Query 023278
Match_columns 284
No_of_seqs 27 out of 29
Neff 1.9
Searched_HMMs 46136
Date Fri Mar 29 02:49:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023278.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023278hhsearch_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 7.8E-05 1.7E-09 56.9 4.2 76 107-187 1-77 (87)
2 PLN02316 synthase/transferase 96.5 0.0071 1.5E-07 64.2 7.3 93 100-196 321-418 (1036)
3 PLN02316 synthase/transferase 96.2 0.011 2.3E-07 62.9 6.6 124 100-229 483-632 (1036)
4 PF14125 DUF4292: Domain of un 56.3 15 0.00032 31.2 3.6 38 161-199 169-208 (210)
5 PF06200 tify: tify domain; I 51.8 12 0.00025 25.9 1.8 14 103-116 1-14 (36)
6 PF06830 Root_cap: Root cap; 46.2 9.7 0.00021 29.0 0.8 22 127-149 23-44 (57)
7 PF14524 Wzt_C: Wzt C-terminal 43.1 36 0.00078 25.5 3.5 78 93-173 17-97 (142)
8 smart00809 Alpha_adaptinC2 Ada 39.0 76 0.0017 23.5 4.7 37 164-200 12-49 (104)
9 cd00418 GlxRS_core catalytic c 37.8 33 0.00071 31.1 3.0 28 181-218 64-92 (230)
10 cd01514 Elongation_Factor_C El 36.4 11 0.00023 27.2 -0.2 39 158-196 1-48 (79)
11 PF02883 Alpha_adaptinC2: Adap 36.1 93 0.002 23.6 4.9 32 168-199 22-54 (115)
12 PRK11385 putativi pili assembl 35.0 36 0.00078 30.7 2.8 37 90-126 110-156 (236)
13 PF05773 RWD: RWD domain; Int 34.1 95 0.0021 22.6 4.5 63 152-215 23-93 (113)
14 PF10102 DUF2341: Domain of un 32.1 56 0.0012 25.6 3.1 41 81-122 16-59 (89)
15 PRK10150 beta-D-glucuronidase; 29.3 41 0.00089 33.0 2.4 47 163-210 43-91 (604)
16 PF01630 Glyco_hydro_56: Hyalu 25.6 43 0.00093 32.4 1.8 33 105-137 44-76 (337)
17 PRK15195 fimbrial chaperone pr 25.2 65 0.0014 28.8 2.7 35 91-125 103-151 (229)
18 PF05393 Hum_adeno_E3A: Human 24.6 44 0.00095 27.7 1.4 30 150-179 55-93 (94)
19 PRK15188 fimbrial chaperone pr 24.3 72 0.0016 28.8 2.9 37 90-126 104-153 (228)
20 PF11619 P53_C: Transcription 23.9 52 0.0011 26.1 1.6 13 185-197 14-26 (71)
21 smart00216 VWD von Willebrand 23.7 91 0.002 24.6 3.0 20 182-201 122-141 (162)
22 PF00094 VWD: von Willebrand f 22.4 1.5E+02 0.0032 22.6 3.8 32 170-201 104-137 (159)
23 cd03713 EFG_mtEFG_C EFG_mtEFG_ 21.8 31 0.00067 24.8 0.0 36 158-196 1-47 (78)
24 TIGR01943 rnfA electron transp 21.0 50 0.0011 29.5 1.2 19 193-211 161-179 (190)
25 PHA02739 hypothetical protein; 21.0 77 0.0017 26.9 2.2 26 189-214 2-27 (116)
26 PF11763 DIPSY: Cell-wall adhe 20.2 1.3E+02 0.0029 26.0 3.5 39 158-204 47-86 (123)
27 PRK15285 putative fimbrial cha 20.1 94 0.002 28.4 2.8 35 91-125 106-150 (250)
