Query 033063
Match_columns 128
No_of_seqs 102 out of 122
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 09:22:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033063.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033063hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10780 MRP_L53: 39S ribosoma 99.7 1.4E-18 3E-23 110.6 4.3 50 12-63 1-51 (51)
2 KOG3445 Mitochondrial/chloropl 99.1 5E-10 1.1E-14 84.2 9.8 85 2-88 20-104 (145)
3 PF05047 L51_S25_CI-B8: Mitoch 98.5 5.2E-07 1.1E-11 56.3 5.4 52 22-75 1-52 (52)
4 KOG3446 NADH:ubiquinone oxidor 96.8 0.0019 4E-08 45.7 3.8 81 3-85 13-93 (97)
5 KOG4079 Putative mitochondrial 96.3 0.0058 1.3E-07 46.8 4.2 78 6-85 29-106 (169)
6 PF14009 DUF4228: Domain of un 89.4 0.37 8.1E-06 35.2 2.9 60 49-112 11-70 (181)
7 PF08806 Sep15_SelM: Sep15/Sel 59.0 30 0.00065 23.4 4.9 49 35-86 27-76 (78)
8 PHA00442 host recBCD nuclease 50.9 16 0.00035 23.8 2.3 31 75-105 15-46 (59)
9 PF13575 DUF4135: Domain of un 50.1 24 0.00052 29.6 3.9 62 51-112 58-128 (370)
10 PF10387 DUF2442: Protein of u 47.0 24 0.00053 23.0 2.8 19 55-73 11-29 (79)
11 smart00295 B41 Band 4.1 homolo 46.5 54 0.0012 24.1 5.0 37 52-88 2-39 (207)
12 cd01767 UBX UBX (ubiquitin reg 39.5 83 0.0018 20.3 4.5 33 55-87 4-37 (77)
13 PF09379 FERM_N: FERM N-termin 39.3 42 0.00091 21.4 3.0 29 58-86 1-30 (80)
14 cd04792 LanM-like LanM-like pr 39.3 36 0.00079 31.3 3.6 61 51-111 101-167 (825)
15 PF00789 UBX: UBX domain; Int 35.4 1.1E+02 0.0023 19.7 4.6 37 53-89 6-43 (82)
16 PF00564 PB1: PB1 domain; Int 33.5 73 0.0016 20.4 3.5 35 55-89 3-38 (84)
17 PRK00509 argininosuccinate syn 33.1 70 0.0015 27.9 4.2 37 51-87 213-249 (399)
18 COG1582 FlgEa Uncharacterized 33.0 73 0.0016 21.4 3.4 41 51-94 23-63 (67)
19 PF09299 Mu-transpos_C: Mu tra 32.6 24 0.00053 22.0 1.0 13 6-18 36-48 (62)
20 cd06407 PB1_NLP A PB1 domain i 32.5 1.3E+02 0.0028 20.3 4.7 32 55-87 2-34 (82)
21 PF03642 MAP: MAP domain; Int 32.3 38 0.00082 23.9 2.0 20 52-71 54-73 (88)
22 PF09465 LBR_tudor: Lamin-B re 31.9 42 0.0009 21.7 2.0 27 44-70 24-51 (55)
23 cd04508 TUDOR Tudor domains ar 31.7 50 0.0011 19.0 2.3 19 53-71 25-44 (48)
24 PF00085 Thioredoxin: Thioredo 31.6 1.4E+02 0.003 18.9 5.1 34 51-85 70-103 (103)
25 TIGR00032 argG argininosuccina 31.4 87 0.0019 27.2 4.5 36 52-87 211-246 (394)
26 PF00659 POLO_box: POLO box du 31.0 60 0.0013 20.5 2.7 20 54-73 14-33 (68)
27 cd01770 p47_UBX p47-like ubiqu 30.6 1.3E+02 0.0029 19.9 4.4 32 55-86 6-38 (79)
28 PLN00200 argininosuccinate syn 30.5 88 0.0019 27.4 4.4 36 52-87 218-253 (404)
29 PF06155 DUF971: Protein of un 30.5 99 0.0021 20.6 3.8 34 46-88 2-35 (89)
30 COG1182 AcpD Acyl carrier prot 29.2 56 0.0012 26.2 2.8 77 9-87 6-83 (202)
31 cd01772 SAKS1_UBX SAKS1-like U 28.7 1.3E+02 0.0028 19.7 4.2 34 54-87 5-39 (79)
32 cd00196 UBQ Ubiquitin-like pro 28.3 1E+02 0.0023 16.5 3.9 30 58-87 2-32 (69)
33 PF07532 Big_4: Bacterial Ig-l 28.2 1.5E+02 0.0032 18.2 4.3 27 43-69 6-33 (59)
34 PF13881 Rad60-SLD_2: Ubiquiti 27.3 1.3E+02 0.0029 21.5 4.2 31 55-86 4-37 (111)
35 smart00666 PB1 PB1 domain. Pho 27.2 1.7E+02 0.0037 18.6 4.5 32 55-87 3-35 (81)
36 PRK13820 argininosuccinate syn 27.1 1.1E+02 0.0023 26.7 4.4 36 52-87 211-246 (394)
37 PRK04527 argininosuccinate syn 26.8 1E+02 0.0022 27.0 4.2 37 51-87 213-249 (400)
38 PF03990 DUF348: Domain of unk 26.5 1E+02 0.0022 18.0 3.0 20 61-80 6-25 (43)
39 PRK10996 thioredoxin 2; Provis 26.3 1.9E+02 0.0041 20.6 5.0 33 51-84 105-137 (139)
40 PF14847 Ras_bdg_2: Ras-bindin 26.1 1.2E+02 0.0025 21.7 3.7 31 55-85 2-33 (105)
41 PRK09981 hypothetical protein; 26.1 1.5E+02 0.0032 21.2 4.2 49 10-60 28-80 (99)
42 cd01999 Argininosuccinate_Synt 26.1 1.2E+02 0.0026 26.2 4.5 36 52-87 211-246 (385)
43 PRK07696 sulfur carrier protei 25.9 37 0.00081 21.8 1.1 26 60-85 4-29 (67)
44 cd05992 PB1 The PB1 domain is 25.6 1.8E+02 0.0039 18.3 4.6 34 55-88 2-36 (81)
45 smart00333 TUDOR Tudor domain. 25.5 89 0.0019 18.5 2.7 18 54-71 30-48 (57)
46 cd06398 PB1_Joka2 The PB1 doma 25.4 1.8E+02 0.0039 20.1 4.5 56 55-112 2-67 (91)
47 smart00166 UBX Domain present 25.4 1.8E+02 0.0039 18.8 4.3 31 54-84 5-36 (80)
48 TIGR03689 pup_AAA proteasome A 25.1 1.3E+02 0.0028 27.1 4.6 47 51-97 415-461 (512)
49 cd02994 PDI_a_TMX PDIa family, 25.1 1.4E+02 0.0031 19.3 3.8 31 51-83 70-100 (101)
50 KOG2086 Protein tyrosine phosp 24.5 1.3E+02 0.0028 26.4 4.3 60 47-106 297-376 (380)
51 TIGR01683 thiS thiamine biosyn 24.4 85 0.0019 19.6 2.5 23 60-83 2-24 (64)
52 cd01807 GDX_N ubiquitin-like d 23.7 2E+02 0.0043 18.2 4.5 45 56-100 3-61 (74)
53 PLN02593 adrenodoxin-like ferr 23.6 1.6E+02 0.0035 20.9 4.1 15 56-70 1-17 (117)
54 PRK08053 sulfur carrier protei 23.5 96 0.0021 19.6 2.6 22 60-82 4-25 (66)
55 PRK05863 sulfur carrier protei 23.3 47 0.001 21.1 1.1 24 60-84 4-27 (65)
56 cd01798 parkin_N amino-termina 22.8 1.8E+02 0.0038 18.2 3.8 31 56-86 1-32 (70)
57 PRK07440 hypothetical protein; 22.7 51 0.0011 21.5 1.2 28 56-85 5-32 (70)
58 PRK06083 sulfur carrier protei 22.6 1.3E+02 0.0028 20.5 3.3 40 43-84 6-45 (84)
59 cd00271 Chemokine_C Chemokine_ 21.3 2.6E+02 0.0056 18.5 4.5 39 50-88 31-69 (72)
60 cd00273 Chemokine_CXC Chemokin 21.1 1.8E+02 0.0039 18.3 3.6 31 53-83 33-63 (64)
61 PF13814 Replic_Relax: Replica 20.4 3.1E+02 0.0066 20.1 5.2 50 53-105 137-191 (191)
62 PF08428 Rib: Rib/alpha-like r 20.4 1.1E+02 0.0024 19.6 2.4 20 51-70 40-59 (65)
No 1
>PF10780 MRP_L53: 39S ribosomal protein L53/MRP-L53; InterPro: IPR019716 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 [, ]. Mitochondrial ribosomal protein L53 (also known as L44) is part of the 39S ribosome [].
