Query 048256
Match_columns 102
No_of_seqs 153 out of 842
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 07:48:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048256.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048256hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06280 DUF1034: Fn3-like dom 97.5 0.0021 4.6E-08 42.3 9.7 87 10-97 2-111 (112)
2 PF10633 NPCBM_assoc: NPCBM-as 96.2 0.035 7.5E-07 34.2 6.6 55 16-70 5-61 (78)
3 PF11614 FixG_C: IG-like fold 90.9 1.7 3.7E-05 28.5 6.8 51 19-70 34-85 (118)
4 COG1470 Predicted membrane pro 88.8 2.6 5.6E-05 35.1 7.5 62 17-78 398-461 (513)
5 smart00635 BID_2 Bacterial Ig- 87.3 3.6 7.8E-05 25.3 6.0 40 44-89 4-43 (81)
6 PF00345 PapD_N: Pili and flag 85.7 5.6 0.00012 26.0 6.7 51 17-69 15-73 (122)
7 PF14874 PapD-like: Flagellar- 82.1 10 0.00022 23.8 12.8 79 17-100 21-100 (102)
8 PF07718 Coatamer_beta_C: Coat 73.9 27 0.00059 24.4 7.1 46 39-87 94-139 (140)
9 PF00635 Motile_Sperm: MSP (Ma 73.4 20 0.00043 22.5 6.3 51 17-70 19-70 (109)
10 PF09244 DUF1964: Domain of un 68.1 10 0.00022 23.3 3.4 42 51-92 15-58 (68)
11 PF00347 Ribosomal_L6: Ribosom 64.2 20 0.00044 21.3 4.4 24 40-63 2-25 (77)
12 TIGR02745 ccoG_rdxA_fixG cytoc 64.1 80 0.0017 25.9 9.2 52 18-70 348-400 (434)
13 PF14874 PapD-like: Flagellar- 60.7 38 0.00083 21.1 5.4 27 44-70 3-31 (102)
14 COG1470 Predicted membrane pro 57.6 1.2E+02 0.0025 25.7 8.9 63 17-80 285-354 (513)
15 PF02368 Big_2: Bacterial Ig-l 56.2 12 0.00025 22.6 2.3 37 44-87 4-40 (79)
16 PF13195 DUF4011: Protein of u 54.5 19 0.00041 25.4 3.4 25 78-102 120-146 (176)
17 cd00237 p23 p23 binds heat sho 50.6 69 0.0015 20.9 5.8 34 36-69 18-54 (106)
18 PF12970 DUF3858: Domain of Un 50.2 35 0.00076 23.2 4.0 36 30-65 36-71 (116)
19 COG4845 Chloramphenicol O-acet 46.3 33 0.00071 25.8 3.6 45 48-101 146-190 (219)
20 PTZ00027 60S ribosomal protein 31.5 1.2E+02 0.0027 21.9 4.7 29 37-65 10-38 (190)
21 TIGR03653 arch_L6P archaeal ri 31.1 1.4E+02 0.003 21.3 4.8 27 37-63 4-30 (170)
22 PRK05518 rpl6p 50S ribosomal p 30.8 1.4E+02 0.003 21.5 4.8 27 37-63 10-36 (180)
23 cd06479 ACD_HspB7_like Alpha c 30.3 1.3E+02 0.0029 18.6 4.1 30 26-55 2-36 (81)
24 PRK13203 ureB urease subunit b 27.9 1.9E+02 0.0041 19.3 4.6 43 16-66 18-82 (102)
25 PF15513 DUF4651: Domain of un 26.9 82 0.0018 19.1 2.6 32 54-89 15-46 (62)
26 PTZ00179 60S ribosomal protein 26.4 1.7E+02 0.0036 21.3 4.6 27 37-63 9-35 (189)
27 PF08310 LGFP: LGFP repeat; I 26.0 34 0.00074 19.5 0.8 20 78-97 21-41 (54)
28 cd04977 Ig1_NCAM-1_like First 25.3 1.7E+02 0.0036 17.8 4.2 26 43-69 1-26 (92)
29 PF09134 Invasin_D3: Invasin, 25.0 1E+02 0.0022 20.4 3.0 7 63-69 64-70 (99)
30 smart00187 INB Integrin beta s 24.9 1.6E+02 0.0035 24.2 4.7 29 42-70 66-95 (423)
31 KOG1226 Integrin beta subunit 24.5 1.5E+02 0.0033 26.4 4.6 43 44-86 101-144 (783)
32 KOG0227 Splicing factor 3a, su 23.8 38 0.00082 25.3 0.8 68 3-70 135-213 (222)
33 PF00553 CBM_2: Cellulose bind 23.5 1.3E+02 0.0029 19.0 3.4 32 21-52 18-52 (101)
34 PF13180 PDZ_2: PDZ domain; PD 22.9 1.4E+02 0.003 17.7 3.2 24 39-67 59-82 (82)
35 CHL00140 rpl6 ribosomal protei 22.8 2.1E+02 0.0046 20.4 4.6 27 36-62 8-34 (178)
36 PTZ00483 proliferating cell nu 22.5 1.3E+02 0.0028 22.9 3.6 39 30-68 136-189 (264)
37 PHA02551 19 tail tube protein; 22.2 2.6E+02 0.0056 20.0 4.8 23 47-69 137-159 (163)
38 PF05738 Cna_B: Cna protein B- 21.9 1.7E+02 0.0037 16.7 4.2 26 30-55 36-62 (70)
39 TIGR03654 L6_bact ribosomal pr 21.2 2.3E+02 0.005 20.1 4.5 26 37-62 8-33 (175)
40 PRK05498 rplF 50S ribosomal pr 20.9 2.2E+02 0.0049 20.2 4.4 25 36-60 8-32 (178)
No 1
>PF06280 DUF1034: Fn3-like domain (DUF1034); InterPro: IPR010435 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain of unknown function is present in bacterial and plant peptidases belonging to MEROPS peptidase family S8 (subfamily S8A subtilisin, clan SB). It is C-terminal to and adjacent to the S8 peptidase domain and can be found in conjunction with the PA (Protease associated) domain (IPR003137 from INTERPRO) and additionally in Gram-positive bacteria with the surface protein anchor domain (IPR001899 from INTERPRO).; GO: 0004252 serine-type endopeptidase activity, 0005618 cell wall, 0016020 membrane; PDB: 3EIF_A 1XF1_B.
Probab=97.51 E-value=0.0021 Score=42.31 Aligned_cols=87 Identities=17% Similarity=0.335 Sum_probs=56.2
Q ss_pred EEecCCCeEEEEEEEEEccC-CceEEEEEeC--------CCce-----------EEEEEcCeEEEeecCcEEEEEEEEEE
Q 048256 10 TVPKLSGSITVTRRVKNVGS-PGTYQARVKT--------PQGV-----------SVTIAPKSLKFINVGEEKSFKVIIKA 69 (102)
Q Consensus 10 ~v~~~~~~~t~~RTVTNVg~-~stY~a~v~~--------p~gv-----------~V~V~P~~l~f~~~~~~~~f~Vt~~~ 69 (102)
++.......+++=+++|.|+ .-+|+..... ..|. .+...|..++. ++||++.++|+|+.