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=97.60 E-value=7.8e-05 Score=56.89 Aligned_cols=76 Identities=25% Similarity=0.528 Sum_probs=39.5
Q ss_pred CCceEEEEccccCCCCCCCceeeeecCCCCCccccCCchhhhhhhhhCCCCCCceEEEeeeccceeeEEEEeecC-CCCC
Q 023278 107 GEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQPFMCGGEPRAMLRKNRGQNDSPFYTIQICVPKHAINLIFSFTNG-VEWD 185 (284)
Q Consensus 107 Ge~L~lfyNp~as~l~PNe~fGiaFNGGFNQPIMCGGEPR~M~~k~RGkad~PiYtI~I~vPkHa~~LiFSFTnG-~~WD 185 (284)
|+.++|||||..+.|.-.. -|=+-+|||. -. ....-.|.+... .....-++..|.||+.|..|.|-|+|| -.||
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 111223433221 111678999999999999999999998 4788
Q ss_pred Cc
Q 023278 186 GP 187 (284)
Q Consensus 186 Gp 187 (284)
--
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=96.47 E-value=0.0071 Score=64.17 Aligned_cols=93 Identities=20% Similarity=0.352 Sum_probs=69.1
Q ss_pred CCCCCCCCCceEEEEccccCCCCCCCceeeeecCCCCCccccCCchhhhhhhhhCCCCCCceEEEeeeccceeeEEEEee
Q 023278 100 NGLPPMSGEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQPFMCGGEPRAMLRKNRGQNDSPFYTIQICVPKHAINLIFSFT 179 (284)
Q Consensus 100 nGlpP~sGe~L~lfyNp~as~l~PNe~fGiaFNGGFNQPIMCGGEPR~M~~k~RGkad~PiYtI~I~vPkHa~~LiFSFT 179 (284)
....|-+|+.++|||||+-+.|.-.+ -|=+.||||.=..-.+.+-.|.+-+.+.-+ .+.-.|.||+-|..|-|-|+
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 35678999999999999999996433 467788888644333322234443433333 88999999999999999999
Q ss_pred cC-----CCCCCceeEEEecCc
Q 023278 180 NG-----VEWDGPYRIKFLVPR 196 (284)
Q Consensus 180 nG-----~~WDGpY~L~f~VP~ 196 (284)
|| ..||--....|.+|=
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=96.16 E-value=0.011 Score=62.88 Aligned_cols=124 Identities=21% Similarity=0.330 Sum_probs=87.6
Q ss_pred CCCCCCCCCceEEEEccccCCCCCCCceeeeecCCCCCccccCC--chhhhhhhhhCCCCCCceEEEeeeccceeeEEEE
Q 023278 100 NGLPPMSGEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQPFMCGG--EPRAMLRKNRGQNDSPFYTIQICVPKHAINLIFS 177 (284)
Q Consensus 100 nGlpP~sGe~L~lfyNp~as~l~PNe~fGiaFNGGFNQPIMCGG--EPR~M~~k~RGkad~PiYtI~I~vPkHa~~LiFS 177 (284)
.=+-|.+|+.++|||||.-+-|.-..+ |=|-||||.=.---| .|-.|.+.+-| .-+.-.|.||.-|..+-|-
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 345689999999999999888875544 779999997555555 58888888766 5778999999999999999
Q ss_pred eecCC---CCCCceeEEEecCcc---------------cccCCh------hhhhhhHHHhhhccCcccccccCCCc
Q 023278 178 FTNGV---EWDGPYRIKFLVPRA---------------WRNKPM------DFFNKGLADQLSKDGACEKAIFPDTD 229 (284)
Q Consensus 178 FTnG~---~WDGpY~L~f~VP~~---------------~~nkP~------~fFnegLa~eLs~eGACd~AIfPd~~ 229 (284)
|.+|- .||--....+.+|-. +---|. .=.=-+|+++|.+.|.--.-|-|.-.