Probab=99.74 E-value=1.4e-18 Score=110.60 Aligned_cols=50 Identities=30% Similarity=0.531 Sum_probs=48.4
Q ss_pred ecCCCCCcHHHHHHHhhc-CchhhhhcCCCceEEEEecCCCCCCeEEEEeeCC
Q 033063 12 FNALDPRIASCMEFLAQC-NAPKAKESNPACQIQVKRRTDDHPPEIKVTFVTG 63 (128)
Q Consensus 12 FnPF~~~aksaR~FL~~i-~~~k~r~sNp~c~I~~~v~~d~~~P~I~Vtf~dG 63 (128)
||||++++++||+||++| ++.+++.+|++|+|.++++ +++|+|+|+|+||
T Consensus 1 FnPF~~~aksaR~FL~~ip~s~k~~~tni~~~vl~~~~--~~~P~v~V~fkdg 51 (51)
T PF10780_consen 1 FNPFSPNAKSARLFLSLIPPSAKARGTNINCEVLPRVS--RSEPSVTVTFKDG 51 (51)
T ss_pred CCCCCcccHHHHHHHHhcCCccccccCCCceEEecCCC--CCCCeEEEEeccC
Confidence 899999999999999999 8999999999999999999 7999999999998
No 2
>KOG3445 consensus Mitochondrial/chloroplast ribosomal protein 36a [Translation, ribosomal structure and biogenesis]
Probab=99.13 E-value=5e-10 Score=84.24 Aligned_cols=85 Identities=19% Similarity=0.275 Sum_probs=77.0
Q ss_pred CccceEEEEEecCCCCCcHHHHHHHhhcCchhhhhcCCCceEEEEecCCCCCCeEEEEeeCCcEEEEecCCCCHHHHHHH
Q 033063 2 LKFLSKVRIEFNALDPRIASCMEFLAQCNAPKAKESNPACQIQVKRRTDDHPPEIKVTFVTGAEEVFDATSTSAHTIRSM 81 (128)
Q Consensus 2 lK~lkkV~V~FnPF~~~aksaR~FL~~i~~~k~r~sNp~c~I~~~v~~d~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~ 81 (128)
+.++++|+|+||=++++++.+|+||..- .+.+.+.||+++|-++.+.. ++|.|...|-||.+.++++.||+..||...
T Consensus 20 v~ql~rit~sfCnwggSSrGmR~Fle~~-L~~~a~enP~v~i~v~~rrg-~hP~lraeY~NGre~vicvrnms~eevs~~ 97 (145)
T KOG3445|consen 20 VWQLRRITVSFCNWGGSSRGMREFLESE-LPDLARENPGVVIYVEPRRG-QHPLLRAEYLNGRERVICVRNMSQEEVSKK 97 (145)
T ss_pred hheeeEEEEEEecCCCccHHHHHHHHHH-HHHHHhhCCCeEEEEeccCC-CCceEEEEecCCceEEEeeccCCHHHHHHH
Confidence 3578999999999999999999999985 67788899999999999977 899999999999999999999999999988
Q ss_pred HHHhccc
Q 033063 82 ILEKGQM 88 (128)
Q Consensus 82 i~~~s~~ 88 (128)
++..-.+
T Consensus 98 ~~lL~ds 104 (145)
T KOG3445|consen 98 ATLLRDS 104 (145)
T ss_pred HHHHhcc
Confidence 7765444
No 3
>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.
Probab=98.45 E-value=5.2e-07 Score=56.26 Aligned_cols=52 Identities=31% Similarity=0.569 Sum_probs=36.3
Q ss_pred HHHHHhhcCchhhhhcCCCceEEEEecCCCCCCeEEEEeeCCcEEEEecCCCCH
Q 033063 22 CMEFLAQCNAPKAKESNPACQIQVKRRTDDHPPEIKVTFVTGAEEVFDATSTSA 75 (128)
Q Consensus 22 aR~FL~~i~~~k~r~sNp~c~I~~~v~~d~~~P~I~Vtf~dG~e~~~d~~~~t~ 75 (128)
+|.||.. .-+.++..||+++|.+... ...+|.|.+.|.||.+..+|++|++.
T Consensus 1 ~R~F~~~-~lp~l~~~NP~v~~~v~~~-~~~~P~~~~~y~~G~~~~i~~~n~~~ 52 (52)
T PF05047_consen 1 ARDFLKN-NLPTLKYHNPQVQFEVRRR-RGRHPFLTAEYLNGREKTIDVKNKSS 52 (52)
T ss_dssp HHHHHHH-THHHHHHHSTT--EEEE----SSS-EEEEEESS--EEEEE-TT---
T ss_pred CHhHHHH-hHHHHHHHCCCcEEEEEEC-CCCCCEEEEEEcCCCEEEEECCCCCC
Confidence 6999977 6688899999999999994 44789999999999999999999863
No 4
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=96.79 E-value=0.0019 Score=45.74 Aligned_cols=81 Identities=21% Similarity=0.296 Sum_probs=68.7
Q ss_pred ccceEEEEEecCCCCCcHHHHHHHhhcCchhhhhcCCCceEEEEecCCCCCCeEEEEeeCCcEEEEecCCCCHHHHHHHH
Q 033063 3 KFLSKVRIEFNALDPRIASCMEFLAQCNAPKAKESNPACQIQVKRRTDDHPPEIKVTFVTGAEEVFDATSTSAHTIRSMI 82 (128)
Q Consensus 3 K~lkkV~V~FnPF~~~aksaR~FL~~i~~~k~r~sNp~c~I~~~v~~d~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i 82 (128)
..++.++|--|+=++.++.+|+|+..-- ...++.||+.-|-.. -|+.--|.+-..|.+|.|..+.-+|++..+|...+
T Consensus 13 ~~lkElRI~lcqkspaSagvR~fvEk~Y-~~lKkaNP~lPILIR-EcSgVqPrl~ARY~~G~E~~v~L~~~s~~~i~kal 90 (97)
T KOG3446|consen 13 LKLKELRIHLCQKSPASAGVREFVEKFY-VNLKKANPDLPILIR-ECSGVQPRLWARYGNGVERSVSLANLSAPQIHKAL 90 (97)
T ss_pred hhhhhheeeecCCCCcchhHHHHHHHhh-hhhhhcCCCCcEeeh-hhcCCchHHHHHhcCCceEEeehhhcchHHHHHHH
Confidence 4588999999999999999999999855 557899998877432 35568999999999999999999999999998776
Q ss_pred HHh
Q 033063 83 LEK 85 (128)
Q Consensus 83 ~~~ 85 (128)
...
T Consensus 91 e~l 93 (97)
T KOG3446|consen 91 ENL 93 (97)
T ss_pred HHH
Confidence 543
No 5
>KOG4079 consensus Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis]
Probab=96.32 E-value=0.0058 Score=46.78 Aligned_cols=78 Identities=18% Similarity=0.321 Sum_probs=64.6
Q ss_pred eEEEEEecCCCCCcHHHHHHHhhcCchhhhhcCCCceEEEEecCCCCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHh
Q 033063 6 SKVRIEFNALDPRIASCMEFLAQCNAPKAKESNPACQIQVKRRTDDHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEK 85 (128)
Q Consensus 6 kkV~V~FnPF~~~aksaR~FL~~i~~~k~r~sNp~c~I~~~v~~d~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~ 85 (128)
+=.+|.||-.++.-..||.|..- +-++++=.||..++-. ..+-...|.+..-|.||.++.||.+.++-.||.+++..-
T Consensus 29 ~vfsvnynt~g~~~~GARdFVfw-NipQiQykNP~VQ~~~-~knmtpsPF~R~YlddGr~vL~Dld~~~r~eI~~hl~K~ 106 (169)
T KOG4079|consen 29 NVFSVNYNTNGPEQSGARDFVFW-NIPQIQYKNPKVQLVK-HKNMTPSPFARAYLDDGREVLFDLDGMKREEIEKHLAKT 106 (169)
T ss_pred eEEEEeccCCCccccCccceEEe-cchhhcccCCceEEEe-eccCCCChHHHheecCcceEEEEcccccHHHHHHHHHHH
Confidence 34589999999999999999887 5577777799777643 233478899999999999999999999999999887653
No 6
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=89.35 E-value=0.37 Score=35.17 Aligned_cols=60 Identities=23% Similarity=0.168 Sum_probs=46.0
Q ss_pred CCCCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhccccchHHHHHhcCCCCCcccCccccc
Q 033063 49 TDDHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQMLENEQMFRDAGLNWPVLIPDEELQ 112 (128)
Q Consensus 49 ~d~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~~L~~~e~~~~~g~~~~~~~p~e~~~ 112 (128)
.....-.|+|-+.||+.++|+. -+++.||+...=.|.= +.......|..|++|.|+|+|.
T Consensus 11 ~~~~~~~vkvv~~~G~v~~~~~-pv~a~evm~~~P~h~v---~~~~~~~~~~~~~~l~~d~~L~ 70 (181)
T PF14009_consen 11 SSSSAATVKVVHPDGKVEEFKR-PVTAAEVMLENPGHFV---CDSDSFRFGRRIKPLPPDEELQ 70 (181)
T ss_pred ccCCCceEEEEcCCCcEEEeCC-CcCHHHHHHHCCCCEE---eccccccCCCcccCCCccCeec
Confidence 4457889999999999999965 6999999888766641 1111223589999999999975
No 7
>PF08806 Sep15_SelM: Sep15/SelM redox domain; InterPro: IPR014912 Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif []. This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum []. ; PDB: 2A4H_A 2A2P_A.
Probab=59.04 E-value=30 Score=23.37 Aligned_cols=49 Identities=20% Similarity=0.292 Sum_probs=34.7
Q ss_pred hhcCCCceEEEEecCCCCCCeEEEEeeCCc-EEEEecCCCCHHHHHHHHHHhc
Q 033063 35 KESNPACQIQVKRRTDDHPPEIKVTFVTGA-EEVFDATSTSAHTIRSMILEKG 86 (128)
Q Consensus 35 r~sNp~c~I~~~v~~d~~~P~I~Vtf~dG~-e~~~d~~~~t~~eI~~~i~~~s 86 (128)
....++++|+.... ++|.+.+-=.+|+ .++++.++++..+|.+.+..+.