T Consensus 2 ~L~d~~~~~~~~itl~N~~~~~~ty~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~vTV-~ag~s~~v~vti~~ 80 (112)
T PF06280_consen 2 SLKDTGNKFSFTITLHNYGDKPVTYTLSHVPVLTDKTDTEEGYSILVPPVPSISTVSFSPDTVTV-PAGQSKTVTVTITP 80 (112)
T ss_dssp EEEEE-SEEEEEEEEEE-SSS-EEEEEEEE-EEEEEE--ETTEEEEEEEE----EEE---EEEEE--TTEEEEEEEEEE-
T ss_pred CccccCCceEEEEEEEECCCCCEEEEEeeEEEEeeEeeccCCcccccccccceeeEEeCCCeEEE-CCCCEEEEEEEEEe
Confidence 44444456778888999998 8888876541 1221 56677888888 58999999999998
Q ss_pred eecc--CCCCeEEEEEEEecCCCC-EEECeE
Q 048256 70 KNAS--VTKDYVFGELIWSDEKQH-QVRSPI 97 (102)
Q Consensus 70 ~~~~--~~~~~~fG~l~W~~~~gh-~VrsPi 97 (102)
.... ....+..|.|..++..++ .++.|.
T Consensus 81 p~~~~~~~~~~~eG~I~~~~~~~~~~lsIPy 111 (112)
T PF06280_consen 81 PSGLDASNGPFYEGFITFKSSDGEPDLSIPY 111 (112)
T ss_dssp -GGGHHTT-EEEEEEEEEESSTTSEEEEEEE
T ss_pred hhcCCcccCCEEEEEEEEEcCCCCEEEEeee
Confidence 4212 346789999999987766 788885
No 2
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=96.20 E-value=0.035 Score=34.23 Aligned_cols=55 Identities=25% Similarity=0.431 Sum_probs=36.3
Q ss_pred CeEEEEEEEEEccC-C-ceEEEEEeCCCceEEEEEcCeEEEeecCcEEEEEEEEEEe
Q 048256 16 GSITVTRRVKNVGS-P-GTYQARVKTPQGVSVTIAPKSLKFINVGEEKSFKVIIKAK 70 (102)
Q Consensus 16 ~~~t~~RTVTNVg~-~-stY~a~v~~p~gv~V~V~P~~l~f~~~~~~~~f~Vt~~~~ 70 (102)
...+++=+|+|-|. . ...+.++..|.|-.+...|..+.--+.||.++++++++..
T Consensus 5 ~~~~~~~tv~N~g~~~~~~v~~~l~~P~GW~~~~~~~~~~~l~pG~s~~~~~~V~vp 61 (78)
T PF10633_consen 5 ETVTVTLTVTNTGTAPLTNVSLSLSLPEGWTVSASPASVPSLPPGESVTVTFTVTVP 61 (78)
T ss_dssp EEEEEEEEEE--SSS-BSS-EEEEE--TTSE---EEEEE--B-TTSEEEEEEEEEE-
T ss_pred CEEEEEEEEEECCCCceeeEEEEEeCCCCccccCCccccccCCCCCEEEEEEEEECC
Confidence 35778889999997 4 5688899999999988999988755789999999999985
No 3
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=90.89 E-value=1.7 Score=28.49 Aligned_cols=51 Identities=22% Similarity=0.335 Sum_probs=36.0
Q ss_pred EEEEEEEEccC-CceEEEEEeCCCceEEEEEcCeEEEeecCcEEEEEEEEEEe
Q 048256 19 TVTRRVKNVGS-PGTYQARVKTPQGVSVTIAPKSLKFINVGEEKSFKVIIKAK 70 (102)
Q Consensus 19 t~~RTVTNVg~-~stY~a~v~~p~gv~V~V~P~~l~f~~~~~~~~f~Vt~~~~ 70 (102)
.++=.++|.+. +-.|+.++..++|+++......+.. ++|+...+.+.+...
T Consensus 34 ~Y~lkl~Nkt~~~~~~~i~~~g~~~~~l~~~~~~i~v-~~g~~~~~~v~v~~p 85 (118)
T PF11614_consen 34 QYTLKLTNKTNQPRTYTISVEGLPGAELQGPENTITV-PPGETREVPVFVTAP 85 (118)
T ss_dssp EEEEEEEE-SSS-EEEEEEEES-SS-EE-ES--EEEE--TT-EEEEEEEEEE-
T ss_pred EEEEEEEECCCCCEEEEEEEecCCCeEEECCCcceEE-CCCCEEEEEEEEEEC
Confidence 46667899999 9999999999999998654478888 689999999999886
No 4
>COG1470 Predicted membrane protein [Function unknown]
Probab=88.84 E-value=2.6 Score=35.12 Aligned_cols=62 Identities=21% Similarity=0.366 Sum_probs=50.3
Q ss_pred eEEEEEEEEEccC--CceEEEEEeCCCceEEEEEcCeEEEeecCcEEEEEEEEEEeeccCCCCe
Q 048256 17 SITVTRRVKNVGS--PGTYQARVKTPQGVSVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDY 78 (102)
Q Consensus 17 ~~t~~RTVTNVg~--~stY~a~v~~p~gv~V~V~P~~l~f~~~~~~~~f~Vt~~~~~~~~~~~~ 78 (102)
..++.=-+.|-|. -..-+.++..|+|-++.|.|.++---++|+..+..+++++...+..++|
T Consensus 398 e~~i~i~I~NsGna~LtdIkl~v~~PqgWei~Vd~~~I~sL~pge~~tV~ltI~vP~~a~aGdY 461 (513)
T COG1470 398 EKTIRISIENSGNAPLTDIKLTVNGPQGWEIEVDESTIPSLEPGESKTVSLTITVPEDAGAGDY 461 (513)
T ss_pred cceEEEEEEecCCCccceeeEEecCCccceEEECcccccccCCCCcceEEEEEEcCCCCCCCcE
Confidence 4566667899997 3677899999999999999999887789999999999998643444554
No 5
>smart00635 BID_2 Bacterial Ig-like domain 2.
Probab=87.34 E-value=3.6 Score=25.30 Aligned_cols=40 Identities=20% Similarity=0.411 Sum_probs=30.1
Q ss_pred EEEEEcCeEEEeecCcEEEEEEEEEEeeccCCCCeEEEEEEEecCC
Q 048256 44 SVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGELIWSDEK 89 (102)
Q Consensus 44 ~V~V~P~~l~f~~~~~~~~f~Vt~~~~~~~~~~~~~fG~l~W~~~~ 89 (102)
.|++.|..+.+. .|+++.|++++... . ... -+.+.|+...
T Consensus 4 ~i~i~p~~~~l~-~G~~~~l~a~~~~~-~--~~~--~~~v~w~Ssn 43 (81)
T smart00635 4 SVTVTPTTASVK-KGLTLQLTATVTPS-S--AKV--TGKVTWTSSN 43 (81)
T ss_pred EEEEeCCeeEEe-CCCeEEEEEEEECC-C--CCc--cceEEEEECC
Confidence 578999999995 89999999997653 1 122 5778897654
No 6
>PF00345 PapD_N: Pili and flagellar-assembly chaperone, PapD N-terminal domain; InterPro: IPR016147 Most Gram-negative bacteria possess a supramolecular structure - the pili - on their surface, which mediates attachment to specific receptors. Many interactive subunits are required to assemble pili, but their assembly only takes place after translocation across the cytoplasmic membrane. Periplasmic chaperones assist pili assembly by binding to the subunits, thereby preventing premature aggregation [, ]. Pili chaperones are structurally, and possibly evolutionarily, related to the immunoglobulin superfamily [, ]: they contain two globular domains, with a topology identical to an immunoglobulin fold. This entry represents the N-terminal domain of pili assembly chaperone, and has a beta-sandwich fold consisting of seven strands in two sheets with a Greek key topology.; GO: 0007047 cellular cell wall organization, 0030288 outer membrane-bounded periplasmic space; PDB: 2CO6_B 2CO7_B 1L4I_B 3GFU_A 3F65_F 3F6L_A 3F6I_A 3GEW_B 3DSN_D 2OS7_B ....
