Query 038221
Match_columns 113
No_of_seqs 18 out of 20
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 08:50:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038221hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09459 EB_dh: Ethylbenzene d 98.4 8.4E-08 1.8E-12 75.1 1.3 49 54-106 2-52 (261)
2 TIGR03477 DMSO_red_II_gam DMSO 96.9 0.0012 2.7E-08 51.9 4.2 57 45-105 9-67 (205)
3 PF06452 DUF1083: Domain of un 95.0 0.035 7.6E-07 38.8 3.7 53 49-108 1-54 (185)
4 cd00005 CBM9 Family 9 carbohyd 94.6 0.057 1.2E-06 40.1 4.1 52 43-105 6-58 (186)
5 TIGR03785 marine_sort_HK prote 89.3 0.48 1E-05 41.6 3.9 63 36-107 70-136 (703)
6 PF10670 DUF4198: Domain of un 78.5 4.1 8.8E-05 29.1 4.1 51 42-98 114-164 (215)
7 COG1566 EmrA Multidrug resista 71.5 6.1 0.00013 33.4 4.0 56 31-86 260-335 (352)
8 KOG4063 Major epididymal secre 68.8 9.1 0.0002 30.1 4.1 45 1-46 2-68 (158)
9 TIGR03154 sulfolob_CbsA cytoch 58.5 41 0.00088 30.3 6.7 64 36-104 35-100 (465)
10 COG2509 Uncharacterized FAD-de 52.6 20 0.00043 32.4 3.9 45 29-73 289-333 (486)
11 PF07893 DUF1668: Protein of u 47.4 64 0.0014 26.3 5.8 26 83-112 179-206 (342)
12 TIGR02375 pseudoazurin pseudoa 46.2 32 0.0007 24.6 3.5 59 41-111 11-71 (116)
13 PRK02710 plastocyanin; Provisi 44.6 79 0.0017 21.9 5.2 17 41-57 43-60 (119)
14 PF00900 Ribosomal_S4e: Riboso 42.9 14 0.00029 25.1 1.1 16 79-99 40-55 (77)
15 PF14451 Ub-Mut7C: Mut7-C ubiq 42.6 20 0.00044 24.4 1.9 44 29-72 28-79 (81)
16 PRK14891 50S ribosomal protein 41.6 22 0.00047 27.2 2.1 19 77-101 14-33 (131)
17 COG4731 Uncharacterized protei 39.3 14 0.0003 28.7 0.8 19 68-87 119-137 (162)
18 COG1471 RPS4A Ribosomal protei 38.1 23 0.00051 29.4 2.0 17 79-100 132-148 (241)
19 COG2218 FwdC Formylmethanofura 37.0 44 0.00095 28.2 3.4 55 24-78 84-140 (264)
20 PF07172 GRP: Glycine rich pro 35.2 21 0.00046 25.1 1.1 15 5-19 9-23 (95)
21 PRK11372 lysozyme inhibitor; P 34.8 1.3E+02 0.0029 21.4 5.2 49 24-84 31-81 (109)
22 PRK10894 lipopolysaccharide tr 33.9 71 0.0015 23.7 3.8 25 29-53 25-54 (180)
23 PF12322 T4_baseplate: T4 bact 33.6 27 0.00058 27.4 1.6 69 26-100 77-146 (205)
24 cd07694 Ig2_CD4 Second immunog 33.2 19 0.00042 25.4 0.7 14 21-34 59-72 (88)
25 PRK09920 acetyl-CoA:acetoacety 32.6 29 0.00063 27.4 1.6 43 43-86 114-168 (219)
26 PF09048 Cro: Cro; InterPro: 31.8 23 0.00049 23.9 0.8 19 91-109 32-50 (59)
27 PF03951 Gln-synt_N: Glutamine 28.5 33 0.00072 22.7 1.2 29 42-71 31-60 (84)
28 PF15240 Pro-rich: Proline-ric 28.4 42 0.00091 26.6 1.9 15 10-24 8-22 (179)
29 TIGR03122 one_C_dehyd_C formyl 27.4 71 0.0015 26.2 3.1 58 29-86 84-150 (260)
30 TIGR01451 B_ant_repeat conserv 26.9 39 0.00085 20.8 1.2 12 40-51 41-52 (53)
31 PF06832 BiPBP_C: Penicillin-B 26.9 1.1E+02 0.0025 19.7 3.5 37 60-109 18-54 (89)
32 COG2421 Predicted acetamidase/ 26.8 69 0.0015 27.4 3.0 29 78-110 156-184 (305)
33 PF08194 DIM: DIM protein; In 26.7 54 0.0012 20.2 1.8 12 44-55 23-34 (36)
34 PRK15292 putative major fimbri 26.1 90 0.0019 26.4 3.6 25 29-53 20-45 (365)
35 PRK04313 30S ribosomal protein 25.7 52 0.0011 26.9 2.0 17 79-100 129-145 (237)
36 PF09864 MliC: Membrane-bound 25.6 1.1E+02 0.0025 19.1 3.2 48 28-86 1-51 (72)
37 PF07215 DUF1419: Protein of u 24.6 63 0.0014 24.3 2.1 45 54-110 43-95 (111)
38 PTZ00033 60S ribosomal protein 24.3 66 0.0014 24.4 2.2 22 78-101 14-36 (125)
39 PF14699 hGDE_N: N-terminal do 22.6 1.4E+02 0.003 20.4 3.4 34 77-110 27-60 (86)
40 PRK00807 50S ribosomal protein 21.1 1E+02 0.0022 19.5 2.3 16 80-101 15-30 (52)
41 TIGR02940 anfO_nitrog Fe-only 21.1 62 0.0013 26.2 1.6 36 36-71 10-46 (214)
42 cd04032 C2_Perforin C2 domain 20.4 1E+02 0.0022 21.9 2.5 28 66-98 12-40 (127)
43 PF09917 DUF2147: Uncharacteri 20.4 43 0.00093 23.0 0.5 16 70-86 75-90 (114)
44 PF07676 PD40: WD40-like Beta 20.4 1.1E+02 0.0024 16.6 2.1 18 91-108 16-35 (39)
45 PF04972 BON: BON domain; Int 20.4 47 0.001 19.8 0.7 23 37-59 18-40 (64)
46 PF08084 PROCT: PROCT (NUC072) 20.2 1E+02 0.0023 23.1 2.5 71 36-111 2-73 (125)
47 PRK03427 cell division protein 20.1 51 0.0011 28.3 1.0 18 2-19 5-22 (333)
No 1
>PF09459 EB_dh: Ethylbenzene dehydrogenase; InterPro: IPR019020 This entry represents a haem-binding domain found in cytochromes b558/566 (subunit A), c-551 and c-552, as well as in members of the type-II members of the microbial dimethyl sulphoxide (DMSO) reductase family. The DMSO reductase family is a large and rapidly expanding group of enzymes found in bacteria and archaea that share a common form of molybdenum cofactor known as bis(molybdopterin guanine dinucleotide)Mo []. In addition to the molybdopterin subunit, these enzymes also contain an iron-sulphur subunit. These include two distinct but very closely related periplasmic proteins of anaerobic respiration: selenate reductase and chlorate reductase []. Other proteins containing this subunit include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase [, , ]. One member of the DMSO reductase family is eythylbenzene dehydrogenase, which is a heterotrimer of three subunits that catalyses the anaerobic degradation of hydrocarbons (alpha, beta and gamma subunits). This entry matches the gamma subunit, whose structure is known []. The alpha subunit contains the catalytic centre as a Molybdenum cofactor-complex. This removes an electron-pair from the hydrocarbon and passes it along an electron transport system involving iron-sulphur complexes held in the beta subunit and a Haem b molecule contained in the gamma subunit. The electron-pair is then subsequently passed to an as yet unknown receiver. The enzyme is found in a variety of different bacteria.; GO: 0020037 heme binding; PDB: 2IVF_C.