T Consensus 27 ~~~y~~v~vk~i~G---~~P~L~l~d~~g~~~E~i~i~~w~~d~i~efL~~kg 76 (78)
T PF08806_consen 27 PPLYPNVEVKYIPG---APPELVLLDEDGEEVERINIEKWKTDEIEEFLNEKG 76 (78)
T ss_dssp GHHBTTEEEEEESS------EEEEE-SSS--SEEEE-SSSSHCHHHHHHHHHT
T ss_pred hhccCceEEEEeCC---CCCEEEEEcCCCCEEEEEEcccCCHHHHHHHHHHhC
Confidence 34578999988765 5688888666776 5889999999999988887764
No 8
>PHA00442 host recBCD nuclease inhibitor
Probab=50.90 E-value=16 Score=23.78 Aligned_cols=31 Identities=16% Similarity=0.225 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhccccchHHHHHhcCCC-CCcc
Q 033063 75 AHTIRSMILEKGQMLENEQMFRDAGLN-WPVL 105 (128)
Q Consensus 75 ~~eI~~~i~~~s~~L~~~e~~~~~g~~-~~~~ 105 (128)
-.+|--+||..-+..+..+.|+.||.+ |.-+
T Consensus 15 wnd~q~yidsLek~~~~L~~Lea~GVDNW~Gy 46 (59)
T PHA00442 15 WNDMQGYIDSLEKDNEFLKALRACGVDNWDGY 46 (59)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHcCCcchhhH
Confidence 357888999999999999999999999 8754
No 9
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=50.08 E-value=24 Score=29.65 Aligned_cols=62 Identities=19% Similarity=0.299 Sum_probs=44.5
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHHHHH----HHHHHhccc--cchH--HHHHhc-CCCCCcccCccccc
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAHTIR----SMILEKGQM--LENE--QMFRDA-GLNWPVLIPDEELQ 112 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~----~~i~~~s~~--L~~~--e~~~~~-g~~~~~~~p~e~~~ 112 (128)
+...++.|+|.+|.+...+|.++....+. +.+..+... +.+. ..|... |+.|.-.|+.++..
T Consensus 58 ~Gr~V~~l~f~~g~kivYKPRsl~~d~~f~~l~~~ln~~~~~~~~~l~~~~~l~~g~~YgW~EfI~~~~c~ 128 (370)
T PF13575_consen 58 GGRSVAILEFSSGKKIVYKPRSLSIDKAFNDLLEWLNEKNGTPSLDLPTPKVLDRGDGYGWQEFIEHEPCN 128 (370)
T ss_pred CCceEEEEEECCCCEEEEeCcccHHHHHHHHHHHHHhhhccccccccccceeeeccCcceeEEEecCCCCC
Confidence 55889999999999999999999876654 444455332 3333 667554 68898887766643
No 10
>PF10387 DUF2442: Protein of unknown function (DUF2442); InterPro: IPR018841 Several proteins in this entry are annotated as being putative molybdopterin-guanine dinucleotide biosynthesis proteins, but this has not been confirmed. The function of these proteins is therefore not known. ; PDB: 2AUW_B 2X8N_A 3K8R_B.
Probab=46.95 E-value=24 Score=22.97 Aligned_cols=19 Identities=32% Similarity=0.683 Sum_probs=16.5
Q ss_pred eEEEEeeCCcEEEEecCCC
Q 033063 55 EIKVTFVTGAEEVFDATST 73 (128)
Q Consensus 55 ~I~Vtf~dG~e~~~d~~~~ 73 (128)
.|.|+|.||.+..+|.+.+
T Consensus 11 ~L~v~f~dG~~~~~dl~~~ 29 (79)
T PF10387_consen 11 RLRVTFSDGETRIFDLSPL 29 (79)
T ss_dssp EEEEEETTS-EEEEECCCS
T ss_pred EEEEEEcCCCEEEEEhHHh
Confidence 8999999999999998665
No 11
>smart00295 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
Probab=46.50 E-value=54 Score=24.10 Aligned_cols=37 Identities=24% Similarity=0.364 Sum_probs=30.1
Q ss_pred CCCeEEEEeeCCcEEEEecC-CCCHHHHHHHHHHhccc
Q 033063 52 HPPEIKVTFVTGAEEVFDAT-STSAHTIRSMILEKGQM 88 (128)
Q Consensus 52 ~~P~I~Vtf~dG~e~~~d~~-~~t~~eI~~~i~~~s~~ 88 (128)
.+-.|.|.+-||....+... ..++.||++.+..+..-
T Consensus 2 ~~~~~~V~l~dg~~~~~~~~~~~t~~ev~~~v~~~~~l 39 (207)
T smart00295 2 KPRVLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGI 39 (207)
T ss_pred CcEEEEEEecCCCEEEEEECCCCCHHHHHHHHHHHhCC
Confidence 35578999999999888766 88999998888876653
No 12
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=39.53 E-value=83 Score=20.27 Aligned_cols=33 Identities=12% Similarity=0.237 Sum_probs=25.4
Q ss_pred eEEEEeeCCcEEEE-ecCCCCHHHHHHHHHHhcc
Q 033063 55 EIKVTFVTGAEEVF-DATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 55 ~I~Vtf~dG~e~~~-d~~~~t~~eI~~~i~~~s~ 87 (128)
.|.|.|-||..++- -..+-++++|.+.|+.+..
T Consensus 4 ~i~iRlpdG~~~~~~F~~~~tl~~l~~fv~~~~~ 37 (77)
T cd01767 4 KIQIRLPDGKRLEQRFNSTHKLSDVRDFVESNGP 37 (77)
T ss_pred EEEEEcCCCCEEEEEeCCCCCHHHHHHHHHHcCC
Confidence 47788889986443 3467899999999998764
No 13
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=39.32 E-value=42 Score=21.39 Aligned_cols=29 Identities=17% Similarity=0.391 Sum_probs=22.1
Q ss_pred EEeeCCcEEEEec-CCCCHHHHHHHHHHhc
Q 033063 58 VTFVTGAEEVFDA-TSTSAHTIRSMILEKG 86 (128)
Q Consensus 58 Vtf~dG~e~~~d~-~~~t~~eI~~~i~~~s 86 (128)
|.+-||...++.. .+.+.++++++|..+=
T Consensus 1 V~llD~~~~~~~v~~~~t~~~l~~~v~~~l 30 (80)
T PF09379_consen 1 VRLLDGTTKTFEVDPKTTGQDLLEQVCDKL 30 (80)
T ss_dssp EEESSEEEEEEEEETTSBHHHHHHHHHHHH
T ss_pred CCCcCCCcEEEEEcCCCcHHHHHHHHHHHc
Confidence 6788998888744 4677899988887754
No 14
>cd04792 LanM-like LanM-like proteins. LanM is a bifunctional enzyme, involved in the synthesis of class II lantibiotics. It is responsible for both the dehydration and the cyclization of the precursor-peptide during lantibiotic synthesis. The C-terminal domain shows similarity to LanC, the cyclase component of the lan operon, but the N terminus seems to be unrelated to the dehydratase, LanB.
Probab=39.27 E-value=36 Score=31.34 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=44.5
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHH----HHHHHHHHhccc--cchHHHHHhcCCCCCcccCcccc
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAH----TIRSMILEKGQM--LENEQMFRDAGLNWPVLIPDEEL 111 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~----eI~~~i~~~s~~--L~~~e~~~~~g~~~~~~~p~e~~ 111 (128)
+..-++.++|.||.+.+.+|.++.+. ++++.+..+... +.+-..|..-++.|.-.|+.++.
T Consensus 101 ~g~~V~~l~f~~g~kivYKPr~l~~d~~f~~~l~~ln~~~~~~~~~~~~~l~~~~ygw~EfI~~~~c 167 (825)
T cd04792 101 GGRVVAILTFSSGLKLVYKPRSLSVDALFQELLEWLNSFLGALPLRTPKVLDRGDYGWEEFIEHQPC 167 (825)
T ss_pred CCceEEEEEECCCCEEEECCCCchHHHHHHHHHHHHHhcCCccccccceeeecCCcceEEeecCCCC
Confidence 45557888999999999999999994 455555544333 24557788888889888776543
No 15
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=35.41 E-value=1.1e+02 Score=19.71 Aligned_cols=37 Identities=11% Similarity=0.005 Sum_probs=28.1
Q ss_pred CCeEEEEeeCCcEEEE-ecCCCCHHHHHHHHHHhcccc
Q 033063 53 PPEIKVTFVTGAEEVF-DATSTSAHTIRSMILEKGQML 89 (128)
Q Consensus 53 ~P~I~Vtf~dG~e~~~-d~~~~t~~eI~~~i~~~s~~L 89 (128)
.-.|.|.|-||+.++- -..+-++++|.+.|+.+...-
T Consensus 6 ~~~I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~ 43 (82)
T PF00789_consen 6 VVRIQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSP 43 (82)
T ss_dssp EEEEEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCT
T ss_pred EEEEEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCC
Confidence 3468899999986654 457889999999998775443
No 16
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=33.53 E-value=73 Score=20.37 Aligned_cols=35 Identities=26% Similarity=0.260 Sum_probs=27.7
Q ss_pred eEEEEeeCCcEE-EEecCCCCHHHHHHHHHHhcccc
Q 033063 55 EIKVTFVTGAEE-VFDATSTSAHTIRSMILEKGQML 89 (128)
Q Consensus 55 ~I~Vtf~dG~e~-~~d~~~~t~~eI~~~i~~~s~~L 89 (128)
.|++.|.++..+ ..-+.++++.++.+.|...-...
