFSFTNGVEWDGPYRIKFLVPR 195 (225)
Q Consensus 157 ~PiYtI~I~vPkHA~~-----------LiFSFTnG~dWDGpY~L~f~VP~ 195 (225)
.|+|.+.|.+|...+. -+.+... +++-..++..+|-
T Consensus 1 EPi~~~~I~~p~~~~g~v~~~l~~rrg~i~~~~~---~~~~~~i~~~iP~ 47 (78)
T cd03713 1 EPIMKVEVTVPEEYMGDVIGDLSSRRGQILGTES---RGGWKVIKAEVPL 47 (78)
T ss_pred CCEEEEEEEcCHHHHHHHHHHHHHcCCceEceec---cCCcEEEEEEcCH
Confidence 4899999999965432 1233332 3456789999984
No 26
>PRK15285 putative fimbrial chaperone protein StfD; Provisional
Probab=23.40 E-value=75 Score=28.04 Aligned_cols=36 Identities=22% Similarity=0.617 Sum_probs=27.3
Q ss_pred CCCceEEEecCCCCCCCCC----------ceEEEEccccCCCCCCC
Q 027300 89 GKAPVYWKTMNGLPPMSGE----------KLKIFYNPYAKKLLPNE 124 (225)
Q Consensus 89 G~apVyWkT~nGlpP~sGe----------~L~lfyNp~a~~l~PNe 124 (225)
-|-.|||=..-+.||...+ ++||||-|++-+..+++
T Consensus 105 DRESlfwlnv~~IPp~~~~~n~L~iairtrIKLfYRP~~L~~~~~~ 150 (250)
T PRK15285 105 DRETLFYYNVREIPPQSDKPNTLQIALQTRIKVFYRPQALSKIDMQ 150 (250)
T ss_pred CceEEEEEEEEEcCCCCCCCcEEEEEeeeeeeEEECcccccCChhh
Confidence 3457999999999997532 48999999986555543
No 27
>PF00094 VWD: von Willebrand factor type D domain; InterPro: IPR001846 A family of growth regulators (originally called cef10, connective tissue growth factor, fisp-12, cyr61, or, alternatively, beta IG-M1 and beta IG-M2), all belong to immediate-early genes expressed after induction by growth factors or certain oncogenes. Sequence analysis of this family revealed the presence of four distinct modules. Each module has homologues in other extracellular mosaic proteins such as Von Willebrand factor, slit, thrombospondins, fibrillar collagens, IGF-binding proteins and mucins. Classification and analysis of these modules suggests the location of binding regions and, by analogy to better characterised modules in other proteins, sheds some light onto the structure of this new family []. 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 []. One of the functions of von Willebrand factor (vWF) is to serve as a carrier of clotting factor VIII (FVIII). The native conformation of the D' domain of vWF is not only required for factor VIII (FVIII) binding but also for normal multimerisation and optimal secretion. The interaction between blood clotting factor VIII and VWF is necessary for normal survival of blood clotting factor VIII in blood circulation. The VWFD domain is a highly structured region, in which the first conserved Cys has been found to form a disulphide bridge with the second conserved one [].
Probab=23.04 E-value=1.5e+02 Score=21.74 Aligned_cols=32 Identities=28% Similarity=0.507 Sum_probs=23.3
Q ss_pred ceeeEEEEeecCC--cCCCceeEEEecCcccccC
Q 027300 169 HAINLIFSFTNGV--EWDGPYRIKFLVPRAWRNK 200 (225)
Q Consensus 169 HA~~LiFSFTnG~--dWDGpY~L~f~VP~~~~nk 200 (225)
+-+.+.++..-++ +|||-..+.+.+|..|+++
T Consensus 104 ~~~~v~~~~~~~v~~~~~~~~~~~v~~~~~~~g~ 137 (159)
T PF00094_consen 104 GFVVVVFSSGVRVQVNWDGNMSVYVSVPPWYKGK 137 (159)
T ss_pred ccEEEEEecCCeEEEEEecccccccccccccccc
Confidence 4344445554454 6999889999999999887
No 28
>PF06572 DUF1131: Protein of unknown function (DUF1131); InterPro: IPR010938 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2QZB_B.