Probab=98.41 E-value=8.4e-08 Score=75.14 Aligned_cols=49 Identities=31% Similarity=0.500 Sum_probs=32.8
Q ss_pred CCcccccCcceeccccCCCC--CCCcCCCceeEEeecccceeccccEEEEEEecC
Q 038221 54 DDWEDIDGSEFSLLPALDPH--AEHEYKGRKMNVKECFSALHDGHDVYFLLQVDG 106 (113)
Q Consensus 54 ~DW~~i~g~efsL~pALdPd--~~~~Y~gGkm~VK~~~~a~HDG~difFlLqVdG 106 (113)
.+|++|+..+++|.|.+++. +..++...+|+|| |+|||++||||||.+.
T Consensus 2 ~~W~~~p~~~v~L~pg~~~~p~~~~~~~~~~v~Vk----Aa~dg~~Iyfll~W~d 52 (261)
T PF09459_consen 2 PDWSKAPPVEVPLYPGQSSYPEPPPKGGTIPVEVK----AAHDGENIYFLLEWPD 52 (261)
T ss_dssp HHHHTS-EEEEE-EE--GGG----T-----EEEEE----EEE-SSEEEEEEEEE-
T ss_pred chhccCCCeEEEECCCccCCccccCCCCcEEEEEE----EEECCCeEEEEEEecC
Confidence 58999999999999996543 4458888999999 9999999999999987
No 2
>TIGR03477 DMSO_red_II_gam DMSO reductase family type II enzyme, heme b subunit. This model represents a heme b-binding subunit, typically called the gamma subunit, of various proteins that also contain a molybdopterin subunit and an iron-sulfur protein. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase.
Probab=96.91 E-value=0.0012 Score=51.89 Aligned_cols=57 Identities=21% Similarity=0.270 Sum_probs=45.6
Q ss_pred ceeeecCCCCCcccccCcceeccccCCCCCCCcCCCc--eeEEeecccceeccccEEEEEEec
Q 038221 45 ELITLDGHADDWEDIDGSEFSLLPALDPHAEHEYKGR--KMNVKECFSALHDGHDVYFLLQVD 105 (113)
Q Consensus 45 G~iTlDG~~~DW~~i~g~efsL~pALdPd~~~~Y~gG--km~VK~~~~a~HDG~difFlLqVd 105 (113)
|.+.+|-.+.-|++++..+.+|.|+--=.+...|++- +|+|| |+||++.|||+|+=+
T Consensus 9 g~~~~dp~d~vW~~ap~~~V~l~~q~~~~pn~~~~~~~~~v~Vk----A~~n~~~Iyf~l~W~ 67 (205)
T TIGR03477 9 GDLPLDPDAPVWAGAPATEVPMVSAPLVHPFLADTGVIKTLDVQ----AARNGERLAVRLKWA 67 (205)
T ss_pred CCCCCCcchhHHhcCCcEEEEeccccccccCccCCCcceEEEEE----EEECCCeEEEEEEEC
Confidence 6888888899999999999999777553333334433 89999 999999999999854
No 3
>PF06452 DUF1083: Domain of unknown function (DUF1083); InterPro: IPR010502 This entry represents the family 9 carbohydrate-binding module (CBD9), which exhibit an immunoglobulin-like beta-sandwich fold, with an additional beta-strand at the N terminus []. Bacterial extracellular cellulases and hemicellulases are involved in the hydrolysis of the major structural polysaccharides of plant cell walls. These are usually modular enzymes that contain catalytic and non-catalytic domains. The CBD9 domain binds to cellulose, xylan, as well as to a range of soluble di- and mono-saccharides, and is found in cellulose- and xylan-degrading enzymes, such as endo-1,4-beta-xylanase (3.2.1.8 from EC) [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0016052 carbohydrate catabolic process; PDB: 1I82_A 1I8A_A 1I8U_A.
Probab=95.03 E-value=0.035 Score=38.80 Aligned_cols=53 Identities=19% Similarity=0.406 Sum_probs=33.6
Q ss_pred ecCCCC-CcccccCcceeccccCCCCCCCcCCCceeEEeecccceeccccEEEEEEecCce
Q 038221 49 LDGHAD-DWEDIDGSEFSLLPALDPHAEHEYKGRKMNVKECFSALHDGHDVYFLLQVDGEC 108 (113)
Q Consensus 49 lDG~~~-DW~~i~g~efsL~pALdPd~~~~Y~gGkm~VK~~~~a~HDG~difFlLqVdG~Y 108 (113)
|||..+ .|+..+ ...+.....+..... +.-+.+|| +++|.+.+||+.+|--+.
T Consensus 1 IDG~~d~~W~~a~--~~~~~~~~~~~~~~~-~~~s~~~~----~~wD~~~LY~~~~v~D~~ 54 (185)
T PF06452_consen 1 IDGKLDAEWKGAP--PITIFYQWWGSDWSG-EDLSTRVR----LLWDDENLYFAFEVTDDT 54 (185)
T ss_dssp SSSS--GGGGGS---EEE--EEEES-T--T-TS-EEEEE----EEE-SSEEEEEEEEE-SS
T ss_pred CCCcccchhcCCc--eEeeeeeecccccCC-CCccEEEE----EEEeCCeEEEEEEEECCc
Confidence 699992 499988 556666666654444 66788899 999999999999996544
No 4
>cd00005 CBM9 Family 9 carbohydrate-binding module (CBM), plays a role in microbial degradation of cellulose and hemicellulose found in plants; previously called cellulose-binding domain; the binding sites of the CBMs for which structures have been determined are of two general types: flat surfaces comprising predominantly aromatic residues tryptophan and tyrosine and extended shallow grooves; this domain frequently occurs in tandem.
Probab=94.58 E-value=0.057 Score=40.14 Aligned_cols=52 Identities=27% Similarity=0.457 Sum_probs=38.2
Q ss_pred ecceeeecCCCCC-cccccCcceeccccCCCCCCCcCCCceeEEeecccceeccccEEEEEEec
Q 038221 43 KPELITLDGHADD-WEDIDGSEFSLLPALDPHAEHEYKGRKMNVKECFSALHDGHDVYFLLQVD 105 (113)
Q Consensus 43 ~PG~iTlDG~~~D-W~~i~g~efsL~pALdPd~~~~Y~gGkm~VK~~~~a~HDG~difFlLqVd 105 (113)
..|.|+|||..++ |+..+-..- .....|. ++-+.+|| +++|...+|++.+|-
T Consensus 6 ~~~~p~IDG~~de~W~~a~~~~~--~~~~~~~-----~~~~t~~k----~lwDd~~LYv~~~v~ 58 (186)
T cd00005 6 KYGTPVIDGQVDDIWKKAKPLET--NTYVEGT-----SGATATVR----VLWDEKNLYVLAEVK 58 (186)
T ss_pred ccCCCeecCccchhHhhCcceee--eeEecCC-----CCcceEEE----EEEcCCcEEEEEEEE
Confidence 4678999999999 998764331 1222332 34578999 999999999999974
No 5
>TIGR03785 marine_sort_HK proteobacterial dedicated sortase system histidine kinase. This histidine kinase protein is paired with an adjacent response regulator (TIGR03787) gene. It co-occurs with a variant sortase enzyme (TIGR03784), usually in the same gene neighborhood, in proteobacterial species most of which are marine, and with an LPXTG motif-containing sortase target conserved protein (TIGR03788). Sortases and LPXTG proteins are far more common in Gram-positive bacteria, where sortase systems mediate attachment to the cell wall or cross-linking of pilin structures. We give this predicted sensor histidine kinase the gene symbol psdS, for Proteobacterial Dedicated Sortase system Sensor histidine kinase.