Probab=85.75 E-value=5.6 Score=26.01 Aligned_cols=51 Identities=18% Similarity=0.275 Sum_probs=38.3
Q ss_pred eEEEEEEEEEccC-CceEEEEEeC---CCc----eEEEEEcCeEEEeecCcEEEEEEEEEE
Q 048256 17 SITVTRRVKNVGS-PGTYQARVKT---PQG----VSVTIAPKSLKFINVGEEKSFKVIIKA 69 (102)
Q Consensus 17 ~~t~~RTVTNVg~-~stY~a~v~~---p~g----v~V~V~P~~l~f~~~~~~~~f~Vt~~~ 69 (102)
..+..=+|+|-|+ +..+.+.+.- ..+ -.+.|+|..+.+ +.|+++.+.| +..
T Consensus 15 ~~~~~i~v~N~~~~~~~vq~~v~~~~~~~~~~~~~~~~vsPp~~~L-~pg~~q~vRv-~~~ 73 (122)
T PF00345_consen 15 QRSASITVTNNSDQPYLVQVWVYDQDDEDEDEPTDPFIVSPPIFRL-EPGESQTVRV-YRG 73 (122)
T ss_dssp SSEEEEEEEESSSSEEEEEEEEEETTSTTSSSSSSSEEEESSEEEE-ETTEEEEEEE-EEC
T ss_pred CCEEEEEEEcCCCCcEEEEEEEEcCCCcccccccccEEEeCCceEe-CCCCcEEEEE-Eec
Confidence 3455678999998 7777777763 111 157799999999 5899999999 663
No 7
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=82.12 E-value=10 Score=23.81 Aligned_cols=79 Identities=19% Similarity=0.269 Sum_probs=52.8
Q ss_pred eEEEEEEEEEccC-CceEEEEEeCCCceEEEEEcCeEEEeecCcEEEEEEEEEEeeccCCCCeEEEEEEEecCCCCEEEC
Q 048256 17 SITVTRRVKNVGS-PGTYQARVKTPQGVSVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGELIWSDEKQHQVRS 95 (102)
Q Consensus 17 ~~t~~RTVTNVg~-~stY~a~v~~p~gv~V~V~P~~l~f~~~~~~~~f~Vt~~~~~~~~~~~~~fG~l~W~~~~gh~Vrs 95 (102)
..+.+=+++|.|. ...|+.......+-.++++|..=.. ..|++..++|+|.+. ...+. .-+.|.-.... ..+..
T Consensus 21 ~~~~~v~l~N~s~~p~~f~v~~~~~~~~~~~v~~~~g~l-~PG~~~~~~V~~~~~--~~~g~-~~~~l~i~~e~-~~~~i 95 (102)
T PF14874_consen 21 TYSRTVTLTNTSSIPARFRVRQPESLSSFFSVEPPSGFL-APGESVELEVTFSPT--KPLGD-YEGSLVITTEG-GSFEI 95 (102)
T ss_pred EEEEEEEEEECCCCCEEEEEEeCCcCCCCEEEECCCCEE-CCCCEEEEEEEEEeC--CCCce-EEEEEEEEECC-eEEEE
Confidence 3444456799999 9999987644234456778876555 689999999999964 22333 34777655444 56666
Q ss_pred eEEEE
Q 048256 96 PIVVK 100 (102)
Q Consensus 96 Piav~ 100 (102)
|+-+.
T Consensus 96 ~v~a~ 100 (102)
T PF14874_consen 96 PVKAE 100 (102)
T ss_pred EEEEE
Confidence 66543
No 8
>PF07718 Coatamer_beta_C: Coatomer beta C-terminal region; InterPro: IPR011710 Proteins synthesised 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. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal IPR002553 from INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat
Probab=73.91 E-value=27 Score=24.45 Aligned_cols=46 Identities=17% Similarity=0.333 Sum_probs=36.7
Q ss_pred CCCceEEEEEcCeEEEeecCcEEEEEEEEEEeeccCCCCeEEEEEEEec
Q 048256 39 TPQGVSVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGELIWSD 87 (102)
Q Consensus 39 ~p~gv~V~V~P~~l~f~~~~~~~~f~Vt~~~~~~~~~~~~~fG~l~W~~ 87 (102)
.-.++++.=.|..++. .+++.+..+.++... +...+..||.|.+..
T Consensus 94 t~gdLklve~p~~~tL-~P~~~~~i~~~iKVs--StetGvIfG~I~Yd~ 139 (140)
T PF07718_consen 94 TLGDLKLVERPQPITL-APHGFARIKATIKVS--STETGVIFGNIVYDG 139 (140)
T ss_pred ecCCcEEccCCCceee-CCCcEEEEEEEEEEE--eccCCEEEEEEEEec
Confidence 3456888888999998 589999999999886 345678999999853
No 9
>PF00635 Motile_Sperm: MSP (Major sperm protein) domain; InterPro: IPR000535 Major sperm proteins (MSP) are central components in molecular interactions underlying sperm motility in Caenorhabditis elegans, whose sperm employ an amoebae-like crawling motion using a MSP-containing lamellipod, rather than the flagellar-based swimming motion associated with other sperm. These proteins oligomerise to form an extensive filament system that extends from sperm villipoda, along the leading edge of the pseudopod. About 30 MSP isoforms may exist in C. elegans. MSPs form a fibrous network, whereby MSP dimers form helical subfilaments that coil around one another to produce filaments, which in turn form supercoils to produce bundles. The crystal structure of MSP from C. elegans reveals an immunoglobulin (Ig)-like seven-stranded beta sandwich fold []. ; GO: 0005198 structural molecule activity; PDB: 1MSP_A 3MSP_B 2BVU_B 2MSP_C 1Z9O_F 1Z9L_A 3IKK_A 1WIC_A 2CRI_A 2RR3_A ....
Probab=73.41 E-value=20 Score=22.49 Aligned_cols=51 Identities=12% Similarity=0.230 Sum_probs=37.8
Q ss_pred eEEEEEEEEEccC-CceEEEEEeCCCceEEEEEcCeEEEeecCcEEEEEEEEEEe
Q 048256 17 SITVTRRVKNVGS-PGTYQARVKTPQGVSVTIAPKSLKFINVGEEKSFKVIIKAK 70 (102)
Q Consensus 17 ~~t~~RTVTNVg~-~stY~a~v~~p~gv~V~V~P~~l~f~~~~~~~~f~Vt~~~~ 70 (102)
.....=+++|.++ .-.|++....|..+. |.|..=.. +.|++....|++...