T Consensus 3 ~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~~ 38 (84)
T PF00564_consen 3 RVKVRYGGDIRRIISLPSDVSFDDLRSKIREKFGLL 38 (84)
T ss_dssp EEEEEETTEEEEEEEECSTSHHHHHHHHHHHHHTTS
T ss_pred EEEEEECCeeEEEEEcCCCCCHHHHHHHHHHHhCCC
Confidence 478889988888 55677899999999988765553
No 17
>PRK00509 argininosuccinate synthase; Provisional
Probab=33.11 E-value=70 Score=27.90 Aligned_cols=37 Identities=16% Similarity=0.279 Sum_probs=32.1
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhcc
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~ 87 (128)
+.|-+|.++|..|.--.+|+..|+.-++++.+.....
T Consensus 213 ~~p~~v~i~F~~G~pvalnG~~~~~~~li~~lN~i~g 249 (399)
T PRK00509 213 DEPEYVEIEFEKGVPVAINGEALSPAELIEELNELAG 249 (399)
T ss_pred CCCeEEEEEEEccEEEEEcCeeCCHHHHHHHHHHHHh
Confidence 3677899999999999999999999999888776554
No 18
>COG1582 FlgEa Uncharacterized protein, possibly involved in motility [Cell motility and secretion]
Probab=33.01 E-value=73 Score=21.36 Aligned_cols=41 Identities=17% Similarity=0.297 Sum_probs=33.5
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhccccchHHH
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQMLENEQM 94 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~~L~~~e~ 94 (128)
.+-|-..+++.||++..+. =+++|+.+.|-+.-|++..-..
T Consensus 23 e~~PDttItLinGkkyvVk---EsveEVi~kI~~y~rkI~~~~~ 63 (67)
T COG1582 23 EAFPDTTITLINGKKYVVK---ESVEEVINKIIEYRRKIGSLAK 63 (67)
T ss_pred hccCCcEEEEEcCcEEEEc---ccHHHHHHHHHHHHHHhheehh
Confidence 4567888999999999997 4799999999988887765443
No 19
>PF09299 Mu-transpos_C: Mu transposase, C-terminal; InterPro: IPR015378 This domain is found in various prokaryotic integrases and transposases. It adopts a beta-barrel structure with Greek-key topology []. ; PDB: 1BCO_A 1BCM_B.
Probab=32.55 E-value=24 Score=22.05 Aligned_cols=13 Identities=31% Similarity=0.534 Sum_probs=9.4
Q ss_pred eEEEEEecCCCCC
Q 033063 6 SKVRIEFNALDPR 18 (128)
Q Consensus 6 kkV~V~FnPF~~~ 18 (128)
++|.|+|||.+.+
T Consensus 36 ~~V~vryDp~dl~ 48 (62)
T PF09299_consen 36 QKVRVRYDPDDLS 48 (62)
T ss_dssp SEEEEEE-GGGTT
T ss_pred CEEEEEECcccCC
Confidence 4689999998763
No 20
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=32.48 E-value=1.3e+02 Score=20.32 Aligned_cols=32 Identities=16% Similarity=0.202 Sum_probs=25.0
Q ss_pred eEEEEeeCCcEEEEe-cCCCCHHHHHHHHHHhcc
Q 033063 55 EIKVTFVTGAEEVFD-ATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 55 ~I~Vtf~dG~e~~~d-~~~~t~~eI~~~i~~~s~ 87 (128)
.|+++| +|..+.|. +.++++.++.+.|.....
T Consensus 2 ~vK~~~-~~d~~r~~l~~~~~~~~L~~~i~~r~~ 34 (82)
T cd06407 2 RVKATY-GEEKIRFRLPPSWGFTELKQEIAKRFK 34 (82)
T ss_pred EEEEEe-CCeEEEEEcCCCCCHHHHHHHHHHHhC
Confidence 478888 56788887 668899999999876554
No 21
>PF03642 MAP: MAP domain; InterPro: IPR005298 Map (MHC class II analogous protein), also known as eap (extracellular adherence protein) and p70, is exclusively found in Staphylococcus aureus. It is a cell-wall associated protein, which is capable of binding to a number of different extracellular matrix glycoploteins and plasma proteins, and to the cell surface of S. aureus. Besides the broad binding specificity, map has been shown to be important in the adherence to and internalization of S. aureus by eukaryotic cells as well as being capable of modulating inflammatory response through its interactions with ICAM-1 (intercellular adhesion molecule-1), although its biological role in vivo remains to date unclear []. The protein consists of a signal peptide followed by a unique sequence of about 20 amino acids and four to six repeated MAP domains of 110-amino acid residues. Within each repeat there is a subdomain consisting of 31 residues that was found to be highly homologous to the N-terminal beta-chain of many MHC class II molecules []. This entry represents the MAP domain. The crystal structure of this domain has been solved and shows a core fold that is comprised of an alpha-helix lying diagonally across a five-stranded, mixed beta-sheet. This structure is very similar to the C-terminal domain of bacterial superantigens [].; PDB: 1YN4_A 1YN3_A 1YN5_B.
Probab=32.34 E-value=38 Score=23.89 Aligned_cols=20 Identities=25% Similarity=0.431 Sum_probs=16.2
Q ss_pred CCCeEEEEeeCCcEEEEecC
Q 033063 52 HPPEIKVTFVTGAEEVFDAT 71 (128)
Q Consensus 52 ~~P~I~Vtf~dG~e~~~d~~ 71 (128)
....-+|+|+||.+.++|-.
T Consensus 54 k~A~YTV~fKnG~kkvvdLk 73 (88)
T PF03642_consen 54 KQAKYTVYFKNGSKKVVDLK 73 (88)
T ss_dssp SEEEEEEEETTS-EEEEECC
T ss_pred heeEEEEEEcCCcEEEEEcc
Confidence 56778999999999999854
No 22
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=31.92 E-value=42 Score=21.69 Aligned_cols=27 Identities=19% Similarity=0.225 Sum_probs=18.9
Q ss_pred EEEecC-CCCCCeEEEEeeCCcEEEEec
Q 033063 44 QVKRRT-DDHPPEIKVTFVTGAEEVFDA 70 (128)
Q Consensus 44 ~~~v~~-d~~~P~I~Vtf~dG~e~~~d~ 70 (128)
..+|.. |.+.-.=+|.|.||.++.+.-
T Consensus 24 e~kV~~~d~~~~~y~V~Y~DGtel~lke 51 (55)
T PF09465_consen 24 EGKVLSYDSKSDRYTVLYEDGTELELKE 51 (55)
T ss_dssp EEEEEEEETTTTEEEEEETTS-EEEEEC
T ss_pred EEEEEEecccCceEEEEEcCCCEEEecc
Confidence 344444 346778899999999998864
No 23
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=31.75 E-value=50 Score=18.98 Aligned_cols=19 Identities=32% Similarity=0.487 Sum_probs=16.0
Q ss_pred CCeEEEEeeC-CcEEEEecC
Q 033063 53 PPEIKVTFVT-GAEEVFDAT 71 (128)
Q Consensus 53 ~P~I~Vtf~d-G~e~~~d~~ 71 (128)
...+.|.|.| |....+..+
T Consensus 25 ~~~~~V~f~DyG~~~~v~~~ 44 (48)
T cd04508 25 DGKVEVFFVDYGNTEVVPLS 44 (48)
T ss_pred CCcEEEEEEcCCCcEEEeHH
Confidence 6779999999 999888754
No 24
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=31.61 E-value=1.4e+02 Score=18.91 Aligned_cols=34 Identities=21% Similarity=0.207 Sum_probs=26.6
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHh
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEK 85 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~ 85 (128)
+.-|++. -|.+|++..--...++..+|.+.|+.|
T Consensus 70 ~~~Pt~~-~~~~g~~~~~~~g~~~~~~l~~~i~~~ 103 (103)
T PF00085_consen 70 KSVPTII-FFKNGKEVKRYNGPRNAESLIEFIEKH 103 (103)
T ss_dssp SSSSEEE-EEETTEEEEEEESSSSHHHHHHHHHHH
T ss_pred CCCCEEE-EEECCcEEEEEECCCCHHHHHHHHHcC
Confidence 5688876 578888885444458999999999876
No 25
>TIGR00032 argG argininosuccinate synthase. argG in bacteria, ARG1 in Saccharomyces cerevisiae. There is a very unusual clustering in the alignment, with a deep split between one cohort of E. coli, H. influenzae, and Streptomyces, and the other cohort of eukaryotes, archaea, and the rest of the eubacteria.
Probab=31.45 E-value=87 Score=27.18 Aligned_cols=36 Identities=14% Similarity=0.180 Sum_probs=31.4
Q ss_pred CCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhcc
Q 033063 52 HPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 52 ~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~ 87 (128)
.|-.|.++|..|.--.+|+..|+.-++++.+.+...
T Consensus 211 ~p~~v~i~F~~G~pv~ing~~~~~~~li~~lN~i~g 246 (394)
T TIGR00032 211 EPEVVTIDFEQGVPVALNGVSLDPVELILEANEIAG 246 (394)
T ss_pred CCeEEEEEEEcceEEEECCccCCHHHHHHHHHHHHH
Confidence 566999999999999999999999999888776544
No 26
>PF00659 POLO_box: POLO box duplicated region; InterPro: IPR000959 A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain []. The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster []. This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule []. The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two alpha-helices and two six-stranded beta-sheets []. The topology of one polypeptide subunit of the dimer consists of, from its N- to C terminus, an extended strand segment, five beta-strands, one alpha-helix (A) and a C-terminal beta-strand. Beta-strands from one subunit form a contiguous antiparallel beta-sheet with beta-strands from the second subunit. The two beta-sheets pack with a crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with beta-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic beta-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface. Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures [].; GO: 0005515 protein binding; PDB: 1MBY_B 3P37_A 3MHN_A 1Q4K_A 3HIK_A 3Q1I_A 3P35_A 3MHQ_A 1UMW_B 3MQ8_B ....