Probab=89.30 E-value=0.48 Score=41.61 Aligned_cols=63 Identities=25% Similarity=0.352 Sum_probs=45.7
Q ss_pred eEEEEEeecceeeecCCCCCcccccCcceeccccCCCCCCCcCCCceeEEeecccceec----cccEEEEEEecCc
Q 038221 36 IRVLAEFKPELITLDGHADDWEDIDGSEFSLLPALDPHAEHEYKGRKMNVKECFSALHD----GHDVYFLLQVDGE 107 (113)
Q Consensus 36 ~~v~Aef~PG~iTlDG~~~DW~~i~g~efsL~pALdPd~~~~Y~gGkm~VK~~~~a~HD----G~difFlLqVdG~ 107 (113)
--+-|-=.+|-|.|||..+||...+. .|..+|.+- ...+..-..++ +.|. |...|.++||.++
T Consensus 70 ~~~~~~~~~~~~~~~g~~~~~~~~~~-~~~~~~~~~----~~~~~~~~~~~----~~~~~~~~~~~ly~~~~~~~~ 136 (703)
T TIGR03785 70 RDLYAYPLDTAIYLDGYLDDWPEYQH-RFQQYGQLQ----TAGKPKPLSLS----FTHMVGKYDQYLYLLFQVTDN 136 (703)
T ss_pred cceeeccCCCCeecCCcccccccccc-hhhhchhhh----hcCCCCCcceE----EEEeccccCceEEEEEEEcCC
Confidence 45677778999999999999999887 556666421 11111234555 8899 9999999999764
No 6
>PF10670 DUF4198: Domain of unknown function (DUF4198)
Probab=78.51 E-value=4.1 Score=29.09 Aligned_cols=51 Identities=22% Similarity=0.533 Sum_probs=41.5
Q ss_pred eecceeeecCCCCCcccccCcceeccccCCCCCCCcCCCceeEEeecccceeccccE
Q 038221 42 FKPELITLDGHADDWEDIDGSEFSLLPALDPHAEHEYKGRKMNVKECFSALHDGHDV 98 (113)
Q Consensus 42 f~PG~iTlDG~~~DW~~i~g~efsL~pALdPd~~~~Y~gGkm~VK~~~~a~HDG~di 98 (113)
|--=.|+.++..++|...-|..+-+.|.=+| .+-..|..+++| +++||+-+
T Consensus 114 ~aK~~v~~~~~~~~~~~~~g~~lEIvPl~~P--~~l~~g~~~~~~----vl~~GkPl 164 (215)
T PF10670_consen 114 YAKTLVNVGGPSEDWSKPVGLPLEIVPLTNP--YKLKAGDPLPFQ----VLFDGKPL 164 (215)
T ss_pred EEEEEEEccCCccccccccCCcEEEEECcCc--ccccCCCEEEEE----EEECCeEc
Confidence 3334557788889999999999999999888 445788899999 99999754
No 7
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=71.46 E-value=6.1 Score=33.43 Aligned_cols=56 Identities=25% Similarity=0.375 Sum_probs=43.2
Q ss_pred cCCCceEEEEEeecceeeecCCCCCcccccCcceecccc-------------------CCCC-CCCcCCCceeEEe
Q 038221 31 KSDYEIRVLAEFKPELITLDGHADDWEDIDGSEFSLLPA-------------------LDPH-AEHEYKGRKMNVK 86 (113)
Q Consensus 31 ~~~~e~~v~Aef~PG~iTlDG~~~DW~~i~g~efsL~pA-------------------LdPd-~~~~Y~gGkm~VK 86 (113)
..|.-+.|...--|+..+++|+.+--+.-.|+.|+|+|+ |||+ .+...+++.|+|.
T Consensus 260 r~Gq~a~I~~da~~~~~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~ld~~~~~~~~l~~g~sv~ 335 (352)
T COG1566 260 RPGQPAEITLDAYPGNGVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIELDPEPLDRHLLRGGLSVV 335 (352)
T ss_pred cCCCeEEEEEEcCCCceEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEecCCchhcccccCceEEE
Confidence 445556777777788788888888888889999999997 6664 6666777777777
No 8
>KOG4063 consensus Major epididymal secretory protein HE1 [Function unknown]
Probab=68.77 E-value=9.1 Score=30.10 Aligned_cols=45 Identities=22% Similarity=0.375 Sum_probs=29.6
Q ss_pred ChHHHHHHHHHHHhhheeeccccccCceeecC----------------------CCceEEEEEeecce
Q 038221 1 MLRLLLLLFVLSTVSIGWVNSHEESGEWSCKS----------------------DYEIRVLAEFKPEL 46 (113)
Q Consensus 1 M~~~l~l~~~~~~~~~~~~~sheesge~sC~~----------------------~~e~~v~Aef~PG~ 46 (113)
||++++.+.++.++..+|+ .|..-+--.|.+ +.+..++..|+|-.
T Consensus 2 ~ms~~~~v~l~alls~a~a-q~~~t~~k~C~ss~g~~~~V~i~~C~t~pC~lkKgt~~si~I~F~~~~ 68 (158)
T KOG4063|consen 2 MMSFLKTVILLALLSLAAA-QAISTGVKQCGSSDGTPLEVKIDGCPTTPCQLKKGTEASIQIDFAPSR 68 (158)
T ss_pred chHHHHHHHHHHHHHHhhh-cccCcccccccCCCCcceEEEecCCCCCceEEecCCeEEEEEEEeecc
Confidence 4777776666666666665 455444447776 56677888888853
No 9
>TIGR03154 sulfolob_CbsA cytochrome b558/566, subunit A. Members of this protein family are CbsA, one subunit of a highly glycosylated, heterodimeric, mono-heme cytochrome b558/566, found in Sulfolobus acidocaldarius and several other members of the Sulfolobales, a branch of the Crenarchaeota.
Probab=58.49 E-value=41 Score=30.25 Aligned_cols=64 Identities=22% Similarity=0.206 Sum_probs=50.0
Q ss_pred eEEEEEeecceeeec--CCCCCcccccCcceeccccCCCCCCCcCCCceeEEeecccceeccccEEEEEEe
Q 038221 36 IRVLAEFKPELITLD--GHADDWEDIDGSEFSLLPALDPHAEHEYKGRKMNVKECFSALHDGHDVYFLLQV 104 (113)
Q Consensus 36 ~~v~Aef~PG~iTlD--G~~~DW~~i~g~efsL~pALdPd~~~~Y~gGkm~VK~~~~a~HDG~difFlLqV 104 (113)
-+|.|-+++|.+-|- |-..=|+.|.=...||.|-+ |-++..=----+-|| |+-.|-.||.|.+-
T Consensus 35 p~I~aYkV~gsadl~nPGs~sfWs~IPw~nisL~~ni-P~~ptSG~Thyv~VK----AAWng~~ifiL~~w 100 (465)
T TIGR03154 35 PQIPVYKVVGSADLSNPGSASYWSQIPWINISLTANI-PMAPTSGLTHYLLVK----AAWNGSWIFILEEW 100 (465)
T ss_pred CcceEEEeecccccCCCCccchhhcCCcccccccccC-CCCCCCCceeEEEEE----eeccCceEEEEEec
Confidence 578899999999885 77888999999999999887 333321111246799 99999999999884
No 10
>COG2509 Uncharacterized FAD-dependent dehydrogenases [General function prediction only]
Probab=52.64 E-value=20 Score=32.41 Aligned_cols=45 Identities=16% Similarity=0.295 Sum_probs=41.0
Q ss_pred eecCCCceEEEEEeecceeeecCCCCCcccccCcceeccccCCCC
Q 038221 29 SCKSDYEIRVLAEFKPELITLDGHADDWEDIDGSEFSLLPALDPH 73 (113)
Q Consensus 29 sC~~~~e~~v~Aef~PG~iTlDG~~~DW~~i~g~efsL~pALdPd 73 (113)
-|+-+.+-.|.+.|-+|.++++||+.-=++-+...|+|+=-.+|.