T Consensus 19 ~~~~~l~l~N~s~~~i~fKiktt~~~~y~--v~P~~G~i-~p~~~~~i~I~~~~~ 70 (109)
T PF00635_consen 19 QQSCELTLTNPSDKPIAFKIKTTNPNRYR--VKPSYGII-EPGESVEITITFQPF 70 (109)
T ss_dssp -EEEEEEEEE-SSSEEEEEEEES-TTTEE--EESSEEEE--TTEEEEEEEEE-SS
T ss_pred eEEEEEEEECCCCCcEEEEEEcCCCceEE--ecCCCEEE-CCCCEEEEEEEEEec
Confidence 3445558999999 889999999998865 68998666 689999999988864
No 10
>PF09244 DUF1964: Domain of unknown function (DUF1964); InterPro: IPR015325 This domain is C-terminal to the catalytic sucrose phosphorylase beta/alpha barrel domain. It adopts a beta-sandwich fold, with Greek-key topology and is functionally uncharacterised []. ; PDB: 1R7A_B 2GDU_A 2GDV_A.
Probab=68.08 E-value=10 Score=23.26 Aligned_cols=42 Identities=19% Similarity=0.317 Sum_probs=23.5
Q ss_pred eEEEeecCcEEEEEEEEEEeeccCCC-CeEEEEEEEecCCC-CE
Q 048256 51 SLKFINVGEEKSFKVIIKAKNASVTK-DYVFGELIWSDEKQ-HQ 92 (102)
Q Consensus 51 ~l~f~~~~~~~~f~Vt~~~~~~~~~~-~~~fG~l~W~~~~g-h~ 92 (102)
.|+|+=.|+.-+-+++|+........ ...-.+|.|+|..| |.
T Consensus 15 Sitf~W~g~~t~atLtFePg~Glg~~n~~pVatl~W~DsaG~H~ 58 (68)
T PF09244_consen 15 SITFTWTGATTSATLTFEPGRGLGVDNTTPVATLAWTDSAGDHR 58 (68)
T ss_dssp EEEEEEE-SS-EEEEEE-GGGC-STT--S--EEEEEEETTEEEE
T ss_pred EEEEEEeccccEEEEEEccCcccCccCCcceeEEEEeccCCCcc
Confidence 35666677778888899875222222 23568999999765 64
No 11
>PF00347 Ribosomal_L6: Ribosomal protein L6; InterPro: IPR020040 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites []. This entry represents the alpha-beta domain found duplicated in ribosomal L6 proteins. This domain consists of two beta-sheets and one alpha-helix packed around single core [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 2HGJ_H 2HGQ_H 2HGU_H 1S1I_H 3O5H_I 3O58_I 3J16_F 3IZS_F 2V47_H 2WDJ_H ....
Probab=64.20 E-value=20 Score=21.33 Aligned_cols=24 Identities=33% Similarity=0.340 Sum_probs=17.1
Q ss_pred CCceEEEEEcCeEEEeecCcEEEE
Q 048256 40 PQGVSVTIAPKSLKFINVGEEKSF 63 (102)
Q Consensus 40 p~gv~V~V~P~~l~f~~~~~~~~f 63 (102)
|.|++|+++...+.+.....+.++
T Consensus 2 P~gV~v~~~~~~i~v~G~~g~l~~ 25 (77)
T PF00347_consen 2 PEGVKVTIKGNIITVKGPKGELSR 25 (77)
T ss_dssp STTCEEEEETTEEEEESSSSEEEE
T ss_pred CCcEEEEEeCcEEEEECCCEeEEE
Confidence 788888888888888644444444
No 12
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=64.15 E-value=80 Score=25.88 Aligned_cols=52 Identities=19% Similarity=0.289 Sum_probs=43.2
Q ss_pred EEEEEEEEEccC-CceEEEEEeCCCceEEEEEcCeEEEeecCcEEEEEEEEEEe
Q 048256 18 ITVTRRVKNVGS-PGTYQARVKTPQGVSVTIAPKSLKFINVGEEKSFKVIIKAK 70 (102)
Q Consensus 18 ~t~~RTVTNVg~-~stY~a~v~~p~gv~V~V~P~~l~f~~~~~~~~f~Vt~~~~ 70 (102)
-.++=.+.|-+. +..|..+++.++|..+...++.+.. +.||+.++.|.+...
T Consensus 348 N~Y~~~i~Nk~~~~~~~~l~v~g~~~~~~~~~~~~i~v-~~g~~~~~~v~v~~~ 400 (434)
T TIGR02745 348 NTYTLKILNKTEQPHEYYLSVLGLPGIKIEGPGAPIHV-KAGEKVKLPVFLRTP 400 (434)
T ss_pred EEEEEEEEECCCCCEEEEEEEecCCCcEEEcCCceEEE-CCCCEEEEEEEEEec
Confidence 346667899998 9999999999999988876557888 589999999998874
No 13
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=60.70 E-value=38 Score=21.05 Aligned_cols=27 Identities=33% Similarity=0.535 Sum_probs=19.8
Q ss_pred EEEEEcCeEEEeec--CcEEEEEEEEEEe
Q 048256 44 SVTIAPKSLKFINV--GEEKSFKVIIKAK 70 (102)
Q Consensus 44 ~V~V~P~~l~f~~~--~~~~~f~Vt~~~~ 70 (102)
.++++|+.|.|... |+....++++...
T Consensus 3 ~l~v~P~~ldFG~v~~g~~~~~~v~l~N~ 31 (102)
T PF14874_consen 3 TLEVSPKELDFGNVFVGQTYSRTVTLTNT 31 (102)
T ss_pred EEEEeCCEEEeeEEccCCEEEEEEEEEEC
Confidence 47789999999754 6677777777654
No 14
>COG1470 Predicted membrane protein [Function unknown]
Probab=57.64 E-value=1.2e+02 Score=25.66 Aligned_cols=63 Identities=21% Similarity=0.350 Sum_probs=45.1
Q ss_pred eEEEEEEEEEccC-CceEEEEEe-CCCceEEEEEcC-----eEEEeecCcEEEEEEEEEEeeccCCCCeEE
Q 048256 17 SITVTRRVKNVGS-PGTYQARVK-TPQGVSVTIAPK-----SLKFINVGEEKSFKVIIKAKNASVTKDYVF 80 (102)
Q Consensus 17 ~~t~~RTVTNVg~-~stY~a~v~-~p~gv~V~V~P~-----~l~f~~~~~~~~f~Vt~~~~~~~~~~~~~f 80 (102)
+..|+=++-|-|. +..|+..+. .|+|....-.=. .+.. +.||.+.+++.+.....+..+.|.+
T Consensus 285 t~sf~V~IeN~g~~~d~y~Le~~g~pe~w~~~Fteg~~~vt~vkL-~~gE~kdvtleV~ps~na~pG~Ynv 354 (513)
T COG1470 285 TASFTVSIENRGKQDDEYALELSGLPEGWTAEFTEGELRVTSVKL-KPGEEKDVTLEVYPSLNATPGTYNV 354 (513)
T ss_pred ceEEEEEEccCCCCCceeEEEeccCCCCcceEEeeCceEEEEEEe-cCCCceEEEEEEecCCCCCCCceeE
Confidence 4568888899999 999999998 788865443332 3455 4799999999998753334455543
No 15
>PF02368 Big_2: Bacterial Ig-like domain (group 2); InterPro: IPR003343 Proteins that contain this domain are found in a variety of bacterial and phage surface proteins such as intimins as well as in some uncharacterised eukaryote proteins. Intimin is a bacterial cell-adhesion molecule that mediates the intimate bacterial host-cell interaction. It contains three domains; two immunoglobulin-like domains and a C-type lectin-like module implying that carbohydrate recognition may be important in intimin-mediated cell adhesion [].; PDB: 3NCX_B 3NCW_D 4AQ1_A 2ZQK_B 2ZWK_C 1F02_I 1E5U_I 1F00_I 2L04_A.