T Consensus 557 Fs~~~~g~~yDn~~~~dyh~~v~g~~~~~~pM~Il~VSsE~~P~aKvGGLgDVV~sLp~ALa~~Gh~V~VitP~Y~ 632 (1036)
T PLN02316 557 FSEKEEGGIFDNRNGLDYHIPVFGGIAKEPPMHIVHIAVEMAPIAKVGGLGDVVTSLSRAVQDLNHNVDIILPKYD 632 (1036)
T ss_pred EecCCCCCCcCCCCCcCCcccccCCCCCCCCcEEEEEEcccCCCCCcCcHHHHHHHHHHHHHHcCCEEEEEecCCc
Confidence 96653 476655554444321 111121 12336788999999976566666543
No 4
>PF14125 DUF4292: Domain of unknown function (DUF4292)
Probab=56.31 E-value=15 Score=31.16 Aligned_cols=38 Identities=24% Similarity=0.610 Sum_probs=30.2
Q ss_pred eEEEeeecc--ceeeEEEEeecCCCCCCceeEEEecCcccc
Q 023278 161 YTIQICVPK--HAINLIFSFTNGVEWDGPYRIKFLVPRAWR 199 (284)
Q Consensus 161 YtI~I~vPk--Ha~~LiFSFTnG~~WDGpY~L~f~VP~~~~ 199 (284)
..|+|.++. .-+.|.+.|.+ ++++.|..+.|.||++++
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 888999999999999876
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=51.82 E-value=12 Score=25.87 Aligned_cols=14 Identities=36% Similarity=0.664 Sum_probs=11.2
Q ss_pred CCCCCCceEEEEcc
Q 023278 103 PPMSGEKLKIFYNP 116 (284)
Q Consensus 103 pP~sGe~L~lfyNp 116 (284)
|+....+|+||||=
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=46.15 E-value=9.7 Score=29.00 Aligned_cols=22 Identities=27% Similarity=0.395 Sum_probs=16.9
Q ss_pred eeeeecCCCCCccccCCchhhhh
Q 023278 127 FGIGFNGGFNQPFMCGGEPRAML 149 (284)
Q Consensus 127 fGiaFNGGFNQPIMCGGEPR~M~ 149 (284)
|=--.+.|-+.||| |||++..+
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 99998654
No 7
>PF14524 Wzt_C: Wzt C-terminal domain; PDB: 2R5O_B.
Probab=43.12 E-value=36 Score=25.49 Aligned_cols=78 Identities=18% Similarity=0.207 Sum_probs=48.3
Q ss_pred ceEeEecCCCCC---CCCCceEEEEccccCCCCCCCceeeeecCCCCCccccCCchhhhhhhhhCCCCCCceEEEeeecc
Q 023278 93 PVYWKTMNGLPP---MSGEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQPFMCGGEPRAMLRKNRGQNDSPFYTIQICVPK 169 (284)
Q Consensus 93 pVyWkt~nGlpP---~sGe~L~lfyNp~as~l~PNe~fGiaFNGGFNQPIMCGGEPR~M~~k~RGkad~PiYtI~I~vPk 169 (284)
-|.....+|.+- .+||.++|-+.=.+.+-.++-.+|+.+-.-..|+|+.--. ..+. ..=.....=.|++++.+|+
T Consensus 17 ~v~i~~~~g~~~~~~~~ge~~~i~i~~~~~~~i~~~~~~~~i~~~~g~~v~~~~t-~~~~-~~~~~~~~g~~~~~~~i~~ 94 (142)
T PF14524_consen 17 SVRILDSDGEPTSSFESGEPIRIRIDYEVNEDIDDPVFGFAIRDSDGQRVFGTNT-YDSG-FPIPLSEGGTYEVTFTIPK 94 (142)
T ss_dssp EEEEEETTEES-SSEETTSEEEEEEEEEESS-EEEEEEEEEEEETT--EEEEEEH-HHHT---EEE-TT-EEEEEEEEE-
T ss_pred EEEEEeCCCCEeeEEeCCCEEEEEEEEEECCCCCccEEEEEEEcCCCCEEEEECc-cccC-ccccccCCCEEEEEEEEcC
Confidence 355666777766 3799999999888888889999999999888898875222 2221 1111111557889999998
Q ss_pred ceee
Q 023278 170 HAIN 173 (284)
Q Consensus 170 Ha~~ 173 (284)
+ |+
T Consensus 95 ~-L~ 97 (142)
T PF14524_consen 95 P-LN 97 (142)
T ss_dssp --B-
T ss_pred c-cC
Confidence 8 54
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=38.96 E-value=76 Score=23.48 Aligned_cols=37 Identities=16% Similarity=0.212 Sum_probs=28.5
Q ss_pred EeeeccceeeEEEEeecCCCCCCc-eeEEEecCccccc
Q 023278 164 QICVPKHAINLIFSFTNGVEWDGP-YRIKFLVPRAWRN 200 (284)
Q Consensus 164 ~I~vPkHa~~LiFSFTnG~~WDGp-Y~L~f~VP~~~~n 200 (284)
+|.-..+.+.+...|+|-.+|+=- +.+++.|||.|+-
T Consensus 12 ~~~~~~~~~~i~~~~~N~s~~~it~f~~~~avpk~~~l 49 (104)