T Consensus 289 FCmcP~G~VV~e~~e~g~~~vNG~S~~~r~s~NtNfAllV~i~~t 333 (486)
T COG2509 289 FCMCPGGEVVAENYEDGFVVVNGHSYYARKSENTNFALLVTIEFT 333 (486)
T ss_pred EEECCCCeEEeeeccCceEEEcccchhcccccCcceEEEEecccc
Confidence 799898889999999999999999999999899999999877765
No 11
>PF07893 DUF1668: Protein of unknown function (DUF1668); InterPro: IPR012871 The hypothetical proteins found in this family are expressed by Oryza sativa (Rice) and are of unknown function.
Probab=47.37 E-value=64 Score=26.27 Aligned_cols=26 Identities=15% Similarity=0.383 Sum_probs=21.0
Q ss_pred eEEeecccceeccccEEEEEEec--CceeecC
Q 038221 83 MNVKECFSALHDGHDVYFLLQVD--GECVYSK 112 (113)
Q Consensus 83 m~VK~~~~a~HDG~difFlLqVd--G~Y~y~k 112 (113)
++== |||||+.||.=.+=. |.|.|+.
T Consensus 179 i~sY----avv~g~~I~vS~~~~~~GTysfDt 206 (342)
T PF07893_consen 179 ITSY----AVVDGRTIFVSVNGRRWGTYSFDT 206 (342)
T ss_pred EEEE----EEecCCeEEEEecCCceEEEEEEc
Confidence 5555 888999999977755 9999975
No 12
>TIGR02375 pseudoazurin pseudoazurin. Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related plastocyanins. Several examples of pseudoazurin are encoded by a neighboring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (TIGR02376) of the same species.
Probab=46.17 E-value=32 Score=24.64 Aligned_cols=59 Identities=14% Similarity=0.246 Sum_probs=31.0
Q ss_pred Eeecceeeec-CCCCCcccccCcce-eccccCCCCCCCcCCCceeEEeecccceeccccEEEEEEecCceeec
Q 038221 41 EFKPELITLD-GHADDWEDIDGSEF-SLLPALDPHAEHEYKGRKMNVKECFSALHDGHDVYFLLQVDGECVYS 111 (113)
Q Consensus 41 ef~PG~iTlD-G~~~DW~~i~g~ef-sL~pALdPd~~~~Y~gGkm~VK~~~~a~HDG~difFlLqVdG~Y~y~ 111 (113)
-|.|..||+. |..--|.-.++..- ...+.+.|+....+..+. |..+=.-++-+|.|.|.
T Consensus 11 ~F~P~~v~V~~GdTV~f~n~d~~Hnv~~~~~~~p~g~~~~~s~~------------g~~~~~tF~~~G~Y~Y~ 71 (116)
T TIGR02375 11 VFEPAYIRAAPGDTVTFVPTDKGHNVETIKGMIPEGAEAFKSKI------------NEEYTVTVTEEGVYGVK 71 (116)
T ss_pred EEeCCEEEECCCCEEEEEECCCCeeEEEccCCCcCCcccccCCC------------CCEEEEEeCCCEEEEEE
Confidence 5777777774 55555543333221 122445565555555321 22333445778988884
No 13
>PRK02710 plastocyanin; Provisional
Probab=44.58 E-value=79 Score=21.95 Aligned_cols=17 Identities=29% Similarity=0.800 Sum_probs=11.3
Q ss_pred Eeecceeeec-CCCCCcc
Q 038221 41 EFKPELITLD-GHADDWE 57 (113)
Q Consensus 41 ef~PG~iTlD-G~~~DW~ 57 (113)
.|.|-.|++. |..-.|.
T Consensus 43 ~F~P~~i~v~~Gd~V~~~ 60 (119)
T PRK02710 43 AFEPSTLTIKAGDTVKWV 60 (119)
T ss_pred EEeCCEEEEcCCCEEEEE
Confidence 6888888775 5455554
No 14
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=42.93 E-value=14 Score=25.08 Aligned_cols=16 Identities=38% Similarity=0.688 Sum_probs=11.8
Q ss_pred CCceeEEeecccceeccccEE
Q 038221 79 KGRKMNVKECFSALHDGHDVY 99 (113)
Q Consensus 79 ~gGkm~VK~~~~a~HDG~dif 99 (113)
+||+..+- .||||+|-
T Consensus 40 ~gG~~ql~-----~hDGrni~ 55 (77)
T PF00900_consen 40 KGGKPQLN-----THDGRNIR 55 (77)
T ss_dssp GGGEEEEE-----ETTTEEEE
T ss_pred cCCcEEEE-----ecCceEEE
Confidence 56666664 89999974
No 15
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=42.59 E-value=20 Score=24.40 Aligned_cols=44 Identities=20% Similarity=0.425 Sum_probs=30.7
Q ss_pred eecCCCceE--EEEEeec----ceeeecCCCCCcccc--cCcceeccccCCC
Q 038221 29 SCKSDYEIR--VLAEFKP----ELITLDGHADDWEDI--DGSEFSLLPALDP 72 (113)
Q Consensus 29 sC~~~~e~~--v~Aef~P----G~iTlDG~~~DW~~i--~g~efsL~pALdP 72 (113)
.|.++++++ |++-=.| |.|++||...+|+.+ +|-..+++|+--|
T Consensus 28 ~~~~~~tvkd~IEsLGVP~tEV~~i~vNG~~v~~~~~~~~Gd~v~V~P~~~~ 79 (81)
T PF14451_consen 28 PFDGGATVKDVIESLGVPHTEVGLILVNGRPVDFDYRLKDGDRVAVYPVFRP 79 (81)
T ss_pred ecCCCCcHHHHHHHcCCChHHeEEEEECCEECCCcccCCCCCEEEEEecccC
Confidence 666666643 2332233 889999999999876 6777888887554
No 16
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=41.60 E-value=22 Score=27.25 Aligned_cols=19 Identities=32% Similarity=0.424 Sum_probs=15.4
Q ss_pred cCCC-ceeEEeecccceeccccEEEE
Q 038221 77 EYKG-RKMNVKECFSALHDGHDVYFL 101 (113)
Q Consensus 77 ~Y~g-Gkm~VK~~~~a~HDG~difFl 101 (113)
-||| |+|-|+ .||+-++|+
T Consensus 14 IyPG~G~~fVR------~DGkvf~Fc 33 (131)
T PRK14891 14 IEPGTGTMFVR------KDGTVLHFV 33 (131)
T ss_pred ccCCCCcEEEe------cCCCEEEEe
Confidence 4554 999999 899988886
No 17
>COG4731 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.32 E-value=14 Score=28.66 Aligned_cols=19 Identities=32% Similarity=0.529 Sum_probs=16.3
Q ss_pred ccCCCCCCCcCCCceeEEee
Q 038221 68 PALDPHAEHEYKGRKMNVKE 87 (113)
Q Consensus 68 pALdPd~~~~Y~gGkm~VK~ 87 (113)
-+.||+.++-|. |||+|+|
T Consensus 119 ~v~dP~~gKtYs-~k~~v~~ 137 (162)
T COG4731 119 KVYDPANGKTYS-GKVTVDE 137 (162)
T ss_pred EEeccCCCCEEE-EEEEEcc
Confidence 578999999998 8888884
No 18
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=38.05 E-value=23 Score=29.40 Aligned_cols=17 Identities=35% Similarity=0.876 Sum_probs=13.1
Q ss_pred CCceeEEeecccceeccccEEE
Q 038221 79 KGRKMNVKECFSALHDGHDVYF 100 (113)
Q Consensus 79 ~gGkm~VK~~~~a~HDG~difF 100 (113)
+||+.++- .||||||.+
T Consensus 132 kgG~~QLn-----~hDGrni~~ 148 (241)
T COG1471 132 KGGRIQLN-----LHDGRNIRL 148 (241)
T ss_pred cCCEEEEE-----ecCCceeec