Probab=22.76 E-value=36 Score=29.44 Aligned_cols=25 Identities=28% Similarity=0.779 Sum_probs=12.9
Q ss_pred EeeeccceeeEEEEeecCCcCCCceeE
Q 027300 163 QICVPKHAINLIFSFTNGVEWDGPYRI 189 (225)
Q Consensus 163 ~I~vPkHA~~LiFSFTnG~dWDGpY~L 189 (225)
-||+-.-.-.+.|-|+ | +|+||+-|
T Consensus 128 V~C~ap~s~~VsYvF~-g-~W~GPegl 152 (171)
T PF06572_consen 128 VECVAPQSQHVSYVFS-G-GWSGPEGL 152 (171)
T ss_dssp EEEE-TT-SSEEEEEE------S-TTS
T ss_pred eEEecCCCCcEEEEec-C-CccCCCCC
Confidence 4787666667777777 5 99999854
No 29
>PF14545 DBB: Dof, BCAP, and BANK (DBB) motif,
Probab=22.50 E-value=82 Score=26.36 Aligned_cols=27 Identities=26% Similarity=0.710 Sum_probs=21.9
Q ss_pred eeeEEEEeecCC------cCCCceeEEEecCcc
Q 027300 170 AINLIFSFTNGV------EWDGPYRIKFLVPRA 196 (225)
Q Consensus 170 A~~LiFSFTnG~------dWDGpY~L~f~VP~~ 196 (225)
.+-++|...|.. .|.-||+++|.+|+-
T Consensus 28 ~~eVef~~~n~~~~~~~~~~~N~yt~~~~aPd~ 60 (142)
T PF14545_consen 28 TVEVEFESNNKPIRRVPAKWENPYTLQFKAPDF 60 (142)
T ss_pred eEEEEEEeCCCeeEeccceEECCEEEEEECchh
Confidence 456677777765 599999999999987
No 30
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=21.88 E-value=58 Score=24.05 Aligned_cols=13 Identities=31% Similarity=0.902 Sum_probs=12.0
Q ss_pred CCCceEEEEcccc
Q 027300 105 SGEKLKIFYNPYA 117 (225)
Q Consensus 105 sGe~L~lfyNp~a 117 (225)
.|+.++++|||.-
T Consensus 94 ~G~~V~V~Y~P~~ 106 (148)
T PF12158_consen 94 IGDTVTVYYNPNN 106 (148)
T ss_pred CcCEEEEEECCcC
Confidence 8999999999984
No 31
>PRK15192 fimbrial chaperone BcfG; Provisional
Probab=21.41 E-value=84 Score=27.50 Aligned_cols=36 Identities=17% Similarity=0.369 Sum_probs=27.0
Q ss_pred CCCceEEEecCCCCCCCC-C---------ceEEEEccccCCCCCCC
Q 027300 89 GKAPVYWKTMNGLPPMSG-E---------KLKIFYNPYAKKLLPNE 124 (225)
Q Consensus 89 G~apVyWkT~nGlpP~sG-e---------~L~lfyNp~a~~l~PNe 124 (225)
-|-.+||=....+||... + ++||||-|.+-+..+++
T Consensus 105 DRESlf~lnv~~IPp~~~~~n~l~iair~riKlFYRP~~L~~~~~~ 150 (234)
T PRK15192 105 DRESLFTLSIAAIPSGKPEANRVQMAFRSALKLLYRPEGLAGNPQQ 150 (234)
T ss_pred cceEEEEEEEEecCCCCCCCcEEEEEEEeeeeEEEccccccCChhh
Confidence 344799999999999543 2 38999999987655543
No 32
>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
Probab=21.00 E-value=53 Score=23.54 Aligned_cols=44 Identities=14% Similarity=0.205 Sum_probs=25.6
Q ss_pred eeEEEEeecCCcCCCceeEEEecCcccccCChhhh-------hHHHHHHhhcc
Q 027300 171 INLIFSFTNGVEWDGPYRIKFLVPRAWRNKPMDFF-------NKVITKQMSVT 216 (225)
Q Consensus 171 ~~LiFSFTnG~dWDGpY~L~f~VP~~~~nkP~~fF-------negLa~eLs~e 216 (225)
...++-||||.+++++ ---++=+.++++.+..| ++...++|+..