T smart00809 12 KFERRPGLIRITLTFTNKSPSPITNFSFQAAVPKSLKL 49 (104)
T ss_pred EEEcCCCeEEEEEEEEeCCCCeeeeEEEEEEcccceEE
Confidence 333345778899999999888743 8899999997763
No 9
>cd00418 GlxRS_core catalytic core domain of glutamyl-tRNA and glutaminyl-tRNA synthetase. Glutamyl-tRNA synthetase(GluRS)/Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Glu or Gln, respectively, to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea, cellular organelles, and some bacteria lack GlnRS. In these cases, the "non-discriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme. The discriminating form of GluRS differs from GlnRS and the non-discriminating form of GluRS in their C-terminal anti-codon bind
Probab=37.81 E-value=33 Score=31.12 Aligned_cols=28 Identities=39% Similarity=0.998 Sum_probs=19.4
Q ss_pred CCCCCC-ceeEEEecCcccccCChhhhhhhHHHhhhccC
Q 023278 181 GVEWDG-PYRIKFLVPRAWRNKPMDFFNKGLADQLSKDG 218 (284)
Q Consensus 181 G~~WDG-pY~L~f~VP~~~~nkP~~fFnegLa~eLs~eG 218 (284)
|.+||+ ||. |-.=.+.+-+ .+++|-++|
T Consensus 64 Gl~wd~~~~~---------QS~r~~~y~~-~~~~L~~~g 92 (230)
T cd00418 64 GLDWDEGPYR---------QSDRFDLYRA-YAEELIKKG 92 (230)
T ss_pred CCCCCCCeee---------hhcCHHHHHH-HHHHHHHcC
Confidence 778998 653 5555666655 567888888
No 10
>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=36.40 E-value=11 Score=27.17 Aligned_cols=39 Identities=21% Similarity=0.330 Sum_probs=25.0
Q ss_pred CCceEEEeeeccceeeEEEE--------eecCCCCC-CceeEEEecCc
Q 023278 158 SPFYTIQICVPKHAINLIFS--------FTNGVEWD-GPYRIKFLVPR 196 (284)
Q Consensus 158 ~PiYtI~I~vPkHa~~LiFS--------FTnG~~WD-GpY~L~f~VP~ 196 (284)
+|+|.+.|.+|..++.-+++ +.+-..++ +=+.|+..+|-
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 58999999999665433222 12222333 56899999994
No 11
>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=36.11 E-value=93 Score=23.60 Aligned_cols=32 Identities=13% Similarity=0.257 Sum_probs=24.4
Q ss_pred ccceeeEEEEeecCCCCCCc-eeEEEecCcccc
Q 023278 168 PKHAINLIFSFTNGVEWDGP-YRIKFLVPRAWR 199 (284)
Q Consensus 168 PkHa~~LiFSFTnG~~WDGp-Y~L~f~VP~~~~ 199 (284)
-.|.+.+.+.|+|-..++=- +.+++.|||.|+
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 45788899999998777644 889999998775
No 12
>PRK11385 putativi pili assembly chaperone; Provisional
Probab=34.99 E-value=36 Score=30.70 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=28.4
Q ss_pred CCCceEeEecCCCCCCCCC----------ceEEEEccccCCCCCCCc
Q 023278 90 GKAPVYWKTMNGLPPMSGE----------KLKIFYNPYAKKLLPNED 126 (284)
Q Consensus 90 G~apVyWkt~nGlpP~sGe----------~L~lfyNp~as~l~PNe~ 126 (284)
-|-.+||=.-.++||...+ ++||||.|..-+..|++.
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 3447999999999997532 389999999877666653
No 13
>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=34.11 E-value=95 Score=22.63 Aligned_cols=63 Identities=19% Similarity=0.366 Sum_probs=42.9
Q ss_pred hhCCCCCCceEEEe--------eeccceeeEEEEeecCCCCCCceeEEEecCcccccCChhhhhhhHHHhhh
Q 023278 152 NRGQNDSPFYTIQI--------CVPKHAINLIFSFTNGVEWDGPYRIKFLVPRAWRNKPMDFFNKGLADQLS 215 (284)
Q Consensus 152 ~RGkad~PiYtI~I--------~vPkHa~~LiFSFTnG~~WDGpY~L~f~VP~~~~nkP~~fFnegLa~eLs 215 (284)
...+..++.|+|+| .-..+.+.|.|.|+.+-- +-|=++.++.++.+++.=..-.++-|.+.+.