Confidence 67777775 899999553
No 19
>COG2218 FwdC Formylmethanofuran dehydrogenase subunit C [Energy production and conversion]
Probab=37.03 E-value=44 Score=28.23 Aligned_cols=55 Identities=27% Similarity=0.468 Sum_probs=37.5
Q ss_pred ccCceeecCCCceEEEEEeecceeeecCCCCCccccc--CcceeccccCCCCCCCcC
Q 038221 24 ESGEWSCKSDYEIRVLAEFKPELITLDGHADDWEDID--GSEFSLLPALDPHAEHEY 78 (113)
Q Consensus 24 esge~sC~~~~e~~v~Aef~PG~iTlDG~~~DW~~i~--g~efsL~pALdPd~~~~Y 78 (113)
..|+-.-+++-..|+=|+-+-|.|++.|.++||--++ |-+.-+.---..--...|
T Consensus 84 ~aGeI~V~GdVg~~~G~~MkgGkI~V~G~a~sw~G~Em~gge~~i~gna~dyVg~~Y 140 (264)
T COG2218 84 SAGEIIVEGDVGMHVGAGMKGGKIVVNGNADSWAGIEMKGGEIKIFGNAGDYVGCAY 140 (264)
T ss_pred cccEEEEeccccceeeeeeeccEEEEeCCCCCcccceeeCCeEEEeechHHhcccee
Confidence 3456666777788999999999999999999997643 334444433333333334
No 20
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=35.17 E-value=21 Score=25.06 Aligned_cols=15 Identities=27% Similarity=0.065 Sum_probs=7.0
Q ss_pred HHHHHHHHHhhheee
Q 038221 5 LLLLFVLSTVSIGWV 19 (113)
Q Consensus 5 l~l~~~~~~~~~~~~ 19 (113)
|.|+|++.+++++.+
T Consensus 9 L~l~LA~lLlisSev 23 (95)
T PF07172_consen 9 LGLLLAALLLISSEV 23 (95)
T ss_pred HHHHHHHHHHHHhhh
Confidence 334444445555554
No 21
>PRK11372 lysozyme inhibitor; Provisional
Probab=34.81 E-value=1.3e+02 Score=21.40 Aligned_cols=49 Identities=10% Similarity=0.217 Sum_probs=26.3
Q ss_pred ccCceeecCCCceEEEEEeecc--eeeecCCCCCcccccCcceeccccCCCCCCCcCCCceeE
Q 038221 24 ESGEWSCKSDYEIRVLAEFKPE--LITLDGHADDWEDIDGSEFSLLPALDPHAEHEYKGRKMN 84 (113)
Q Consensus 24 esge~sC~~~~e~~v~Aef~PG--~iTlDG~~~DW~~i~g~efsL~pALdPd~~~~Y~gGkm~ 84 (113)
+..++.|++ . ++.+.|.+. .++| .+++.++.|-.+.- ..+..|.+|..+
T Consensus 31 ~~~~Y~C~~-~--~~~v~~~~~~~~v~l--------~~~~~~~~L~~~~S-ASGArY~~g~~~ 81 (109)
T PRK11372 31 DTLEYQCDE-K--PLTVKLNNPRQEVSF--------VYDNQLLHLKQGIS-ASGARYTDGIYV 81 (109)
T ss_pred CcEEEEeCC-c--EEEEEEECCCCeEEE--------EECCEEEEEEEeec-cCcCcEeCCcEE
Confidence 345889977 3 556666542 2221 13555555555443 346677666544
No 22
>PRK10894 lipopolysaccharide transport periplasmic protein LptA; Provisional
Probab=33.89 E-value=71 Score=23.73 Aligned_cols=25 Identities=16% Similarity=0.417 Sum_probs=16.4
Q ss_pred eecCCCceEEEEE-----eecceeeecCCC
Q 038221 29 SCKSDYEIRVLAE-----FKPELITLDGHA 53 (113)
Q Consensus 29 sC~~~~e~~v~Ae-----f~PG~iTlDG~~ 53 (113)
++.++..|+|.|+ ...|.+++-|+.
T Consensus 25 ~~d~~~pI~I~AD~~~~~~~~~~~~~tGnV 54 (180)
T PRK10894 25 TGDTDQPIHIDSDQQSLDMQGNVVTFTGNV 54 (180)
T ss_pred ccccCCCEEEEeCceEeeccCCEEEEEeeE
Confidence 3555556777665 357888888875
No 23
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=33.61 E-value=27 Score=27.36 Aligned_cols=69 Identities=20% Similarity=0.321 Sum_probs=49.9
Q ss_pred CceeecCCCceEEEEEeecceeeecCCCCCcccccCcceec-cccCCCCCCCcCCCceeEEeecccceeccccEEE
Q 038221 26 GEWSCKSDYEIRVLAEFKPELITLDGHADDWEDIDGSEFSL-LPALDPHAEHEYKGRKMNVKECFSALHDGHDVYF 100 (113)
Q Consensus 26 ge~sC~~~~e~~v~Aef~PG~iTlDG~~~DW~~i~g~efsL-~pALdPd~~~~Y~gGkm~VK~~~~a~HDG~difF 100 (113)
-.|.|....+ ++...+..-.+-|+=+...|...+|....+ +|-++-+ .....-+-+|...+|||..+|=
T Consensus 77 ~~~~C~~cg~-~~~~~i~l~~~~l~~~~~~~~~~~~i~i~~ryP~~~~~-----~~~~~mi~~cI~~I~~~~~~~~ 146 (205)
T PF12322_consen 77 VNYTCPDCGE-EVKVPINLDQIKLTDGKNEIKLSDGIKIKMRYPSLFEF-----DDVFEMIASCIDYIYDGEQVYN 146 (205)
T ss_pred EEEECCCCCc-EEEEEecchhcccCCCCcceEecCCEEEEEeCCccccc-----CCHHHHHHHHHHeEEECCEEEE
Confidence 3789997777 888888888888833388899888887777 5777644 2222334568889999988763
No 24
>cd07694 Ig2_CD4 Second immunoglobulin (Ig) domain of CD4. Ig2_CD4; second immunoglobulin (Ig) domain of CD4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.
Probab=33.21 E-value=19 Score=25.44 Aligned_cols=14 Identities=29% Similarity=0.812 Sum_probs=11.3
Q ss_pred cccccCceeecCCC
Q 038221 21 SHEESGEWSCKSDY 34 (113)
Q Consensus 21 sheesge~sC~~~~ 34 (113)
+-++||.|+|.=-.
T Consensus 59 ~~qdSG~WtC~V~~ 72 (88)
T cd07694 59 GPNDSGTWDCIVSV 72 (88)
T ss_pred CcccCCEEEEEEEE
Confidence 67899999997543
No 25
>PRK09920 acetyl-CoA:acetoacetyl-CoA transferase subunit alpha; Provisional
Probab=32.62 E-value=29 Score=27.36 Aligned_cols=43 Identities=12% Similarity=0.139 Sum_probs=28.9
Q ss_pred ecceeee-------cCCCCCcccccCcceeccccCCCCC-----CCcCCCceeEEe
Q 038221 43 KPELITL-------DGHADDWEDIDGSEFSLLPALDPHA-----EHEYKGRKMNVK 86 (113)
Q Consensus 43 ~PG~iTl-------DG~~~DW~~i~g~efsL~pALdPd~-----~~~Y~gGkm~VK 86 (113)
+||.+|= ||....| .++|.++-|.||+.||= -.+=..|++++.
T Consensus 114 ~Pg~~t~~glGT~v~~gk~~~-~~~G~~~l~~~a~~~DvAlI~a~~AD~~GN~~~~ 168 (219)
T PRK09920 114 LGGFLTPTGVGTVVEEGKQTL-TLDGKTWLLERPLRADLALIRAHRADTLGNLTYQ 168 (219)
T ss_pred CCceeeccccCccccCCCcee-EECCeEEEEEecCCCcEEEEEecccCCCCCEEEE
Confidence 4666663 4555556 47899999999999872 233345777665
No 26
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=31.76 E-value=23 Score=23.88 Aligned_cols=19 Identities=26% Similarity=0.574 Sum_probs=15.8
Q ss_pred ceeccccEEEEEEecCcee
Q 038221 91 ALHDGHDVYFLLQVDGECV 109 (113)
Q Consensus 91 a~HDG~difFlLqVdG~Y~ 109 (113)
|+.-|||||...+=||.|.