T Consensus 104 ~~~iiliTDG~~~~~~--~~~~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~~ 154 (161)
T cd01450 104 PKVIIVLTDGRSDDGG--DPKEAAAKLKDEGIKVFVVGVGPADEEELREIASC 154 (161)
T ss_pred CeEEEEECCCCCCCCc--chHHHHHHHHHCCCEEEEEeccccCHHHHHHHhCC
Confidence 4667889999999985 11223344455555555 33444555555
No 33
>PF14508 GH97_N: Glycosyl-hydrolase 97 N-terminal; PDB: 3A24_A 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A.
Probab=20.81 E-value=59 Score=28.11 Aligned_cols=69 Identities=22% Similarity=0.367 Sum_probs=38.1
Q ss_pred CCCCCCCceeeeecCCCCCccccCCchhhhhhhhhCCC-C---CCceEEEeeeccceeeEEEEeecCCcCCCceeEEEec
Q 027300 118 KKLLPNEDFGIGFNGGFNQPFMCGGEPRAMLRKNRGQN-D---SPFYTIQICVPKHAINLIFSFTNGVEWDGPYRIKFLV 193 (225)
Q Consensus 118 ~~l~PNe~fGIaFNGgFNQPIMCGGEPR~M~~k~RGka-d---~PiYtI~I~vPkHA~~LiFSFTnG~dWDGpY~L~f~V 193 (225)
..++.+...|+-+++|- .-|...+ ..+..|.+. + .|.+--+-.+..|+--|.++|.+... -.++|.|||
T Consensus 28 ~~vl~~S~LGl~~~~~~----~~~~~~~-~~~~~~~~~V~e~y~~~~Gk~~~~~~~yne~~l~~~~~~~--~~l~l~fRa 100 (259)
T PF14508_consen 28 KTVLEPSPLGLVLDDGD----VFGDGLK-VVSVSRRSHVDETYTPVWGKRSEVRNHYNELTLSFKNKYG--RRLNLEFRA 100 (259)
T ss_dssp EEEEEEEEEEEEETTS-----EETTT-E-EEEEEEEEEEEEEEE-TTTTSSEEEEEEEEEEEEECCCCC--EEEEEEEEE
T ss_pred EEEEecCCCcEEECCCC----cccCCCE-EEEeEeeeeccccccccccceeEEeeeEEEEEEEEecCCC--ceeEEEEEE
Confidence 34555667788887773 1122222 122222221 1 12223345677899999999998654 577788877
No 34
>PRK09926 putative chaperone protein EcpD; Provisional
Probab=20.61 E-value=98 Score=26.77 Aligned_cols=35 Identities=29% Similarity=0.693 Sum_probs=26.1
Q ss_pred CCCceEEEecCCCCCCCC------C---------ceEEEEccccCCCCCC
Q 027300 89 GKAPVYWKTMNGLPPMSG------E---------KLKIFYNPYAKKLLPN 123 (225)
Q Consensus 89 G~apVyWkT~nGlpP~sG------e---------~L~lfyNp~a~~l~PN 123 (225)
.|-.+||=.-..+||..- + .+||||.|..-+..+.