T Consensus 23 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~~p~~YP-~~~P~i~l~~~~~~~~~~~~~l~~~l~~~~~ 93 (113)
T PF05773_consen 23 EIESKSPPSLEVKLDESSSSFESSSFPSVTLHFTLPPGYP-ESPPKISLESPKNSRNEQIEKLNKELEQIAE 93 (113)
T ss_dssp SSTSSSSEEEEEEE--CEECCTTTTSEEEEEEEEE-SSTT-SS--EEEEEEESSSHCHHHHHHHHHHHHHHH
T ss_pred ccccCCCCceeeeecccccccccccceeEEEEEeCCCcCC-CcCCEEEEEcCCCCCHHHHHHHHHHHHHHHH
Confidence 44566778899988 356778999999999888 8887888888888774444444555544443
No 14
>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=32.13 E-value=56 Score=25.56 Aligned_cols=41 Identities=20% Similarity=0.543 Sum_probs=30.6
Q ss_pred CCcchhh-c-cCCCceEeEecCCCCCCCCCceEEEE-ccccCCCC
Q 023278 81 RPSWAMF-E-LGKAPVYWKTMNGLPPMSGEKLKIFY-NPYAKKLL 122 (284)
Q Consensus 81 lPsWa~F-E-lG~apVyWkt~nGlpP~sGe~L~lfy-Np~as~l~ 122 (284)
||-|-+. . .+.-.+.|--.+-+|+ ....+.|+| ||.|...-
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 3445788888888888 888999999 78776653
No 15
>PRK10150 beta-D-glucuronidase; Provisional
Probab=29.28 E-value=41 Score=33.03 Aligned_cols=47 Identities=17% Similarity=0.347 Sum_probs=29.0
Q ss_pred EEeeeccceeeEEEEeecCCCCCCc--eeEEEecCcccccCChhhhhhhH
Q 023278 163 IQICVPKHAINLIFSFTNGVEWDGP--YRIKFLVPRAWRNKPMDFFNKGL 210 (284)
Q Consensus 163 I~I~vPkHa~~LiFSFTnG~~WDGp--Y~L~f~VP~~~~nkP~~fFnegL 210 (284)
+.|.||-+- +....-..-.++.|. |+-+|.||+.|++|-+..-=||+
T Consensus 43 ~~i~vP~~~-~~~~~~~~~~~~~G~~WYrr~f~lp~~~~gk~v~L~Fegv 91 (604)
T PRK10150 43 RAMAVPGSF-NDQFADADIRNYVGDVWYQREVFIPKGWAGQRIVLRFGSV 91 (604)
T ss_pred cEecCCCch-hhccccccccCCcccEEEEEEEECCcccCCCEEEEEECcc
Confidence 567788653 222211122234555 99999999999998765444554
No 16
>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=25.65 E-value=43 Score=32.38 Aligned_cols=33 Identities=30% Similarity=0.549 Sum_probs=20.4
Q ss_pred CCCCceEEEEccccCCCCCCCceeeeecCCCCC
Q 023278 105 MSGEKLKIFYNPYAKKLLPNEDFGIGFNGGFNQ 137 (284)
Q Consensus 105 ~sGe~L~lfyNp~as~l~PNe~fGiaFNGGFNQ 137 (284)
-.||.++|||.+.--.--==++-|..+|||.=|
T Consensus 44 f~G~~itIfY~~~lG~yP~~~~~~~~~NGGlPQ 76 (337)
T PF01630_consen 44 FRGQNITIFYEPRLGLYPYYDEQGKPVNGGLPQ 76 (337)
T ss_dssp SSSSSEEEEESTSSST--EEEETSEEETTSSGG
T ss_pred ccCCeEEEEeCCCCCCcceECCCCCeecCCCCC
Confidence 369999999998332211112234888888765
No 17
>PRK15195 fimbrial chaperone protein FimC; Provisional
Probab=25.16 E-value=65 Score=28.79 Aligned_cols=35 Identities=23% Similarity=0.723 Sum_probs=25.8
Q ss_pred CCceEeEecCCCCCCCCC--------------ceEEEEccccCCCCCCC
Q 023278 91 KAPVYWKTMNGLPPMSGE--------------KLKIFYNPYAKKLLPNE 125 (284)
Q Consensus 91 ~apVyWkt~nGlpP~sGe--------------~L~lfyNp~as~l~PNe 125 (284)
|-.+||=.-..+||...+ .+||||.|..-+-.|++
T Consensus 103 rESlf~Lnv~eIP~~~~~~~~~~n~l~iair~~iKlFyRP~~l~~~~~~ 151 (229)