Probab=31.01 E-value=60 Score=20.54 Aligned_cols=20 Identities=15% Similarity=0.263 Sum_probs=16.0
Q ss_pred CeEEEEeeCCcEEEEecCCC
Q 033063 54 PEIKVTFVTGAEEVFDATST 73 (128)
Q Consensus 54 P~I~Vtf~dG~e~~~d~~~~ 73 (128)
-.|.|-|.|+.++.+.+..-
T Consensus 14 g~vqv~FnD~tkivl~~~~~ 33 (68)
T PF00659_consen 14 GTVQVNFNDHTKIVLSPDGR 33 (68)
T ss_dssp SEEEEEETTS-EEEEETTCC
T ss_pred CCEEEEEeCCCEEEECCCCC
Confidence 37999999999999987655
No 27
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=30.64 E-value=1.3e+02 Score=19.94 Aligned_cols=32 Identities=19% Similarity=0.302 Sum_probs=24.8
Q ss_pred eEEEEeeCCcEEEE-ecCCCCHHHHHHHHHHhc
Q 033063 55 EIKVTFVTGAEEVF-DATSTSAHTIRSMILEKG 86 (128)
Q Consensus 55 ~I~Vtf~dG~e~~~-d~~~~t~~eI~~~i~~~s 86 (128)
.|.|.|-||+.++- -...-++.+|.++|+.+.
T Consensus 6 ~iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~ 38 (79)
T cd01770 6 SIQIRLADGKRLVQKFNSSHRVSDVRDFIVNAR 38 (79)
T ss_pred EEEEECCCCCEEEEEeCCCCcHHHHHHHHHHhC
Confidence 47888999988753 235678999999999764
No 28
>PLN00200 argininosuccinate synthase; Provisional
Probab=30.52 E-value=88 Score=27.35 Aligned_cols=36 Identities=22% Similarity=0.352 Sum_probs=31.5
Q ss_pred CCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhcc
Q 033063 52 HPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 52 ~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~ 87 (128)
.|-.|.++|..|.--.+|+..|+.-++++.+.....
T Consensus 218 ~p~~v~i~Fe~G~pv~lnG~~~~~~~li~~lN~i~g 253 (404)
T PLN00200 218 QPEYIEIEFEKGLPVAINGKTLSPATLLTKLNEIGG 253 (404)
T ss_pred CCeEEEEEEEccEEEEECCeeCCHHHHHHHHHHHHh
Confidence 566899999999999999999999999888776554
No 29
>PF06155 DUF971: Protein of unknown function (DUF971); InterPro: IPR010376 This domain is found in gamma-butyrobetaine dioxygenase and trimethyllysine dioxygenase proteins.; PDB: 2L6N_A 3LUU_A 2L6P_A 3MS5_A 3O2G_A 3N6W_A.
Probab=30.46 E-value=99 Score=20.63 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=24.1
Q ss_pred EecCCCCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhccc
Q 033063 46 KRRTDDHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQM 88 (128)
Q Consensus 46 ~v~~d~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~~ 88 (128)
+|+-+...-.+.|++.||.+..+. ...++.+++=
T Consensus 2 ~i~l~~~~~~l~i~w~DG~~~~~~---------~~~LRd~C~C 35 (89)
T PF06155_consen 2 EIKLDKDERHLEIEWSDGQESRFP---------YEWLRDNCPC 35 (89)
T ss_dssp EEEEECCTTEEEEEETTSEEEEEE---------HHHHHHT-SS
T ss_pred eEEEecCCCEEEEEECCCCEEEEC---------HHHHhccCCC
Confidence 344344568999999999999998 3666666553
No 30
>COG1182 AcpD Acyl carrier protein phosphodiesterase [Lipid metabolism]
Probab=29.20 E-value=56 Score=26.21 Aligned_cols=77 Identities=9% Similarity=-0.025 Sum_probs=52.0
Q ss_pred EEEecCCCCCcHHHHHHHhhcCchhhhhcCCCceEEEEecCCCCCCeEEEEeeCCcEEEEecC-CCCHHHHHHHHHHhcc
Q 033063 9 RIEFNALDPRIASCMEFLAQCNAPKAKESNPACQIQVKRRTDDHPPEIKVTFVTGAEEVFDAT-STSAHTIRSMILEKGQ 87 (128)
Q Consensus 9 ~V~FnPF~~~aksaR~FL~~i~~~k~r~sNp~c~I~~~v~~d~~~P~I~Vtf~dG~e~~~d~~-~~t~~eI~~~i~~~s~ 87 (128)
.|+=+|.+..|.|-++-=..+ ..+|+.||+-+|...=+....=|.|+-.+.+|-...-++. ...-++.++..+.+..
T Consensus 6 ~I~as~~~~~S~S~~l~~~Fi--~~yk~~~P~dev~~~DL~~e~iP~ld~~~~~a~~~~~~~~~t~~~~~~~~~sd~l~~ 83 (202)
T COG1182 6 VIKASPLGENSVSRKLADEFI--ETYKEKHPNDEVIERDLAAEPIPHLDEELLAAWFKPQAGEGTAEEKEALARSDKLLE 83 (202)
T ss_pred EEecCCCccccHHHHHHHHHH--HHHHHhCCCCeEEEeecccCCCcccCHHHHhcccCCccCCCCHHHHHHHHHHHHHHH
Confidence 778889877776654433332 2368889999999999999899999999888755444443 3334444455554433
No 31
>cd01772 SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-substrate-1), also known as Y33K, is a widely expressed protein containing N-terminal UBA (ubiquitin-associated) and C-terminal UBX (ubiqiutin-like) domains that was identified as a substrate of stress-activated protein kinases (SAPKs). SAKS1 is related evolutionarily to two other UBA/UBX-containing proteins, p47 and Faf1. The UBA and UBX domains of SAKS1 bind ubiquitin tetramers and valosin-containing protein (VCP), respectively suggesting a role for SAKS1 as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=28.68 E-value=1.3e+02 Score=19.73 Aligned_cols=34 Identities=9% Similarity=0.104 Sum_probs=26.3
Q ss_pred CeEEEEeeCCcEEEE-ecCCCCHHHHHHHHHHhcc
Q 033063 54 PEIKVTFVTGAEEVF-DATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 54 P~I~Vtf~dG~e~~~-d~~~~t~~eI~~~i~~~s~ 87 (128)
-.|.|.|-||..+.- -.++-++.+|.+.++.+..
T Consensus 5 ~~i~iRlp~G~~~~~~F~~~~tl~~v~~fV~~~~~ 39 (79)
T cd01772 5 TRIQIRLLDGTTLKQTFKAREQLAAVRLFVELNTG 39 (79)
T ss_pred EEEEEECCCCCEEEEEeCCCChHHHHHHHHHHcCC
Confidence 357888999986643 4457999999999998753
No 32
>cd00196 UBQ Ubiquitin-like proteins. Ubiquitin homologs; Includes ubiquitin and ubiquitin-like proteins. Ubiquitin-mediated proteolysis is part of the regulated turnover of proteins required for controlling cell cycle progression. Other family members are protein modifiers that perform a wide range of functions. Ubiquitination usually results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. The three-step mechanism requires an activating enzyme (E1) that forms a thiol ester with the C-terminal carboxy group, a conjugating enzyme (E2) that transiently carries the activated ubiquitin molecule as a thiol ester, and a ligase (E3) that transfers the activated ubiquitin from the E2 to the substrate lysine residue. In poly-ubiquitination, ubiquitin itself is the substrate.
Probab=28.32 E-value=1e+02 Score=16.46 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=22.0
Q ss_pred EEeeCCcEEEEecC-CCCHHHHHHHHHHhcc
Q 033063 58 VTFVTGAEEVFDAT-STSAHTIRSMILEKGQ 87 (128)
Q Consensus 58 Vtf~dG~e~~~d~~-~~t~~eI~~~i~~~s~ 87 (128)
|.+.+|....+... +.++.++.+++..+..
T Consensus 2 v~~~~~~~~~~~~~~~~tv~~l~~~i~~~~~ 32 (69)
T cd00196 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLG 32 (69)
T ss_pred eEecCCCEEEEEcCCCCcHHHHHHHHHHHHC
Confidence 34447777777554 8999999999887643
No 33
>PF07532 Big_4: Bacterial Ig-like domain (group 4); InterPro: IPR011081 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.
Probab=28.22 E-value=1.5e+02 Score=18.20 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=19.2
Q ss_pred EEEEecCC-CCCCeEEEEeeCCcEEEEe
Q 033063 43 IQVKRRTD-DHPPEIKVTFVTGAEEVFD 69 (128)
Q Consensus 43 I~~~v~~d-~~~P~I~Vtf~dG~e~~~d 69 (128)
+.+..... .=|..|.|+|.||....+.
T Consensus 6 vt~~~g~~~~LP~~V~v~~~dGs~~~~~ 33 (59)
T PF07532_consen 6 VTTAVGEKPQLPETVTVTYSDGSTEEVP 33 (59)
T ss_pred EEEeCCCcCCCCCEEEEEECCCCEEEEE
Confidence 33444333 5688999999999987664
No 34
>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A.