T Consensus 107 DrESlf~lnv~eIP~~~~~~~~~~~n~l~iair~~IKLFyRP~~l~~~~~ 156 (246)
T PRK09926 107 DRESVFWFNVLEVPPKPDAEKVANQSLLQLAFRTRIKLFYRPDGLKGNPS 156 (246)
T ss_pred CceEEEEEEeeecCCCCccccccccceEEEeeeeeEEEEEcCccCCCChh
Confidence 455799999999999631 1 3899999998655443
No 35
>PF11763 DIPSY: Cell-wall adhesin ligand-binding C-terminal; InterPro: IPR021746 The DIPSY domain is characterised by the distinctive D*I*PSY motif at the very C terminus of yeast cell-wall glycoproteins. It appears not to be conserved in any other species, however. In fungi, cell adhesion is required for flocculation, mating and virulence, and is mediated by covalently bound cell wall proteins termed adhesins. Map4, an adhesin required for mating in Schizosaccharomyces pombe, is N-glycosylated and O-glycosylated, and is an endogenous substrate for the mannosyl transferase Oma4p. Map4 has a modular structure with an N-terminal signal peptide, a serine and threonine (S/T)-rich domain that includes nine repeats of 36 amino acids (rich in serine and threonine residues, but lacking glutamines), and a C-terminal DIPSY domain with no glycosyl-phosphatidyl inositol (GPI)-anchor signal. The N-terminal S/T-rich regions, are required for cell wall attachment, but the C-terminal DIPSY domain is required for agglutination and mating in liquid and solid media [].
Probab=20.51 E-value=1.3e+02 Score=25.19 Aligned_cols=28 Identities=32% Similarity=0.593 Sum_probs=20.9
Q ss_pred CCceEEEeeec-cceeeEEEEeecCCcCCCceeEE
Q 027300 157 SPFYTIQICVP-KHAINLIFSFTNGVEWDGPYRIK 190 (225)
Q Consensus 157 ~PiYtI~I~vP-kHA~~LiFSFTnG~dWDGpY~L~ 190 (225)
.|+|++++-=| +|..+++ ++=||-|+.+
T Consensus 47 rP~Y~v~~~D~~~~sf~I~------kn~dG~~~Ft 75 (123)
T PF11763_consen 47 RPIYRVYHDDPNKSSFNII------KNNDGTYQFT 75 (123)
T ss_pred ccEEEEeecCCCcceEEEE------ecCCCcEEEE
Confidence 59999999999 8888876 4556655433
No 36
>PRK15253 putative fimbrial assembly chaperone protein StcB; Provisional
Probab=20.25 E-value=82 Score=27.63 Aligned_cols=36 Identities=19% Similarity=0.571 Sum_probs=27.1
Q ss_pred CCCceEEEecCCCCCCC----CC---------ceEEEEccccCCCCCCC
Q 027300 89 GKAPVYWKTMNGLPPMS----GE---------KLKIFYNPYAKKLLPNE 124 (225)
Q Consensus 89 G~apVyWkT~nGlpP~s----Ge---------~L~lfyNp~a~~l~PNe 124 (225)
-|-.|||=.-.+.||.. ++ ++||||-|+.-+..+++
T Consensus 114 DRESlfwlnv~~IPp~~~~~~~~n~l~iairtriKLFYRP~~L~~~~~~ 162 (242)
T PRK15253 114 NKESLFYLNVLDIPPNSQENAGKNVLKFAMQNRIKLIWRPSRIAAVTKD 162 (242)
T ss_pred ceeEEEEEEEEEcCCCCCCcCcCcEEEEEeeeEEEEEEcchhcccchhh
Confidence 34579999999999953 22 38999999986555554
No 37
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=20.14 E-value=38 Score=23.94 Aligned_cols=37 Identities=24% Similarity=0.355 Sum_probs=23.9
Q ss_pred CCCceEEEeeeccceee-----------EEEEeecCCcCCCceeEEEecCc
Q 027300 156 DSPFYTIQICVPKHAIN-----------LIFSFTNGVEWDGPYRIKFLVPR 195 (225)
Q Consensus 156 d~PiYtI~I~vPkHA~~-----------LiFSFTnG~dWDGpY~L~f~VP~ 195 (225)
..|+|.+.|.+|...+. -+.+.++ .+.-..+++.+|-
T Consensus 2 lEPi~~~~I~~p~~~~g~v~~~l~~rrG~i~~~~~---~~~~~~i~~~iP~ 49 (85)
T smart00838 2 LEPIMKVEVTVPEEYMGDVIGDLNSRRGKIEGMEQ---RGGAQVIKAKVPL 49 (85)
T ss_pred cCCEEEEEEEeCHHHHHHHHHHHHHcCCEEECeec---cCCcEEEEEECCH
Confidence 46999999999964322 1233333 3345889999983
Done!