T Consensus 32 Alr~gR~I~v~~~~dGs~~ 50 (59)
T PF09048_consen 32 ALRAGRNIFVTIMPDGSVE 50 (59)
T ss_dssp HHHCT-EEEEEEETTSEEE
T ss_pred HHHcCCcEEEEEcCCCeEE
Confidence 7778999999999999874
No 27
>PF03951 Gln-synt_N: Glutamine synthetase, beta-Grasp domain; InterPro: IPR008147 Glutamine synthetase (6.3.1.2 from EC) (GS) [] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. There seem to be three different classes of GS [, , ]: Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see IPR001637 from INTERPRO). Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast. Class III enzymes (GSIII) has, currently, only been found in Bacteroides fragilis and in Butyrivibrio fibrisolvens. It is a hexamer of identical chains. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes. While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.; GO: 0004356 glutamate-ammonia ligase activity, 0006542 glutamine biosynthetic process, 0006807 nitrogen compound metabolic process; PDB: 3NG0_A 2D3A_A 2D3C_E 2D3B_H 1LGR_C 2GLS_I 1F1H_B 1FPY_C 2LGS_D 1F52_A ....
Probab=28.47 E-value=33 Score=22.72 Aligned_cols=29 Identities=21% Similarity=0.408 Sum_probs=23.8
Q ss_pred eecceeeecCCCC-CcccccCcceeccccCC
Q 038221 42 FKPELITLDGHAD-DWEDIDGSEFSLLPALD 71 (113)
Q Consensus 42 f~PG~iTlDG~~~-DW~~i~g~efsL~pALd 71 (113)
+.=|. +.||.+- -|..|+.|..-|.|.++
T Consensus 31 ~~~g~-~fDGSSi~g~~~~~~SDm~l~Pd~~ 60 (84)
T PF03951_consen 31 LEDGI-GFDGSSIRGFATIEESDMYLKPDPS 60 (84)
T ss_dssp GGS-E-EEECCGTTTSSBSCCEEEEEEEEGG
T ss_pred hhCCC-CCCcccCcCcccCCCCCEEEecCcc
Confidence 33455 9999999 99999999999999854
No 28
>PF15240 Pro-rich: Proline-rich
Probab=28.39 E-value=42 Score=26.63 Aligned_cols=15 Identities=13% Similarity=-0.011 Sum_probs=6.4
Q ss_pred HHHHhhheeeccccc
Q 038221 10 VLSTVSIGWVNSHEE 24 (113)
Q Consensus 10 ~~~~~~~~~~~shee 24 (113)
|+.+.|+.+.+..|+
T Consensus 8 vALLALSSAQ~~dEd 22 (179)
T PF15240_consen 8 VALLALSSAQSTDED 22 (179)
T ss_pred HHHHHhhhccccccc
Confidence 333444544444443
No 29
>TIGR03122 one_C_dehyd_C formylmethanofuran dehydrogenase subunit C. Members of this largely archaeal protein family are subunit C of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdC) from molybdenum-containing (FmdC) forms of this enzyme.
Probab=27.40 E-value=71 Score=26.25 Aligned_cols=58 Identities=26% Similarity=0.402 Sum_probs=29.8
Q ss_pred eecCCCceEEEEEeecceeeecCCCCCc--ccccCcceeccccCCCCCCCc-------CCCceeEEe
Q 038221 29 SCKSDYEIRVLAEFKPELITLDGHADDW--EDIDGSEFSLLPALDPHAEHE-------YKGRKMNVK 86 (113)
Q Consensus 29 sC~~~~e~~v~Aef~PG~iTlDG~~~DW--~~i~g~efsL~pALdPd~~~~-------Y~gGkm~VK 86 (113)
.++++..-++=+..+-|.|++.|.+.|| ....|-+.-..+--..-.... -.||++.|+
T Consensus 84 ~v~G~~G~~~G~~M~gG~I~V~G~ag~~~G~~m~GG~I~V~GnAg~~~G~~~~G~~~gM~GG~I~V~ 150 (260)
T TIGR03122 84 VVEGDVGMHVGAEMKGGKIVVNGNADSWLGCEMKGGEIEVKGNAGDYVGSAYRGEWRGMSGGKIIVE 150 (260)
T ss_pred EEEccchhHHhccCCCCEEEEEecCchhhhCcccCCEEEEECCCcccccceeecccccccCCEEEEE
Confidence 3444433344455666777777777777 333444444444333333333 345666665
No 30
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=26.93 E-value=39 Score=20.80 Aligned_cols=12 Identities=25% Similarity=0.589 Sum_probs=10.5
Q ss_pred EEeecceeeecC
Q 038221 40 AEFKPELITLDG 51 (113)
Q Consensus 40 Aef~PG~iTlDG 51 (113)
.+|.||++|++|
T Consensus 41 ~~~v~~S~~~~g 52 (53)
T TIGR01451 41 TTFVSNSVTVNG 52 (53)
T ss_pred CEEEeCcEEECC
Confidence 579999999988
No 31
>PF06832 BiPBP_C: Penicillin-Binding Protein C-terminus Family; InterPro: IPR009647 This conserved region of approximately 90 residues is found in a sub-group of bacterial Penicillin-Binding Proteins (PBPs). A variable length loop region separates this region from the transpeptidase unit (IPR001460 from INTERPRO). It is predicted to be a beta fold.
Probab=26.86 E-value=1.1e+02 Score=19.68 Aligned_cols=37 Identities=30% Similarity=0.537 Sum_probs=24.4
Q ss_pred cCcceeccccCCCCCCCcCCCceeEEeecccceeccccEEEEEEecCcee
Q 038221 60 DGSEFSLLPALDPHAEHEYKGRKMNVKECFSALHDGHDVYFLLQVDGECV 109 (113)
Q Consensus 60 ~g~efsL~pALdPd~~~~Y~gGkm~VK~~~~a~HDG~difFlLqVdG~Y~ 109 (113)
+|..+.+.|... ...+|.+| |.+....+|.++ ||.|.