Probab=56.18 E-value=12 Score=22.64 Aligned_cols=37 Identities=24% Similarity=0.607 Sum_probs=27.7
Q ss_pred EEEEEcCeEEEeecCcEEEEEEEEEEeeccCCCCeEEEEEEEec
Q 048256 44 SVTIAPKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGELIWSD 87 (102)
Q Consensus 44 ~V~V~P~~l~f~~~~~~~~f~Vt~~~~~~~~~~~~~fG~l~W~~ 87 (102)
+|++.|..+.. ..|+++.|++.+.... ... +.+.|+.
T Consensus 4 ~I~i~~~~~~l-~~G~~~~l~~~~~~~~-~~~-----~~v~w~s 40 (79)
T PF02368_consen 4 SITITPTSVTL-KVGQTQQLTATVTPSD-GSN-----SKVTWSS 40 (79)
T ss_dssp SEEETTTEEEC-ETTCEETTEEEEEEEE-STT-----SCEEEEE
T ss_pred EEEEECCEEEE-ECCCEEEEEEEEEECC-CcE-----eEEEEEe
Confidence 47789999999 5899999999998762 222 5667764
No 16
>PF13195 DUF4011: Protein of unknown function (DUF4011)
Probab=54.49 E-value=19 Score=25.44 Aligned_cols=25 Identities=28% Similarity=0.662 Sum_probs=19.4
Q ss_pred eEEEEEEEec--CCCCEEECeEEEEEC
Q 048256 78 YVFGELIWSD--EKQHQVRSPIVVKAV 102 (102)
Q Consensus 78 ~~fG~l~W~~--~~gh~VrsPiav~~~ 102 (102)
.+||-|.|.+ +.+...++|+....|
T Consensus 120 La~G~L~W~~~~~~~~~~~APLlL~PV 146 (176)
T PF13195_consen 120 LAFGFLEWYESDDSDKPRRAPLLLIPV 146 (176)
T ss_pred eeeeEEEeccCCCCCCEEECCEEEEeE
Confidence 3799999997 233899999987654
No 17
>cd00237 p23 p23 binds heat shock protein (Hsp)90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis.
Probab=50.61 E-value=69 Score=20.93 Aligned_cols=34 Identities=15% Similarity=0.157 Sum_probs=22.1
Q ss_pred EEeCCCceEEEEEcCeEEEeecC---cEEEEEEEEEE
Q 048256 36 RVKTPQGVSVTIAPKSLKFINVG---EEKSFKVIIKA 69 (102)
Q Consensus 36 ~v~~p~gv~V~V~P~~l~f~~~~---~~~~f~Vt~~~ 69 (102)
.+..+..+.|.++|..|.|...+ ....|.+.|-.
T Consensus 18 ~v~d~~d~~v~l~~~~l~f~~~~~~g~~y~~~l~l~~ 54 (106)
T cd00237 18 CVEDSKDVKVDFEKSKLTFSCLNGDNVKIYNEIELYD 54 (106)
T ss_pred EeCCCCCcEEEEecCEEEEEEECCCCcEEEEEEEeec
Confidence 33345788999999999998633 44444445543
No 18
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=50.22 E-value=35 Score=23.23 Aligned_cols=36 Identities=25% Similarity=0.347 Sum_probs=22.6
Q ss_pred CceEEEEEeCCCceEEEEEcCeEEEeecCcEEEEEE
Q 048256 30 PGTYQARVKTPQGVSVTIAPKSLKFINVGEEKSFKV 65 (102)
Q Consensus 30 ~stY~a~v~~p~gv~V~V~P~~l~f~~~~~~~~f~V 65 (102)
+++|.-.|..|+|+++...|..-..+.+-.|.+++|
T Consensus 36 ~E~ytyti~~pegm~l~t~~~~K~I~N~~Gk~~isv 71 (116)
T PF12970_consen 36 DETYTYTIELPEGMKLVTPPMEKKIDNPVGKVSISV 71 (116)
T ss_dssp EEEEEEEEEE-TT-EE-S--S-EEEEETTEEEEEEE
T ss_pred CcceEEEEEcCCCCeeecCccceeccCCcceEEEEE
Confidence 578999999999999988888888776655555444
No 19
>COG4845 Chloramphenicol O-acetyltransferase [Defense mechanisms]
Probab=46.30 E-value=33 Score=25.79 Aligned_cols=45 Identities=20% Similarity=0.202 Sum_probs=28.1
Q ss_pred EcCeEEEeecCcEEEEEEEEEEeeccCCCCeEEEEEEEecCCCCEEECeEEEEE
Q 048256 48 APKSLKFINVGEEKSFKVIIKAKNASVTKDYVFGELIWSDEKQHQVRSPIVVKA 101 (102)
Q Consensus 48 ~P~~l~f~~~~~~~~f~Vt~~~~~~~~~~~~~fG~l~W~~~~gh~VrsPiav~~ 101 (102)
.=.-|+|+ ++.+.......-..--+.+|...|.||+ |..|++|..
T Consensus 146 ~lPWlsFt------slS~~~~~~k~~~~PiF~~Grf~~~~Gk---l~lPlavq~ 190 (219)
T COG4845 146 NLPWLSFT------SLSHHYRRNKIYGQPIFYAGRFYEEDGK---LTLPLAVQA 190 (219)
T ss_pred ccccccee------eeeeeccCCccccceeEeecceeccCCe---EEEeEEEEe
Confidence 33456775 3444444321111223578999999999 999999864
No 20
>PTZ00027 60S ribosomal protein L6; Provisional
Probab=31.45 E-value=1.2e+02 Score=21.93 Aligned_cols=29 Identities=21% Similarity=0.382 Sum_probs=21.6
Q ss_pred EeCCCceEEEEEcCeEEEeecCcEEEEEE
Q 048256 37 VKTPQGVSVTIAPKSLKFINVGEEKSFKV 65 (102)
Q Consensus 37 v~~p~gv~V~V~P~~l~f~~~~~~~~f~V 65 (102)
+.-|+|++|++.-..+.++.+..+.++.+
T Consensus 10 I~IP~~V~V~i~~~~v~VkGp~G~L~~~~ 38 (190)
T PTZ00027 10 IRIPEGVTVTVKSRKVTVTGKYGELTRSF 38 (190)
T ss_pred EecCCCCEEEEECCEEEEECCCceEEEEe
Confidence 66788999988888888876666555443
No 21
>TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model.