T PRK15195 103 RESLFWMNVKAIPSVDKNALEGRNVLQLAILSRIKLFVRPINLQELPEE 151 (229)
T ss_pred eeEEEEEEeeecCCCCcccccccceEEEEEEeEEEEEEcccccCCChhh
Confidence 446999999999995321 38999999876554443
No 18
>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=24.58 E-value=44 Score=27.74 Aligned_cols=30 Identities=37% Similarity=0.602 Sum_probs=21.4
Q ss_pred hhhhCCCCCCceEEEeee-cc--------ceeeEEEEee
Q 023278 150 RKNRGQNDSPFYTIQICV-PK--------HAINLIFSFT 179 (284)
Q Consensus 150 ~k~RGkad~PiYtI~I~v-Pk--------Ha~~LiFSFT 179 (284)
-|.|-|+.+|||.=-|-+ |+ -.-++.|||+
T Consensus 55 C~kRkrsRrPIYrPvI~~~P~~~~~~~~~GL~~~~fs~~ 93 (94)
T PF05393_consen 55 CKKRKRSRRPIYRPVIGLEPQNLQIHRDDGLRNLLFSFQ 93 (94)
T ss_pred HHHhhhccCCccccccccCCCcccccccCCcceeEEEee
Confidence 378999999999876663 22 2336788886
No 19
>PRK15188 fimbrial chaperone protein BcfB; Provisional
Probab=24.34 E-value=72 Score=28.78 Aligned_cols=37 Identities=16% Similarity=0.421 Sum_probs=28.2
Q ss_pred CCCceEeEecCCCCCCCCC-------------ceEEEEccccCCCCCCCc
Q 023278 90 GKAPVYWKTMNGLPPMSGE-------------KLKIFYNPYAKKLLPNED 126 (284)
Q Consensus 90 G~apVyWkt~nGlpP~sGe-------------~L~lfyNp~as~l~PNe~ 126 (284)
-|-.+||=...++||..-. ++||||-|..-+..+++.
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 3447999999999996421 389999999877666654
No 20
>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=23.90 E-value=52 Score=26.15 Aligned_cols=13 Identities=38% Similarity=0.866 Sum_probs=12.2
Q ss_pred CCceeEEEecCcc
Q 023278 185 DGPYRIKFLVPRA 197 (284)
Q Consensus 185 DGpY~L~f~VP~~ 197 (284)
||.|+|.+.+|++
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 21
>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=23.70 E-value=91 Score=24.64 Aligned_cols=20 Identities=30% Similarity=0.571 Sum_probs=16.7
Q ss_pred CCCCCceeEEEecCcccccC
Q 023278 182 VEWDGPYRIKFLVPRAWRNK 201 (284)
Q Consensus 182 ~~WDGpY~L~f~VP~~~~nk 201 (284)
+.|||--.|+++||..|+|+
T Consensus 122 v~~dg~~~~~V~~~~~~~g~ 141 (162)
T smart00216 122 VTFDGLTLLSVQLPSRYRGK 141 (162)
T ss_pred EEECCCcEEEEEECHHHCCC
Confidence 35898777999999988887
No 22
>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=22.37 E-value=1.5e+02 Score=22.64 Aligned_cols=32 Identities=28% Similarity=0.507 Sum_probs=23.3
Q ss_pred ceeeEEEEeecCC--CCCCceeEEEecCcccccC
Q 023278 170 HAINLIFSFTNGV--EWDGPYRIKFLVPRAWRNK 201 (284)
Q Consensus 170 Ha~~LiFSFTnG~--~WDGpY~L~f~VP~~~~nk 201 (284)
+-+.+.++..-++ .|||-..+.+.+|..|+++
T Consensus 104 ~~~~v~~~~~~~v~~~~~~~~~~~v~~~~~~~g~ 137 (159)
T PF00094_consen 104 GFVVVVFSSGVRVQVNWDGNMSVYVSVPPWYKGK 137 (159)
T ss_pred ccEEEEEecCCeEEEEEecccccccccccccccc
Confidence 4344445454454 6899889999999999887
No 23