T Consensus 18 ~g~~~~~~~~~~-------~~~~l~l~----a~~~~~~~~W~v--dg~~~ 54 (89)
T PF06832_consen 18 DGAVLALDPGIP-------ERQPLVLK----AAGGRGPVYWFV--DGEPL 54 (89)
T ss_pred CCCEEEeCCCCC-------ccceEEEE----EeCCCCcEEEEE--CCEEc
Confidence 455555555433 46899999 998855666664 77664
No 32
>COG2421 Predicted acetamidase/formamidase [Energy production and conversion]
Probab=26.82 E-value=69 Score=27.42 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=26.1
Q ss_pred CCCceeEEeecccceeccccEEEEEEecCceee
Q 038221 78 YKGRKMNVKECFSALHDGHDVYFLLQVDGECVY 110 (113)
Q Consensus 78 Y~gGkm~VK~~~~a~HDG~difFlLqVdG~Y~y 110 (113)
+.||+|-+| -+--|-.||+=.+|+|++-+
T Consensus 156 ~~GGNlD~k----~l~~GstvylPV~V~GAlls 184 (305)
T COG2421 156 EHGGNLDIK----DLTEGSTVYLPVFVEGALLS 184 (305)
T ss_pred ccCCcCChh----hccCCCEEEEEEEEcCceee
Confidence 779999999 88899999999999998743
No 33
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=26.73 E-value=54 Score=20.20 Aligned_cols=12 Identities=25% Similarity=0.554 Sum_probs=9.1
Q ss_pred cceeeecCCCCC
Q 038221 44 PELITLDGHADD 55 (113)
Q Consensus 44 PG~iTlDG~~~D 55 (113)
||.++++|.=.|
T Consensus 23 pG~ViING~C~d 34 (36)
T PF08194_consen 23 PGNVIINGKCID 34 (36)
T ss_pred CCeEEECceeee
Confidence 889999886443
No 34
>PRK15292 putative major fimbrial protein SthE; Provisional
Probab=26.14 E-value=90 Score=26.39 Aligned_cols=25 Identities=36% Similarity=0.388 Sum_probs=16.2
Q ss_pred eecCC-CceEEEEEeecceeeecCCC
Q 038221 29 SCKSD-YEIRVLAEFKPELITLDGHA 53 (113)
Q Consensus 29 sC~~~-~e~~v~Aef~PG~iTlDG~~ 53 (113)
+|... .+..+.--=.|..||++=++
T Consensus 20 ~c~~~~~~~~~~~~~lp~~i~V~~g~ 45 (365)
T PRK15292 20 SCKRSGNEGAVSITPLPEQIVVDSGS 45 (365)
T ss_pred eeecccCCCceeeeeCCCceeecCCC
Confidence 78853 44444334459999998666
No 35
>PRK04313 30S ribosomal protein S4e; Validated
Probab=25.75 E-value=52 Score=26.93 Aligned_cols=17 Identities=41% Similarity=0.884 Sum_probs=13.3
Q ss_pred CCceeEEeecccceeccccEEE
Q 038221 79 KGRKMNVKECFSALHDGHDVYF 100 (113)
Q Consensus 79 ~gGkm~VK~~~~a~HDG~difF 100 (113)
+||+..+- +||||+|-+
T Consensus 129 ~gG~~ql~-----~hDGrni~~ 145 (237)
T PRK04313 129 KGGKIQLN-----LHDGRNILV 145 (237)
T ss_pred cCCEEEEE-----ecCCceEEc
Confidence 67777775 999999765
No 36
>PF09864 MliC: Membrane-bound lysozyme-inhibitor of c-type lysozyme; InterPro: IPR018660 This entry contains proteins that represent a novel family of bacterial lysozyme inhibitors with widespread homologues in Gram-negative bacteria, that may function as colonization or virulence factors in bacteria interacting with an animal host []. ; PDB: 3OE3_F 2F09_A 3F6Z_D.
Probab=25.64 E-value=1.1e+02 Score=19.05 Aligned_cols=48 Identities=17% Similarity=0.308 Sum_probs=31.6
Q ss_pred eeecCCCceEEEEEeecce---eeecCCCCCcccccCcceeccccCCCCCCCcCCCceeEEe
Q 038221 28 WSCKSDYEIRVLAEFKPEL---ITLDGHADDWEDIDGSEFSLLPALDPHAEHEYKGRKMNVK 86 (113)
Q Consensus 28 ~sC~~~~e~~v~Aef~PG~---iTlDG~~~DW~~i~g~efsL~pALdPd~~~~Y~gGkm~VK 86 (113)
|.|+++. +|.+.|.+.. ++|- +++.++.|-++.. ..+..|.+|.++.-
T Consensus 1 y~C~~~~--~i~v~~~~~~~~~a~l~--------~~~~~~~L~~~~S-aSGarY~~~~~~~w 51 (72)
T PF09864_consen 1 YQCDNGQ--RISVTYINDDDPSAVLR--------YDDQEYTLPQAPS-ASGARYSNGGYEFW 51 (72)
T ss_dssp EEECCSC--EEEEEEEECTTEEEEEE--------CCTEEEEEEEECT-SSSEEEECCTEEEE
T ss_pred CCCCCCC--EEEEEEcCCCCcEEEEE--------ECCEEEEEEEeec-CCCCcEeCCCEEEE
Confidence 5798665 6777776654 5552 2235666666666 77889988866654
No 37
>PF07215 DUF1419: Protein of unknown function (DUF1419); InterPro: IPR009862 This family consists of several bacterial proteins of around 110 residues in length. Members of this family seem to be specific to Agrobacterium species and to Rhizobium loti (Mesorhizobium loti). The function of this family is unknown.
Probab=24.58 E-value=63 Score=24.26 Aligned_cols=45 Identities=29% Similarity=0.617 Sum_probs=30.5
Q ss_pred CCcccccCcc----eeccccCCCCC----CCcCCCceeEEeecccceeccccEEEEEEecCceee
Q 038221 54 DDWEDIDGSE----FSLLPALDPHA----EHEYKGRKMNVKECFSALHDGHDVYFLLQVDGECVY 110 (113)
Q Consensus 54 ~DW~~i~g~e----fsL~pALdPd~----~~~Y~gGkm~VK~~~~a~HDG~difFlLqVdG~Y~y 110 (113)
..|=.|.-.+ |-+||-|.=-. -.||..|++| .|||-|.|||..+|
T Consensus 43 GeWFEI~e~~hdyMleiLPPL~~rg~mFamrEf~tgsVT------------SVFf~l~Idg~~R~ 95 (111)
T PF07215_consen 43 GEWFEITEAEHDYMLEILPPLWMRGDMFAMREFLTGSVT------------SVFFALRIDGRIRY 95 (111)
T ss_pred cccEEecchhhhhHHhhCCchheecchhhhhhhccCCee------------eEEEEEEECCceeE
Confidence 3454444333 56777765433 3588888776 57999999999877
No 38
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=24.28 E-value=66 Score=24.41 Aligned_cols=22 Identities=27% Similarity=0.313 Sum_probs=17.9
Q ss_pred CCC-ceeEEeecccceeccccEEEE
Q 038221 78 YKG-RKMNVKECFSALHDGHDVYFL 101 (113)
Q Consensus 78 Y~g-Gkm~VK~~~~a~HDG~difFl 101 (113)
||| |+|-|+ |..+.||.-.+|+
T Consensus 14 yPG~G~~~Vr--~~~~~Dgkv~~F~ 36 (125)
T PTZ00033 14 HPGHGRRYVP--FAFLSTKPVLTFL 36 (125)
T ss_pred cCCCCcEeee--cccCCCCCEEEEe
Confidence 444 899999 7778999988886
No 39
>PF14699 hGDE_N: N-terminal domain from the human glycogen debranching enzyme
Probab=22.61 E-value=1.4e+02 Score=20.37 Aligned_cols=34 Identities=12% Similarity=0.143 Sum_probs=16.5
Q ss_pred cCCCceeEEeecccceeccccEEEEEEecCceee
Q 038221 77 EYKGRKMNVKECFSALHDGHDVYFLLQVDGECVY 110 (113)
Q Consensus 77 ~Y~gGkm~VK~~~~a~HDG~difFlLqVdG~Y~y 110 (113)
+|...|-...+--+.-|...-|=.-+..+|.|.|
T Consensus 27 ~F~R~~f~~~~~~~~~~~d~~idi~i~~aGsF~y 60 (86)
T PF14699_consen 27 PFDRDKFRELKWESSFDKDIYIDIPIYKAGSFCY 60 (86)
T ss_pred ccccCceEEeeccCCCCcCeEEEEEcccCceEEE
Confidence 4444444444333333332223334567888887
No 40
>PRK00807 50S ribosomal protein L24e; Validated
Probab=21.09 E-value=1e+02 Score=19.48 Aligned_cols=16 Identities=50% Similarity=0.698 Sum_probs=12.7
Q ss_pred CceeEEeecccceeccccEEEE
Q 038221 80 GRKMNVKECFSALHDGHDVYFL 101 (113)
Q Consensus 80 gGkm~VK~~~~a~HDG~difFl 101 (113)
.|+|.|+ +||+-.||.
T Consensus 15 ~G~~~vr------~Dgkv~~Fc 30 (52)
T PRK00807 15 TGKMYVK------KDGTILYFC 30 (52)
T ss_pred CCeEEEE------eCCcEEEEe
Confidence 3788787 899988875
No 41
>TIGR02940 anfO_nitrog Fe-only nitrogenase accessory protein AnfO. Members of this protein family, called Anf1 in Rhodobacter capsulatus and AnfO in Azotobacter vinelandii, are found only in species with the Fe-only nitrogenase and are encoded immediately downstream of the structural genes in the above named species.