Probab=31.15 E-value=1.4e+02 Score=21.31 Aligned_cols=27 Identities=30% Similarity=0.363 Sum_probs=15.9
Q ss_pred EeCCCceEEEEEcCeEEEeecCcEEEE
Q 048256 37 VKTPQGVSVTIAPKSLKFINVGEEKSF 63 (102)
Q Consensus 37 v~~p~gv~V~V~P~~l~f~~~~~~~~f 63 (102)
+..|+|++|++.-..+.++.+..++++
T Consensus 4 I~IP~~V~v~i~~~~i~vkGp~G~L~~ 30 (170)
T TIGR03653 4 IEIPEGVSVTIEGNIVTVKGPKGEVTR 30 (170)
T ss_pred EecCCCCEEEEeCCEEEEECCCeEEEE
Confidence 445667777776666666544444443
No 22
>PRK05518 rpl6p 50S ribosomal protein L6P; Reviewed
Probab=30.80 E-value=1.4e+02 Score=21.52 Aligned_cols=27 Identities=22% Similarity=0.292 Sum_probs=18.5
Q ss_pred EeCCCceEEEEEcCeEEEeecCcEEEE
Q 048256 37 VKTPQGVSVTIAPKSLKFINVGEEKSF 63 (102)
Q Consensus 37 v~~p~gv~V~V~P~~l~f~~~~~~~~f 63 (102)
+.-|+|++|++.-..+.++.+..+.+.
T Consensus 10 I~IP~~V~v~i~~~~v~VkGp~G~L~~ 36 (180)
T PRK05518 10 IEIPEGVTVEIEGLVVTVKGPKGELTR 36 (180)
T ss_pred EEcCCCCEEEEECCEEEEECCCeEEEE
Confidence 556788888888777887655544443
No 23
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=30.32 E-value=1.3e+02 Score=18.61 Aligned_cols=30 Identities=27% Similarity=0.357 Sum_probs=24.9
Q ss_pred EccC-CceEEEEEeCC----CceEEEEEcCeEEEe
Q 048256 26 NVGS-PGTYQARVKTP----QGVSVTIAPKSLKFI 55 (102)
Q Consensus 26 NVg~-~stY~a~v~~p----~gv~V~V~P~~l~f~ 55 (102)
||.+ +..|.+.++.| ..+.|+|....|+..
T Consensus 2 ~v~e~~~~~~v~~dlpG~~pedi~V~v~~~~L~I~ 36 (81)
T cd06479 2 NVKTLGDTYQFAVDVSDFSPEDIIVTTSNNQIEVH 36 (81)
T ss_pred CccCcCCeEEEEEECCCCCHHHeEEEEECCEEEEE
Confidence 5667 78899999877 468999999999985
No 24
>PRK13203 ureB urease subunit beta; Reviewed
Probab=27.87 E-value=1.9e+02 Score=19.28 Aligned_cols=43 Identities=33% Similarity=0.680 Sum_probs=26.5
Q ss_pred CeEEEEEEEEEccC-C----ceEEE-----------------EEeCCCceEEEEEcCeEEEeecCcEEEEEEE
Q 048256 16 GSITVTRRVKNVGS-P----GTYQA-----------------RVKTPQGVSVTIAPKSLKFINVGEEKSFKVI 66 (102)
Q Consensus 16 ~~~t~~RTVTNVg~-~----stY~a-----------------~v~~p~gv~V~V~P~~l~f~~~~~~~~f~Vt 66 (102)
+..+++-+|+|.|+ + |-|+. ....|+|.+ +.| ++||+++.++.
T Consensus 18 gr~~~~l~V~NtGDRPIQVGSH~HF~E~N~aL~FDR~~A~G~RLdIpaGTa-------vRF-EPG~~k~V~LV 82 (102)
T PRK13203 18 GRETVTLTVANTGDRPIQVGSHYHFFEVNPALSFDREAARGMRLNIPAGTA-------VRF-EPGQTREVELV 82 (102)
T ss_pred CCCEEEEEEEeCCCCceEEccccchhhcCcchhccHhhhcCcccccCCCCe-------EeE-CCCCeEEEEEE
Confidence 45567788999996 3 45542 234455555 467 46777766543
No 25
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=26.87 E-value=82 Score=19.12 Aligned_cols=32 Identities=22% Similarity=0.302 Sum_probs=20.6
Q ss_pred EeecCcEEEEEEEEEEeeccCCCCeEEEEEEEecCC
Q 048256 54 FINVGEEKSFKVIIKAKNASVTKDYVFGELIWSDEK 89 (102)
Q Consensus 54 f~~~~~~~~f~Vt~~~~~~~~~~~~~fG~l~W~~~~ 89 (102)
|+..|+-+.+-|.... +.....-|-|+..||+
T Consensus 15 fs~lG~I~vLYvn~~e----S~~~~~~GGvV~eDgR 46 (62)
T PF15513_consen 15 FSQLGEIAVLYVNPYE----SDEDRLTGGVVMEDGR 46 (62)
T ss_pred HHhcCcEEEEEEcccc----cCCCeEeccEEEeCCC
Confidence 4455665555554443 2445678999999998
No 26
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=26.37 E-value=1.7e+02 Score=21.27 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=18.0
Q ss_pred EeCCCceEEEEEcCeEEEeecCcEEEE
Q 048256 37 VKTPQGVSVTIAPKSLKFINVGEEKSF 63 (102)
Q Consensus 37 v~~p~gv~V~V~P~~l~f~~~~~~~~f 63 (102)
+.-|+|++|++.=..++++.+..+.++
T Consensus 9 I~IP~~V~V~i~~~~ItVkGpkG~Ls~ 35 (189)
T PTZ00179 9 ITIPEDVTVSVKDRIVTVKGKRGTLTK 35 (189)
T ss_pred EeCCCCCEEEEeCCEEEEECCCcEEEE
Confidence 556777777777777777655554443
No 27
>PF08310 LGFP: LGFP repeat; InterPro: IPR013207 This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from Corynebacterium glutamicum (Brevibacterium flavum) and Corynebacterium efficiens along with PS1 protein contain this repeat region. The N-terminal region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminal region consists of 4 tandem LGFP repeats. It is hypothesised that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity. Deletion of Q01377 from SWISSPROT protein results in a 10-fold increase in the cell volume of the organism and infers the corresponding involvement of the protein in the cell shape formation []. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix.
Probab=26.03 E-value=34 Score=19.46 Aligned_cols=20 Identities=30% Similarity=0.640 Sum_probs=14.3
Q ss_pred eEEEEEEEecCCC-CEEECeE
Q 048256 78 YVFGELIWSDEKQ-HQVRSPI 97 (102)
Q Consensus 78 ~~fG~l~W~~~~g-h~VrsPi 97 (102)
+.-|.|-|+...| |.|+-.|
T Consensus 21 F~~G~Iywsp~tGa~~v~G~I 41 (54)
T PF08310_consen 21 FQNGTIYWSPATGAHAVHGAI 41 (54)
T ss_pred cCCeEEEEeCCCCcEEECHHH
Confidence 4459999997655 8886554
No 28
>cd04977 Ig1_NCAM-1_like First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1 and similar proteins. Ig1_NCAM-1 like: first immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1. NCAM-1 plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-nonNCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves the Ig1, Ig2, and Ig3 domains. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the s
Probab=25.31 E-value=1.7e+02 Score=17.82 Aligned_cols=26 Identities=31% Similarity=0.413 Sum_probs=20.6
Q ss_pred eEEEEEcCeEEEeecCcEEEEEEEEEE
Q 048256 43 VSVTIAPKSLKFINVGEEKSFKVIIKA 69 (102)
Q Consensus 43 v~V~V~P~~l~f~~~~~~~~f~Vt~~~ 69 (102)
+.|.+.|...... .|+...|...+..