Probab=27.34 E-value=1.3e+02 Score=21.45 Aligned_cols=31 Identities=26% Similarity=0.360 Sum_probs=22.7
Q ss_pred eEEEEeeCCc---EEEEecCCCCHHHHHHHHHHhc
Q 033063 55 EIKVTFVTGA---EEVFDATSTSAHTIRSMILEKG 86 (128)
Q Consensus 55 ~I~Vtf~dG~---e~~~d~~~~t~~eI~~~i~~~s 86 (128)
.|++-+.||+ .+.|++ ++|+.+|.+.|...+
T Consensus 4 ~lkf~l~~G~d~~~~~~~~-~~TV~~lKe~i~~~W 37 (111)
T PF13881_consen 4 ELKFRLADGKDIGPFRFDP-STTVADLKERIWAEW 37 (111)
T ss_dssp EEEEEETTS-EEEEEEE-T-TSBHHHHHHHHHHSS
T ss_pred EEEEEEeCCCcccccccCc-cChHHHHHHHHHHHC
Confidence 3677788998 445555 999999999988766
No 35
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=27.22 E-value=1.7e+02 Score=18.58 Aligned_cols=32 Identities=16% Similarity=0.314 Sum_probs=23.2
Q ss_pred eEEEEeeCCcEEEEec-CCCCHHHHHHHHHHhcc
Q 033063 55 EIKVTFVTGAEEVFDA-TSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 55 ~I~Vtf~dG~e~~~d~-~~~t~~eI~~~i~~~s~ 87 (128)
.|++.| +|....+.. ..+++.++...|...-.
T Consensus 3 ~vK~~~-~~~~~~~~~~~~~s~~dL~~~i~~~~~ 35 (81)
T smart00666 3 DVKLRY-GGETRRLSVPRDISFEDLRSKVAKRFG 35 (81)
T ss_pred cEEEEE-CCEEEEEEECCCCCHHHHHHHHHHHhC
Confidence 478888 556666654 38999999988876554
No 36
>PRK13820 argininosuccinate synthase; Provisional
Probab=27.11 E-value=1.1e+02 Score=26.70 Aligned_cols=36 Identities=11% Similarity=0.216 Sum_probs=31.1
Q ss_pred CCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhcc
Q 033063 52 HPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 52 ~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~ 87 (128)
.|-.|.++|..|.--.+|+..|+.-++++.+.....
T Consensus 211 ~p~~v~i~F~~G~pv~lng~~~~~~~li~~lN~i~g 246 (394)
T PRK13820 211 EPEIVEIEFEEGVPVAINGEKMDGVELIRKLNEIAG 246 (394)
T ss_pred CCeEEEEEEEccEEEEECCeeCCHHHHHHHHHHHHh
Confidence 455899999999999999999999999888776554
No 37
>PRK04527 argininosuccinate synthase; Provisional
Probab=26.78 E-value=1e+02 Score=26.98 Aligned_cols=37 Identities=14% Similarity=0.194 Sum_probs=31.6
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhcc
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~ 87 (128)
+.|-.|.++|..|.--.+|++.|+.-+|++.+.....
T Consensus 213 ~~p~~v~i~Fe~G~pv~lnG~~~~~~~li~~lN~i~g 249 (400)
T PRK04527 213 TEALTVTIKFVEGEAVALDGKPLPGAQILAKLNKLFA 249 (400)
T ss_pred CCCeEEEEEEEccEEEEECCEeCCHHHHHHHHHHHHh
Confidence 3566999999999999999999999999887766543
No 38
>PF03990 DUF348: Domain of unknown function (DUF348) ; InterPro: IPR007137 This domain normally occurs as tandem repeats; however it is found as a single copy in the Saccharomyces cerevisiae (Baker's yeast) DNA-binding nuclear protein YCR593 (P25357 from SWISSPROT).
Probab=26.50 E-value=1e+02 Score=18.03 Aligned_cols=20 Identities=20% Similarity=0.247 Sum_probs=15.8
Q ss_pred eCCcEEEEecCCCCHHHHHH
Q 033063 61 VTGAEEVFDATSTSAHTIRS 80 (128)
Q Consensus 61 ~dG~e~~~d~~~~t~~eI~~ 80 (128)
.||++..+-+...++.++++
T Consensus 6 ~dG~~~~v~T~a~tV~~~L~ 25 (43)
T PF03990_consen 6 VDGKEKTVYTTASTVGDALK 25 (43)
T ss_pred ECCEEEEEEeCCCCHHHHHH
Confidence 38999999988888777753
No 39
>PRK10996 thioredoxin 2; Provisional
Probab=26.32 E-value=1.9e+02 Score=20.63 Aligned_cols=33 Identities=18% Similarity=0.179 Sum_probs=24.9
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHH
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILE 84 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~ 84 (128)
..-|++.+ |+||+....-...++..+|.+.++.
T Consensus 105 ~~~Ptlii-~~~G~~v~~~~G~~~~e~l~~~l~~ 137 (139)
T PRK10996 105 RSIPTIMI-FKNGQVVDMLNGAVPKAPFDSWLNE 137 (139)
T ss_pred CccCEEEE-EECCEEEEEEcCCCCHHHHHHHHHH
Confidence 67899865 8999987665556888888777764
No 40
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=26.10 E-value=1.2e+02 Score=21.71 Aligned_cols=31 Identities=19% Similarity=0.388 Sum_probs=23.0
Q ss_pred eEEEEeeCCcEEEEecCC-CCHHHHHHHHHHh
Q 033063 55 EIKVTFVTGAEEVFDATS-TSAHTIRSMILEK 85 (128)
Q Consensus 55 ~I~Vtf~dG~e~~~d~~~-~t~~eI~~~i~~~ 85 (128)
.|.|-+-||....+|.++ .++.+|+..+..+
T Consensus 2 vi~~I~~dG~tk~VNV~~c~~a~eI~~rvLKK 33 (105)
T PF14847_consen 2 VIRFILEDGSTKTVNVSGCFNAQEIKRRVLKK 33 (105)
T ss_dssp EEEEEETTTEEEEEE--S--HHHHHHHHHHHH
T ss_pred EEEEECCCCcEEEEEECCCCCHHHHHHHHHHH
Confidence 478899999999999988 4788887776654
No 41
>PRK09981 hypothetical protein; Provisional
Probab=26.10 E-value=1.5e+02 Score=21.21 Aligned_cols=49 Identities=12% Similarity=0.190 Sum_probs=30.9
Q ss_pred EEecCCCCCcHHHHHHHhhcCchhhhhcC----CCceEEEEecCCCCCCeEEEEe
Q 033063 10 IEFNALDPRIASCMEFLAQCNAPKAKESN----PACQIQVKRRTDDHPPEIKVTF 60 (128)
Q Consensus 10 V~FnPF~~~aksaR~FL~~i~~~k~r~sN----p~c~I~~~v~~d~~~P~I~Vtf 60 (128)
+.|.-+..+-..|...|+.+. .++|+.. | |.|++++..-...=.+++.|
T Consensus 28 a~~~~~~~~~~~Ae~~l~~l~-ekAk~ve~~sep-c~I~~~i~~~~~g~~L~a~F 80 (99)
T PRK09981 28 SKFSRFFATREEAESFMTKLK-ELAAAASSADEG-ASVAYKIKDLEGQVELDAAF 80 (99)
T ss_pred EEEEEEeCCHHHHHHHHHHHH-HHHHHHhccCCc-ceeEEEEEEcCCcEEEEEEE
Confidence 344444555566777777765 5667665 6 99999987654444444444
No 42
>cd01999 Argininosuccinate_Synthase Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterized by severe vomiting spells and mental retardation. AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity
Probab=26.07 E-value=1.2e+02 Score=26.23 Aligned_cols=36 Identities=11% Similarity=0.195 Sum_probs=31.1
Q ss_pred CCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhcc
Q 033063 52 HPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQ 87 (128)
Q Consensus 52 ~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~ 87 (128)
.|-.|.++|..|.--.+|+..|+.-++++.+.....
T Consensus 211 ~p~~v~i~F~~G~pv~lng~~~~~~~li~~lN~i~g 246 (385)
T cd01999 211 EPEYVEIEFEKGVPVALNGEKLDPVELILELNEIAG 246 (385)
T ss_pred CCeEEEEEEEccEEEEEcCeeCCHHHHHHHHHHHHH
Confidence 567899999999999999999999999888776543
No 43
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=25.92 E-value=37 Score=21.83 Aligned_cols=26 Identities=4% Similarity=0.040 Sum_probs=17.0
Q ss_pred eeCCcEEEEecCCCCHHHHHHHHHHh
Q 033063 60 FVTGAEEVFDATSTSAHTIRSMILEK 85 (128)
Q Consensus 60 f~dG~e~~~d~~~~t~~eI~~~i~~~ 85 (128)
..||+.+.+....+|+.++++.+...
T Consensus 4 ~vNG~~~~~~~~~~tv~~lL~~l~~~ 29 (67)
T PRK07696 4 KINGNQIEVPESVKTVAELLTHLELD 29 (67)
T ss_pred EECCEEEEcCCCcccHHHHHHHcCCC
Confidence 46888888875445677776654443
No 44
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=25.65 E-value=1.8e+02 Score=18.31 Aligned_cols=34 Identities=26% Similarity=0.244 Sum_probs=24.3
Q ss_pred eEEEEeeCCcEEEE-ecCCCCHHHHHHHHHHhccc
Q 033063 55 EIKVTFVTGAEEVF-DATSTSAHTIRSMILEKGQM 88 (128)
Q Consensus 55 ~I~Vtf~dG~e~~~-d~~~~t~~eI~~~i~~~s~~ 88 (128)
.|++.|.++...-. .+.++++.++...|...-..