>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=21.83 E-value=31 Score=24.80 Aligned_cols=36 Identities=25% Similarity=0.369 Sum_probs=23.5
Q ss_pred CCceEEEeeeccceee-----------EEEEeecCCCCCCceeEEEecCc
Q 023278 158 SPFYTIQICVPKHAIN-----------LIFSFTNGVEWDGPYRIKFLVPR 196 (284)
Q Consensus 158 ~PiYtI~I~vPkHa~~-----------LiFSFTnG~~WDGpY~L~f~VP~ 196 (284)
+|+|.+.|.+|...+. -+.+... +++-..++..+|-
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 5899999999964432 1233332 3455789999984
No 24
>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=21.04 E-value=50 Score=29.51 Aligned_cols=19 Identities=37% Similarity=0.767 Sum_probs=16.6
Q ss_pred ecCcccccCChhhhhhhHH
Q 023278 193 LVPRAWRNKPMDFFNKGLA 211 (284)
Q Consensus 193 ~VP~~~~nkP~~fFnegLa 211 (284)
+||+.||+.|+.|.--||-
T Consensus 161 ~vP~~~~G~pI~li~aglm 179 (190)
T TIGR01943 161 DVPKAFRGSPIALITAGLM 179 (190)
T ss_pred CCCccccCcCHHHHHHHHH
Confidence 6999999999999887763
No 25
>PHA02739 hypothetical protein; Provisional
Probab=21.02 E-value=77 Score=26.91 Aligned_cols=26 Identities=23% Similarity=0.547 Sum_probs=22.7
Q ss_pred eEEEecCcccccCChhhhhhhHHHhh
Q 023278 189 RIKFLVPRAWRNKPMDFFNKGLADQL 214 (284)
Q Consensus 189 ~L~f~VP~~~~nkP~~fFnegLa~eL 214 (284)
-|+.-||+.|++.|..+--.=|.+++
T Consensus 2 ~lkiiVP~EW~~~p~~tL~~~L~~~i 27 (116)
T PHA02739 2 SLKLIVPNEWKVLPPATLQTELLRII 27 (116)
T ss_pred cEEEEechhhhhCCHHHHHHHHHHHH
Confidence 37889999999999999888887777
No 26
>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=20.19 E-value=1.3e+02 Score=26.02 Aligned_cols=39 Identities=31% Similarity=0.555 Sum_probs=25.9
Q ss_pred CCceEEEeeec-cceeeEEEEeecCCCCCCceeEEEecCcccccCChh
Q 023278 158 SPFYTIQICVP-KHAINLIFSFTNGVEWDGPYRIKFLVPRAWRNKPMD 204 (284)
Q Consensus 158 ~PiYtI~I~vP-kHa~~LiFSFTnG~~WDGpY~L~f~VP~~~~nkP~~ 204 (284)
.|+|++++-=| +|..+++ ++=||-|+ |..+..=-+-|+.
T Consensus 47 rP~Y~v~~~D~~~~sf~I~------kn~dG~~~--Ft~~e~~~~ep~~ 86 (123)
T PF11763_consen 47 RPIYRVYHDDPNKSSFNII------KNNDGTYQ--FTFVESSFSEPLD 86 (123)
T ss_pred ccEEEEeecCCCcceEEEE------ecCCCcEE--EEEcccCCCCcEE
Confidence 59999999999 8888876 45567654 4444443344443
No 27
>PRK15285 putative fimbrial chaperone protein StfD; Provisional
Probab=20.13 E-value=94 Score=28.44 Aligned_cols=35 Identities=23% Similarity=0.634 Sum_probs=26.8
Q ss_pred CCceEeEecCCCCCCCCC----------ceEEEEccccCCCCCCC
Q 023278 91 KAPVYWKTMNGLPPMSGE----------KLKIFYNPYAKKLLPNE 125 (284)
Q Consensus 91 ~apVyWkt~nGlpP~sGe----------~L~lfyNp~as~l~PNe 125 (284)
|-.|||=..-+.||...+ ++||||-|++-+..+++
T Consensus 106 RESlfwlnv~~IPp~~~~~n~L~iairtrIKLfYRP~~L~~~~~~ 150 (250)
T PRK15285 106 RETLFYYNVREIPPQSDKPNTLQIALQTRIKVFYRPQALSKIDMQ 150 (250)
T ss_pred ceEEEEEEEEEcCCCCCCCcEEEEEeeeeeeEEECcccccCChhh
Confidence 447999999999997532 48999999986555543
Done!