T Consensus 1 ~~v~v~p~~~~v~-~G~~~~l~C~~~G 26 (92)
T cd04977 1 LQVDIVPSQGEIS-VGESKFFLCQVIG 26 (92)
T ss_pred CeEEEecCcEEEC-CCCeEEEEEEeEe
Confidence 3678899998874 7898888887765
No 29
>PF09134 Invasin_D3: Invasin, domain 3; InterPro: IPR015217 This domain adopts a structure consisting of an immunoglobulin-like beta-sandwich, with seven strands in two beta-sheets, arranged in a Greek-key topology. It forms part of the extracellular region of the protein, which can be expressed as a soluble protein (Inv497) that binds integrins and promotes subsequent uptake by cells when attached to bacteria []. ; PDB: 1CWV_A.
Probab=25.05 E-value=1e+02 Score=20.38 Aligned_cols=7 Identities=14% Similarity=0.534 Sum_probs=3.3
Q ss_pred EEEEEEE
Q 048256 63 FKVIIKA 69 (102)
Q Consensus 63 f~Vt~~~ 69 (102)
|+-++..
T Consensus 64 YtATl~G 70 (99)
T PF09134_consen 64 YTATLKG 70 (99)
T ss_dssp EEEEEE-
T ss_pred EEEEEEc
Confidence 5555554
No 30
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=24.87 E-value=1.6e+02 Score=24.23 Aligned_cols=29 Identities=17% Similarity=0.504 Sum_probs=22.0
Q ss_pred ceEEEEEcCeEEEe-ecCcEEEEEEEEEEe
Q 048256 42 GVSVTIAPKSLKFI-NVGEEKSFKVIIKAK 70 (102)
Q Consensus 42 gv~V~V~P~~l~f~-~~~~~~~f~Vt~~~~ 70 (102)
+-.+.++|.++..+ ++||.+.|++++...
T Consensus 66 ~~~vQi~PQ~v~l~LRpG~~~~f~~~~~~a 95 (423)
T smart00187 66 EQAVQVSPQRVRLKLRPGEPQNFTLTVRQA 95 (423)
T ss_pred CCceEeccceEEEEeccCCcEEEEEEEEec
Confidence 35677888876544 679999999999764
No 31
>KOG1226 consensus Integrin beta subunit (N-terminal portion of extracellular region) [Signal transduction mechanisms; Extracellular structures]
Probab=24.49 E-value=1.5e+02 Score=26.37 Aligned_cols=43 Identities=23% Similarity=0.442 Sum_probs=28.0
Q ss_pred EEEEEcCeEEEe-ecCcEEEEEEEEEEeeccCCCCeEEEEEEEe
Q 048256 44 SVTIAPKSLKFI-NVGEEKSFKVIIKAKNASVTKDYVFGELIWS 86 (102)
Q Consensus 44 ~V~V~P~~l~f~-~~~~~~~f~Vt~~~~~~~~~~~~~fG~l~W~ 86 (102)
.+.++|..+... ++|+++.|+|++.....-+.+-|..=.|.|+
T Consensus 101 ~~Qi~PQ~~~l~LRpg~~~~f~l~~r~a~~yPVDLYyLMDlS~S 144 (783)
T KOG1226|consen 101 ITQITPQELRLRLRPGEEQTFQLKVRQAEDYPVDLYYLMDLSYS 144 (783)
T ss_pred eeEeccceEEEEecCCCceeEEEEEeeccCCCeeEEEEeecchh
Confidence 456667655543 6799999999998653334555555555554
No 32
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=23.80 E-value=38 Score=25.28 Aligned_cols=68 Identities=15% Similarity=0.228 Sum_probs=40.3
Q ss_pred CCCcceEEEecCCCeEEEEEEEEEccC-C--ceEEEEEeCC-CceEEEEEcCeEEEeec-------CcEEEEEEEEEEe
Q 048256 3 NFNYPSITVPKLSGSITVTRRVKNVGS-P--GTYQARVKTP-QGVSVTIAPKSLKFINV-------GEEKSFKVIIKAK 70 (102)
Q Consensus 3 dLNyPSi~v~~~~~~~t~~RTVTNVg~-~--stY~a~v~~p-~gv~V~V~P~~l~f~~~-------~~~~~f~Vt~~~~ 70 (102)
++|||+|.......-..+.---.+|-+ + --|-+.+--| +.+.+.+-|..+.+.+. .+++.|+|.|.-.
T Consensus 135 Qv~Yp~i~~~~~Pr~rfmssyeq~ve~~dk~~qyLvfaaePyE~Iafk~p~~Eid~se~Kf~t~wd~~tk~y~lqF~fk 213 (222)
T KOG0227|consen 135 QVNYPEIEEGIMPRHRFMSSYEQKVEPPDKSWQYLVFAAEPYENIAFKVPSREIDKSEGKFWTHWDAETKQYTLQFFFK 213 (222)
T ss_pred EecchhhhhccCCcchhhhhhHhhcCCccccceEEEEEeccccceeeecCchhhhhccCceeeeecCCCceEEEEEEec
Confidence 589999988654432222111234444 3 3455555455 56888888887777541 3567788877654
No 33
>PF00553 CBM_2: Cellulose binding domain; InterPro: IPR001919 The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (3.2.1.4 from EC), cellobiohydrolases (3.2.1.91 from EC) (exoglucanases), or xylanases (3.2.1.8 from EC) []. Structurally, cellulases and xylanases generally consist of a catalytic domain joined to a cellulose-binding domain (CBD) by a short linker sequence rich in proline and/or hydroxy-amino acids. The CBD domain is found either at the N-terminal or at the C-terminal extremity of these enzymes. As it is shown in the following schematic representation, there are two conserved cysteines in this CBD domain - one at each extremity of the domain - which have been shown [] to be involved in a disulphide bond. There are also four conserved tryptophan, two are involved in cellulose binding. The CBD of a number of bacterial cellulases has been shown to consist of about 105 amino acid residues [, ]. +-------------------------------------------------+ | | xCxxxxWxxxxxNxxxWxxxxxxxWxxxxxxxxWNxxxxxGxxxxxxxxxxCx 'C': conserved cysteine involved in a disulphide bond. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 2CZN_A 2CWR_A 1HEH_C 1HEJ_C 3NDZ_E 3NDY_E 2XBD_A 1E5C_A 1XBD_A 1E5B_A ....