T Consensus 2 ~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~ 36 (81)
T cd05992 2 RVKVKYGGEIRRFVVVSRSISFEDLRSKIAEKFGL 36 (81)
T ss_pred cEEEEecCCCEEEEEecCCCCHHHHHHHHHHHhCC
Confidence 37888885544333 44899999999988776554
No 45
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=25.46 E-value=89 Score=18.53 Aligned_cols=18 Identities=33% Similarity=0.499 Sum_probs=15.5
Q ss_pred CeEEEEeeC-CcEEEEecC
Q 033063 54 PEIKVTFVT-GAEEVFDAT 71 (128)
Q Consensus 54 P~I~Vtf~d-G~e~~~d~~ 71 (128)
..+.|.|.| |....+..+
T Consensus 30 ~~~~V~f~D~G~~~~v~~~ 48 (57)
T smart00333 30 QLYEVFFIDYGNEEVVPPS 48 (57)
T ss_pred CEEEEEEECCCccEEEeHH
Confidence 789999999 999888753
No 46
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=25.43 E-value=1.8e+02 Score=20.06 Aligned_cols=56 Identities=20% Similarity=0.256 Sum_probs=34.2
Q ss_pred eEEEEeeCCcEEEEecC------CCCHHHHHHHHHHhccccchHHHH----HhcCCCCCcccCccccc
Q 033063 55 EIKVTFVTGAEEVFDAT------STSAHTIRSMILEKGQMLENEQMF----RDAGLNWPVLIPDEELQ 112 (128)
Q Consensus 55 ~I~Vtf~dG~e~~~d~~------~~t~~eI~~~i~~~s~~L~~~e~~----~~~g~~~~~~~p~e~~~ 112 (128)
+|+|+| +|....|... ++++.++.+.|...=. |.-..-+ .+---.|..|..+++++
T Consensus 2 ~vKv~y-~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~-l~~~~~~~l~Y~Dedgd~V~l~~D~DL~ 67 (91)
T cd06398 2 VVKVKY-GGTLRRFTFPVAENQLDLNMDGLREKVEELFS-LSPDADLSLTYTDEDGDVVTLVDDNDLT 67 (91)
T ss_pred EEEEEe-CCEEEEEEeccccccCCCCHHHHHHHHHHHhC-CCCCCcEEEEEECCCCCEEEEccHHHHH
Confidence 588999 6667777655 6999999888876432 1100011 11123477777777764
No 47
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=25.39 E-value=1.8e+02 Score=18.84 Aligned_cols=31 Identities=13% Similarity=0.187 Sum_probs=23.4
Q ss_pred CeEEEEeeCCcEEEE-ecCCCCHHHHHHHHHH
Q 033063 54 PEIKVTFVTGAEEVF-DATSTSAHTIRSMILE 84 (128)
Q Consensus 54 P~I~Vtf~dG~e~~~-d~~~~t~~eI~~~i~~ 84 (128)
-.|.|.|-||..+.- -..+-++.+|.+.++.
T Consensus 5 ~~I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~ 36 (80)
T smart00166 5 CRLQIRLPDGSRLVRRFPSSDTLRTVYEFVSA 36 (80)
T ss_pred EEEEEEcCCCCEEEEEeCCCCcHHHHHHHHHH
Confidence 357888889986544 4458899999999954
No 48
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=25.14 E-value=1.3e+02 Score=27.12 Aligned_cols=47 Identities=13% Similarity=0.223 Sum_probs=42.4
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhccccchHHHHHh
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQMLENEQMFRD 97 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~~L~~~e~~~~ 97 (128)
....++.++|.||....+--+.+....++..|-....+..+++.|..
T Consensus 415 ~~~~~l~~~~~~g~~~~l~~~d~~sGa~i~~iv~~a~~~ai~~~~~~ 461 (512)
T TIGR03689 415 EENRYVEVTYANGSTEVLYFKDFVSGAMIANIVDRAKKRAIKDHITG 461 (512)
T ss_pred cccceeEEEecCCceeeEeecccccHHHHHHHHHHHHHHHHHHHHhc
Confidence 46789999999999999999999999999999999999999998843
No 49
>cd02994 PDI_a_TMX PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human transmembrane protein, TMX. TMX is a type I integral membrane protein; the N-terminal redox active TRX domain is present in the endoplasmic reticulum (ER) lumen while the C-terminus is oriented towards the cytoplasm. It is expressed in many cell types and its active site motif (CPAC) is unique. In vitro, TMX reduces interchain disulfides of insulin and renatures inactive RNase containing incorrect disulfide bonds. The C. elegans homolog, DPY-11, is expressed only in the hypodermis and resides in the cytoplasm. It is required for body and sensory organ morphogeneis. Another uncharacterized TRX-related transmembrane protein, human TMX4, is included in the alignment. The active site sequence of TMX4 is CPSC.
Probab=25.08 E-value=1.4e+02 Score=19.33 Aligned_cols=31 Identities=16% Similarity=0.136 Sum_probs=22.7
Q ss_pred CCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHH
Q 033063 51 DHPPEIKVTFVTGAEEVFDATSTSAHTIRSMIL 83 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~ 83 (128)
..-|++.+ |.+|....+. ..++..+|.+.|+
T Consensus 70 ~~~Pt~~~-~~~g~~~~~~-G~~~~~~l~~~i~ 100 (101)
T cd02994 70 TALPTIYH-AKDGVFRRYQ-GPRDKEDLISFIE 100 (101)
T ss_pred cccCEEEE-eCCCCEEEec-CCCCHHHHHHHHh
Confidence 56788877 8999865554 4778888877664
No 50
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=24.46 E-value=1.3e+02 Score=26.44 Aligned_cols=60 Identities=25% Similarity=0.329 Sum_probs=41.7
Q ss_pred ecCCCCCC--eEEEEeeCCcEEEEec-CCCCHHHHHHHHHHhcccc-----------------chHHHHHhcCCCCCccc
Q 033063 47 RRTDDHPP--EIKVTFVTGAEEVFDA-TSTSAHTIRSMILEKGQML-----------------ENEQMFRDAGLNWPVLI 106 (128)
Q Consensus 47 v~~d~~~P--~I~Vtf~dG~e~~~d~-~~~t~~eI~~~i~~~s~~L-----------------~~~e~~~~~g~~~~~~~ 106 (128)
+..|..+| .|.+.+.||..++... .+-|+.+|...|+...-.. +-.+.|++||+.=+||+
T Consensus 297 l~~d~~~PtTsIQIRLanG~RlV~~fN~sHTv~DIR~fI~~aRp~~~~~~F~L~~~FPpk~l~D~sqTle~AgL~Nsvlv 376 (380)
T KOG2086|consen 297 LVIDPAEPTTSIQIRLANGTRLVLKFNHSHTVSDIREFIDTARPGDSSTYFILMMAFPPKPLSDDSQTLEEAGLLNSVLV 376 (380)
T ss_pred cccCCCCCcceEEEEecCCceeeeeccCcccHHHHHHHHHhcCCCCcCCceeeeecCCCcccCCcchhHHhccchhhhhh
Confidence 34444444 5999999999988732 2489999999998765433 23567888887755553
No 51
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=24.45 E-value=85 Score=19.61 Aligned_cols=23 Identities=9% Similarity=0.057 Sum_probs=17.5
Q ss_pred eeCCcEEEEecCCCCHHHHHHHHH
Q 033063 60 FVTGAEEVFDATSTSAHTIRSMIL 83 (128)
Q Consensus 60 f~dG~e~~~d~~~~t~~eI~~~i~ 83 (128)
+.||+++.+. +++|+.++++.+.
T Consensus 2 ~iNg~~~~~~-~~~tv~~ll~~l~ 24 (64)
T TIGR01683 2 TVNGEPVEVE-DGLTLAALLESLG 24 (64)
T ss_pred EECCeEEEcC-CCCcHHHHHHHcC
Confidence 4689999985 4678888877664
No 52
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=23.73 E-value=2e+02 Score=18.16 Aligned_cols=45 Identities=18% Similarity=0.368 Sum_probs=30.6
Q ss_pred EEEEeeCCcEEEEec-CCCCHHHHHHHHHHhc-------------cccchHHHHHhcCC
Q 033063 56 IKVTFVTGAEEVFDA-TSTSAHTIRSMILEKG-------------QMLENEQMFRDAGL 100 (128)
Q Consensus 56 I~Vtf~dG~e~~~d~-~~~t~~eI~~~i~~~s-------------~~L~~~e~~~~~g~ 100 (128)
|.|...+|+...++. ...|+.++.+.|.... +.|+-...|.++|.
T Consensus 3 i~vk~~~G~~~~l~v~~~~tV~~lK~~i~~~~gi~~~~q~L~~~G~~L~d~~~L~~~~i 61 (74)
T cd01807 3 LTVKLLQGRECSLQVSEKESVSTLKKLVSEHLNVPEEQQRLLFKGKALADDKRLSDYSI 61 (74)
T ss_pred EEEEeCCCCEEEEEECCCCcHHHHHHHHHHHHCCCHHHeEEEECCEECCCCCCHHHCCC
Confidence 667777888766543 3689999998887753 34555555555554
No 53
>PLN02593 adrenodoxin-like ferredoxin protein
Probab=23.63 E-value=1.6e+02 Score=20.94 Aligned_cols=15 Identities=47% Similarity=0.643 Sum_probs=11.0
Q ss_pred EEEEe--eCCcEEEEec
Q 033063 56 IKVTF--VTGAEEVFDA 70 (128)
Q Consensus 56 I~Vtf--~dG~e~~~d~ 70 (128)
|+|+| .+|.+.++..