Probab=21.06 E-value=62 Score=26.16 Aligned_cols=36 Identities=19% Similarity=0.354 Sum_probs=30.6
Q ss_pred eEEEEEeecceeee-cCCCCCcccccCcceeccccCC
Q 038221 36 IRVLAEFKPELITL-DGHADDWEDIDGSEFSLLPALD 71 (113)
Q Consensus 36 ~~v~Aef~PG~iTl-DG~~~DW~~i~g~efsL~pALd 71 (113)
.++..-|.||.|-| ..|...|+.+.-.+|++-|+..
T Consensus 10 G~~~s~~e~G~i~vye~~~~~W~~~~ei~~~v~~~~g 46 (214)
T TIGR02940 10 GEISSIFDKGFILLFEEDGGEWKVLTRIENAVCPAKG 46 (214)
T ss_pred CCEecccCCeEEEEEecCCCeEEEEEEEEeccCcccC
Confidence 47788899999987 6777799999999999888765
No 42
>cd04032 C2_Perforin C2 domain of Perforin. Perforin contains a single copy of a C2 domain in its C-terminus and plays a role in lymphocyte-mediated cytotoxicity. Mutations in perforin leads to familial hemophagocytic lymphohistiocytosis type 2. The function of perforin is calcium dependent and the C2 domain is thought to confer this binding to target cell membranes. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few
Probab=20.44 E-value=1e+02 Score=21.87 Aligned_cols=28 Identities=7% Similarity=0.076 Sum_probs=18.8
Q ss_pred ccccCCCCCCC-cCCCceeEEeecccceeccccE
Q 038221 66 LLPALDPHAEH-EYKGRKMNVKECFSALHDGHDV 98 (113)
Q Consensus 66 L~pALdPd~~~-~Y~gGkm~VK~~~~a~HDG~di 98 (113)
--|+||||-.. .+.=|+++|+ +|-|+++
T Consensus 12 ~~~~~~~~~~~~~~~~~~L~V~-----V~~A~~L 40 (127)
T cd04032 12 SSPNVNSNCCPTRRGLATLTVT-----VLRATGL 40 (127)
T ss_pred CCCCcCCCcCcCcCCcEEEEEE-----EEECCCC
Confidence 35999999555 4455788887 5555544
No 43
>PF09917 DUF2147: Uncharacterized protein conserved in bacteria (DUF2147); InterPro: IPR019223 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=20.43 E-value=43 Score=22.97 Aligned_cols=16 Identities=25% Similarity=0.574 Sum_probs=9.1
Q ss_pred CCCCCCCcCCCceeEEe
Q 038221 70 LDPHAEHEYKGRKMNVK 86 (113)
Q Consensus 70 LdPd~~~~Y~gGkm~VK 86 (113)
+||+.++.|+ ++|+++
T Consensus 75 ydP~~GktY~-~~i~l~ 90 (114)
T PF09917_consen 75 YDPEDGKTYS-AKITLS 90 (114)
T ss_pred EeCCCCCEEE-EEEEEC
Confidence 5666666665 455544
No 44
>PF07676 PD40: WD40-like Beta Propeller Repeat; InterPro: IPR011659 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This region appears to be related to the IPR001680 from INTERPRO repeat. This model is likely to miss copies within a sequence.; PDB: 2HQS_D 1C5K_A 2IVZ_A 2W8B_D 3IAX_A 1CRZ_A 1N6F_D 1N6D_C 1N6E_C 1K32_A ....
Probab=20.43 E-value=1.1e+02 Score=16.60 Aligned_cols=18 Identities=28% Similarity=0.440 Sum_probs=14.1
Q ss_pred ceeccccEEEEEEec--Cce
Q 038221 91 ALHDGHDVYFLLQVD--GEC 108 (113)
Q Consensus 91 a~HDG~difFlLqVd--G~Y 108 (113)
-..||+-|+|.-+.+ |.+
T Consensus 16 ~SpDGk~i~f~s~~~~~g~~ 35 (39)
T PF07676_consen 16 WSPDGKYIYFTSNRNDRGSF 35 (39)
T ss_dssp E-TTSSEEEEEEECT--SSE
T ss_pred EecCCCEEEEEecCCCCCCc
Confidence 567999999998888 665
No 45
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=20.40 E-value=47 Score=19.84 Aligned_cols=23 Identities=17% Similarity=0.283 Sum_probs=18.2
Q ss_pred EEEEEeecceeeecCCCCCcccc
Q 038221 37 RVLAEFKPELITLDGHADDWEDI 59 (113)
Q Consensus 37 ~v~Aef~PG~iTlDG~~~DW~~i 59 (113)
.|..+...|.|+|-|+.++.+..
T Consensus 18 ~i~v~v~~g~v~L~G~v~s~~~~ 40 (64)
T PF04972_consen 18 NISVSVENGVVTLSGEVPSQEQR 40 (64)
T ss_dssp TEEEEEECTEEEEEEEESSCHHH
T ss_pred eEEEEEECCEEEEEeeCcHHHHH
Confidence 56666779999999999876654
No 46
>PF08084 PROCT: PROCT (NUC072) domain; InterPro: IPR012984 The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family [].; PDB: 2P87_A 2P8R_A 3SBG_A 2OG4_A.
Probab=20.23 E-value=1e+02 Score=23.06 Aligned_cols=71 Identities=21% Similarity=0.265 Sum_probs=32.0
Q ss_pred eEEEEEeecceeeecCCCCCcccccCcceec-cccCCCCCCCcCCCceeEEeecccceeccccEEEEEEecCceeec
Q 038221 36 IRVLAEFKPELITLDGHADDWEDIDGSEFSL-LPALDPHAEHEYKGRKMNVKECFSALHDGHDVYFLLQVDGECVYS 111 (113)
Q Consensus 36 ~~v~Aef~PG~iTlDG~~~DW~~i~g~efsL-~pALdPd~~~~Y~gGkm~VK~~~~a~HDG~difFlLqVdG~Y~y~ 111 (113)
|-|...|.||+|+|-...-. -+|.|... +--+..+..+.|.- ++..| |--.+-|--.=|||.=-+|...|+
T Consensus 2 i~it~sftpGSvsL~Ay~LT---~~G~eWg~~nkD~~~~~p~g~~p-~~~ek-~QllLSdr~~GfFlVP~~~~WNY~ 73 (125)
T PF08084_consen 2 ITITCSFTPGSVSLSAYKLT---PEGYEWGRQNKDLISDNPQGFSP-SFYEK-VQLLLSDRILGFFLVPEDGVWNYN 73 (125)
T ss_dssp EEEEEEEETTEEEEEEEEE----HHHHHHHHCTTT--SS--TT--G-GGEEE-EEEEEETTS--EEEEETTS--B-T
T ss_pred EEEEEeccCCceEEEEEecC---HHHHHHHhhcccccccCCCCCCc-chhhe-eeeeeecceeeEEEccCCCcccce
Confidence 66888999999999765321 12222221 00000111222321 33333 222355666778888888877664
No 47
>PRK03427 cell division protein ZipA; Provisional
Probab=20.06 E-value=51 Score=28.34 Aligned_cols=18 Identities=28% Similarity=0.340 Sum_probs=11.2
Q ss_pred hHHHHHHHHHHHhhheee
Q 038221 2 LRLLLLLFVLSTVSIGWV 19 (113)
Q Consensus 2 ~~~l~l~~~~~~~~~~~~ 19 (113)
+||+++++.+.+.+...+
T Consensus 5 LrLiLivvGAIAIiAlL~ 22 (333)
T PRK03427 5 LRLILIIVGAIAIIALLV 22 (333)
T ss_pred hhhHHHHHHHHHHHHHHH
Confidence 678777766655554443
Done!