Probab=23.48 E-value=1.3e+02 Score=18.98 Aligned_cols=32 Identities=25% Similarity=0.388 Sum_probs=21.7
Q ss_pred EEEEEEccC-C-ceEEEEEeCCCceEEE-EEcCeE
Q 048256 21 TRRVKNVGS-P-GTYQARVKTPQGVSVT-IAPKSL 52 (102)
Q Consensus 21 ~RTVTNVg~-~-stY~a~v~~p~gv~V~-V~P~~l 52 (102)
.=+|+|-++ . .-|++.+..|.|.+|. +.-..+
T Consensus 18 ~v~v~N~~~~~i~~W~v~~~~~~~~~i~~~Wna~~ 52 (101)
T PF00553_consen 18 EVTVTNNGSSPINGWTVTFTFPSGQTITSSWNATV 52 (101)
T ss_dssp EEEEEESSSSTEESEEEEEEESTTEEEEEEESCEE
T ss_pred EEEEEECCCCccCCEEEEEEeCCCCEEeeeeccEE
Confidence 456899887 4 4699999988776643 334443
No 34
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=22.87 E-value=1.4e+02 Score=17.74 Aligned_cols=24 Identities=33% Similarity=0.469 Sum_probs=15.9
Q ss_pred CCCceEEEEEcCeEEEeecCcEEEEEEEE
Q 048256 39 TPQGVSVTIAPKSLKFINVGEEKSFKVII 67 (102)
Q Consensus 39 ~p~gv~V~V~P~~l~f~~~~~~~~f~Vt~ 67 (102)
.++|=.|+ |++.+.+++++++|++
T Consensus 59 ~~~g~~v~-----l~v~R~g~~~~~~v~l 82 (82)
T PF13180_consen 59 GKPGDTVT-----LTVLRDGEELTVEVTL 82 (82)
T ss_dssp SSTTSEEE-----EEEEETTEEEEEEEE-
T ss_pred CCCCCEEE-----EEEEECCEEEEEEEEC
Confidence 34554444 5777888888888875
No 35
>CHL00140 rpl6 ribosomal protein L6; Validated
Probab=22.78 E-value=2.1e+02 Score=20.35 Aligned_cols=27 Identities=26% Similarity=0.326 Sum_probs=17.2
Q ss_pred EEeCCCceEEEEEcCeEEEeecCcEEE
Q 048256 36 RVKTPQGVSVTIAPKSLKFINVGEEKS 62 (102)
Q Consensus 36 ~v~~p~gv~V~V~P~~l~f~~~~~~~~ 62 (102)
.+.-|+|++|++.=..+.++.+..+.+
T Consensus 8 ~I~IP~~V~v~i~~~~v~vkGp~G~l~ 34 (178)
T CHL00140 8 PIKIPDNVNVSIDDQIIKVKGPKGTLS 34 (178)
T ss_pred eeecCCCCEEEEECCEEEEECCCEEEE
Confidence 456677777777777777764444433
No 36
>PTZ00483 proliferating cell nuclear antigen; Provisional
Probab=22.47 E-value=1.3e+02 Score=22.86 Aligned_cols=39 Identities=13% Similarity=0.214 Sum_probs=31.4
Q ss_pred CceEEEEEeCCCc---------------eEEEEEcCeEEEeecCcEEEEEEEEE
Q 048256 30 PGTYQARVKTPQG---------------VSVTIAPKSLKFINVGEEKSFKVIIK 68 (102)
Q Consensus 30 ~stY~a~v~~p~g---------------v~V~V~P~~l~f~~~~~~~~f~Vt~~ 68 (102)
.--|.|.+..|.+ +.+++++..+.|...|+..+..+.+.
T Consensus 136 ~~e~~~~v~m~s~~f~~i~kdl~~vsD~v~i~~~~~~v~f~a~Gd~~~~~~~l~ 189 (264)
T PTZ00483 136 QCEYHCKCVMNSKKFQEFAKYLHSIGDTVSISMKKDEMRLETEGEGIKASKQFH 189 (264)
T ss_pred CCCccEEEEEEHHHHHHHHHHHHHcCCEEEEEEECCEEEEEEeecCcEEEEEEc
Confidence 3468888887742 78889999999998898888887775
No 37
>PHA02551 19 tail tube protein; Provisional
Probab=22.24 E-value=2.6e+02 Score=20.01 Aligned_cols=23 Identities=17% Similarity=0.276 Sum_probs=18.3
Q ss_pred EEcCeEEEeecCcEEEEEEEEEE
Q 048256 47 IAPKSLKFINVGEEKSFKVIIKA 69 (102)
Q Consensus 47 V~P~~l~f~~~~~~~~f~Vt~~~ 69 (102)
|..-.|.++..+|-.+|+|+|.-
T Consensus 137 VgeveLdy~~nn~i~tF~Vtf~y 159 (163)
T PHA02551 137 VGEIDLDWDSNNEIETFEVTFAL 159 (163)
T ss_pred ccceeecccCCCcEEEEEEEEEe
Confidence 34445889888999999999974
No 38
>PF05738 Cna_B: Cna protein B-type domain; InterPro: IPR008454 This entry represents a repeated B region domain found in the collagen-binding surface protein Cna in Staphylococcus aureus, as well as other related domains. The B region domain of Cna has a prealbumin-like beta-sandwich fold of seven strands in two sheets with a Greek key topology []. However, this domain does not mediate collagen binding, the IPR008456 from INTERPRO region carries out that function; instead it appears to form a stalk that presents the ligand binding domain away from the bacterial cell surface. Cna is a collagen-binding MSCRAMM (Microbial Surface Component Recognizing Adhesive Matrix Molecules), and is necessary and sufficient for S. aureus cells to adhere to cartilage.; PDB: 2X5P_A 3RKP_A 3KPT_A 1VLF_T 1TI2_F 1TI6_D 1TI4_J 1VLE_V 1VLD_X 3PF2_A ....
Probab=21.95 E-value=1.7e+02 Score=16.65 Aligned_cols=26 Identities=31% Similarity=0.652 Sum_probs=18.5
Q ss_pred CceEEEE-EeCCCceEEEEEcCeEEEe
Q 048256 30 PGTYQAR-VKTPQGVSVTIAPKSLKFI 55 (102)
Q Consensus 30 ~stY~a~-v~~p~gv~V~V~P~~l~f~ 55 (102)
...|.+. +.+|.|..+.-.|..+...
T Consensus 36 ~G~Y~l~E~~aP~GY~~~~~~~~~~i~ 62 (70)
T PF05738_consen 36 PGTYTLKETKAPDGYQLDDTPYEFTIT 62 (70)
T ss_dssp SEEEEEEEEETTTTEEEEECEEEEEEC
T ss_pred CeEEEEEEEECCCCCEECCCceEEEEe
Confidence 5568887 5679998876666555554
No 39
>TIGR03654 L6_bact ribosomal protein L6, bacterial type.
Probab=21.23 E-value=2.3e+02 Score=20.06 Aligned_cols=26 Identities=31% Similarity=0.358 Sum_probs=14.3
Q ss_pred EeCCCceEEEEEcCeEEEeecCcEEE
Q 048256 37 VKTPQGVSVTIAPKSLKFINVGEEKS 62 (102)
Q Consensus 37 v~~p~gv~V~V~P~~l~f~~~~~~~~ 62 (102)
+.-|+|+.|++.=..+.++.+..+.+
T Consensus 8 I~IP~~V~v~~~~~~v~v~Gp~G~l~ 33 (175)
T TIGR03654 8 IAIPAGVEVTIDGNVVTVKGPKGELS 33 (175)
T ss_pred eecCCCcEEEEeCCEEEEEcCCeEEE
Confidence 45566666666666666654443333
No 40
>PRK05498 rplF 50S ribosomal protein L6; Validated
Probab=20.89 E-value=2.2e+02 Score=20.17 Aligned_cols=25 Identities=28% Similarity=0.359 Sum_probs=15.1
Q ss_pred EEeCCCceEEEEEcCeEEEeecCcE
Q 048256 36 RVKTPQGVSVTIAPKSLKFINVGEE 60 (102)
Q Consensus 36 ~v~~p~gv~V~V~P~~l~f~~~~~~ 60 (102)
.+.-|+|+.|++.-..+.++.+..+
T Consensus 8 ~I~IP~~V~v~~~~~~v~vkGp~G~ 32 (178)
T PRK05498 8 PIAIPAGVEVTINGNVVTVKGPKGE 32 (178)
T ss_pred ceecCCCCEEEEECCEEEEECCCEE
Confidence 3556677777766666666544433
Done!