T Consensus 1 ~~V~fi~~~G~~~~v~~ 17 (117)
T PLN02593 1 ISVTFVDKDGEERTVKA 17 (117)
T ss_pred CEEEEEcCCCCEEEEEE
Confidence 57888 5787777764
No 54
>PRK08053 sulfur carrier protein ThiS; Provisional
Probab=23.45 E-value=96 Score=19.60 Aligned_cols=22 Identities=5% Similarity=0.131 Sum_probs=16.6
Q ss_pred eeCCcEEEEecCCCCHHHHHHHH
Q 033063 60 FVTGAEEVFDATSTSAHTIRSMI 82 (128)
Q Consensus 60 f~dG~e~~~d~~~~t~~eI~~~i 82 (128)
+.||+.+.+. +++|+.++++++
T Consensus 4 ~vNg~~~~~~-~~~tl~~ll~~l 25 (66)
T PRK08053 4 LFNDQPMQCA-AGQTVHELLEQL 25 (66)
T ss_pred EECCeEEEcC-CCCCHHHHHHHc
Confidence 5789999995 467888887654
No 55
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=23.31 E-value=47 Score=21.11 Aligned_cols=24 Identities=13% Similarity=0.059 Sum_probs=16.6
Q ss_pred eeCCcEEEEecCCCCHHHHHHHHHH
Q 033063 60 FVTGAEEVFDATSTSAHTIRSMILE 84 (128)
Q Consensus 60 f~dG~e~~~d~~~~t~~eI~~~i~~ 84 (128)
..||+.+.++ +++|+.++++.+..
T Consensus 4 ~vNG~~~~~~-~~~tl~~ll~~l~~ 27 (65)
T PRK05863 4 VVNEEQVEVD-EQTTVAALLDSLGF 27 (65)
T ss_pred EECCEEEEcC-CCCcHHHHHHHcCC
Confidence 4688888886 46777777665433
No 56
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=22.80 E-value=1.8e+02 Score=18.16 Aligned_cols=31 Identities=13% Similarity=0.224 Sum_probs=22.7
Q ss_pred EEEEeeCCcEEEEec-CCCCHHHHHHHHHHhc
Q 033063 56 IKVTFVTGAEEVFDA-TSTSAHTIRSMILEKG 86 (128)
Q Consensus 56 I~Vtf~dG~e~~~d~-~~~t~~eI~~~i~~~s 86 (128)
|.|+-.+|....++. .+.++.++.++|....
T Consensus 1 i~vk~~~g~~~~~~v~~~~tV~~lK~~i~~~~ 32 (70)
T cd01798 1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQ 32 (70)
T ss_pred CEEEcCCCCEEEEEECCCChHHHHHHHHHHHH
Confidence 345666788877654 3789999998887764
No 57
>PRK07440 hypothetical protein; Provisional
Probab=22.68 E-value=51 Score=21.46 Aligned_cols=28 Identities=18% Similarity=0.159 Sum_probs=18.6
Q ss_pred EEEEeeCCcEEEEecCCCCHHHHHHHHHHh
Q 033063 56 IKVTFVTGAEEVFDATSTSAHTIRSMILEK 85 (128)
Q Consensus 56 I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~ 85 (128)
+++ +.||+.+.+. +++|+.++++.+...
T Consensus 5 m~i-~vNG~~~~~~-~~~tl~~lL~~l~~~ 32 (70)
T PRK07440 5 ITL-QVNGETRTCS-SGTSLPDLLQQLGFN 32 (70)
T ss_pred eEE-EECCEEEEcC-CCCCHHHHHHHcCCC
Confidence 444 4688888884 568888887655443
No 58
>PRK06083 sulfur carrier protein ThiS; Provisional
Probab=22.57 E-value=1.3e+02 Score=20.45 Aligned_cols=40 Identities=15% Similarity=0.026 Sum_probs=27.9
Q ss_pred EEEEecCCCCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHH
Q 033063 43 IQVKRRTDDHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILE 84 (128)
Q Consensus 43 I~~~v~~d~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~ 84 (128)
|.+..-..++...+++ +.||+...++ +++|+.++++.+..
T Consensus 6 ~~~~~~~~~~~~~m~I-~VNG~~~~~~-~~~tl~~LL~~l~~ 45 (84)
T PRK06083 6 IVTCTTEGAAMVLITI-SINDQSIQVD-ISSSLAQIIAQLSL 45 (84)
T ss_pred eeeeeccCCCCceEEE-EECCeEEEcC-CCCcHHHHHHHcCC
Confidence 4555555567777775 5799999996 47788888776543
No 59
>cd00271 Chemokine_C Chemokine_C, C or lymphotactin subgroup, 1 of 4 subgroup designations of chemokines based on the arrangement of two N-terminal, conserved cysteine residues. Most of the known chemokines (cd00169) belong to either the CC (cd00272) or CXC (cd00273) subclass. The two other subclasses each have a single known member: fractalkine for the CX3C (cd00274) class and lymphotactin for the C (cd00271) class. Chemokine_Cs differ structurally since they contain only one of the two disulfide bridges that are conserved in all other chemokines and they possess a unique C-terminal extension, which is required for biological activity and thought to play a role in receptor binding. Lymphotactin, a mediator of mucosal immunity, has been found to chemoattract neutrophils and B cells through the XCR1 receptor and thought to be a factor in acute allograft rejection and inflammatory bowel disease.
Probab=21.29 E-value=2.6e+02 Score=18.50 Aligned_cols=39 Identities=8% Similarity=0.027 Sum_probs=32.8
Q ss_pred CCCCCeEEEEeeCCcEEEEecCCCCHHHHHHHHHHhccc
Q 033063 50 DDHPPEIKVTFVTGAEEVFDATSTSAHTIRSMILEKGQM 88 (128)
Q Consensus 50 d~~~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~~~s~~ 88 (128)
+...|-|.++.+.|++.=.|++.-=++++++++|.+.+.
T Consensus 31 ~~~~~AVIF~Tkkgr~iCadP~~~WVq~~i~~ld~~~~~ 69 (72)
T cd00271 31 EGSVRAVIFITKRGLKICADPQAKWVKSAVKTIDRRAST 69 (72)
T ss_pred CCCCCeEEEEecCCCEEeCCCChHHHHHHHHHHHhhccc
Confidence 335678888889999999999999999999999977653
No 60
>cd00273 Chemokine_CXC Chemokine_CXC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members contain an RCxC motif which may be a general requirement for binding to CXC chemokine receptors; those with the ELR motif are chemotatic for neutrophils and have been shown to be angiogenic, while those without the motif act on T and B cells, and are typically angiostatic; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CC (cd00272), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups.
Probab=21.13 E-value=1.8e+02 Score=18.29 Aligned_cols=31 Identities=19% Similarity=0.262 Sum_probs=27.0
Q ss_pred CCeEEEEeeCCcEEEEecCCCCHHHHHHHHH
Q 033063 53 PPEIKVTFVTGAEEVFDATSTSAHTIRSMIL 83 (128)
Q Consensus 53 ~P~I~Vtf~dG~e~~~d~~~~t~~eI~~~i~ 83 (128)
.+.|-++.++|.+.=+|++.--++.+++.+.
T Consensus 33 ~~~VI~~tk~g~~iC~dP~~~wVk~~i~~l~ 63 (64)
T cd00273 33 NTEIIATLKNGRKVCLNPEAPWVQKIIKKLL 63 (64)
T ss_pred CceEEEEEecCCEEEcCCCcHHHHHHHHHHh
Confidence 7788899999999999999988888877653
No 61
>PF13814 Replic_Relax: Replication-relaxation
Probab=20.44 E-value=3.1e+02 Score=20.09 Aligned_cols=50 Identities=16% Similarity=0.220 Sum_probs=38.9
Q ss_pred CCeEEEEeeCCc-----EEEEecCCCCHHHHHHHHHHhccccchHHHHHhcCCCCCcc
Q 033063 53 PPEIKVTFVTGA-----EEVFDATSTSAHTIRSMILEKGQMLENEQMFRDAGLNWPVL 105 (128)
Q Consensus 53 ~P~I~Vtf~dG~-----e~~~d~~~~t~~eI~~~i~~~s~~L~~~e~~~~~g~~~~~~ 105 (128)
.|=..+.+.++. -.++|.+..+...+.+.|+.+.+-++.. +.-|-.||||
T Consensus 137 ~PDa~~~~~~~~~~~~~fiEvD~~te~~~~l~~Kl~~Y~~~~~~~---~~~~~~~pv~ 191 (191)
T PF13814_consen 137 RPDAVFRWRDGDREVRFFIEVDRGTESPARLRRKLERYRRYLRSG---QKRNGVFPVV 191 (191)
T ss_pred eCCEEEEEecCCeEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH---HhcCCCcCcC
Confidence 344555566653 5688999999999999999999877766 7778888886
No 62
>PF08428 Rib: Rib/alpha-like repeat; InterPro: IPR012706 This entry represents a region of about 79 amino acids found tandemly repeated up to fourteen times within the proteins that contain it. The repeats lack cysteines and are highly conserved, even at the DNA level, within and between proteins []. Proteins containing these repeats include the Rib and alpha surface antigens of group B Streptococcus, Esp of Enterococcus faecalis (Streptococcus faecalis), and related proteins of Lactobacillus. Most members of this protein family also have the cell wall anchor motif, LPXTG, shared by many staphyloccal and streptococcal surface antigens. These repeats are thought to define protective epitopes and may play a role in generating phenotypic and genotypic variation [].
Probab=20.39 E-value=1.1e+02 Score=19.64 Aligned_cols=20 Identities=20% Similarity=0.396 Sum_probs=15.9
Q ss_pred CCCCeEEEEeeCCcEEEEec
Q 033063 51 DHPPEIKVTFVTGAEEVFDA 70 (128)
Q Consensus 51 ~~~P~I~Vtf~dG~e~~~d~ 70 (128)
...-.|.|+|-||....+..
T Consensus 40 ~~~~~V~VtypDgS~~~V~v 59 (65)
T PF08428_consen 40 TKTGKVKVTYPDGSTDEVPV 59 (65)
T ss_pred cEEEEEEEEcCCCCEEEEEe
Confidence 45667999999999887753
Done!