Query 019215
Match_columns 344
No_of_seqs 18 out of 20
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 07:39:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019215.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019215hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02338 OTU: OTU-like cystein 98.9 2.3E-09 4.9E-14 83.8 7.0 33 99-131 2-38 (121)
2 COG0278 Glutaredoxin-related p 70.1 2.3 4.9E-05 36.6 1.2 15 301-315 11-25 (105)
3 PF14359 DUF4406: Domain of un 68.1 2 4.4E-05 34.7 0.5 54 175-235 12-65 (92)
4 KOG2606 OTU (ovarian tumor)-li 64.4 10 0.00023 37.5 4.6 36 254-289 236-271 (302)
5 PF00356 LacI: Bacterial regul 58.2 12 0.00026 27.1 2.9 33 124-156 13-46 (46)
6 KOG2943 Predicted glyoxalase [ 53.9 9 0.0002 37.7 2.2 43 203-247 49-94 (299)
7 PLN03093 Protein SENSITIVITY T 52.2 7.4 0.00016 37.9 1.3 13 288-300 170-182 (273)
8 PRK09358 adenosine deaminase; 50.7 1.3E+02 0.0027 28.2 9.0 86 65-153 234-338 (340)
9 PF05826 Phospholip_A2_2: Phos 50.7 6.8 0.00015 32.3 0.7 17 311-327 2-20 (99)
10 PHA02938 hypothetical protein; 49.8 39 0.00084 34.1 5.8 58 104-164 156-213 (361)
11 PRK09526 lacI lac repressor; R 45.6 19 0.00042 32.0 2.8 33 124-156 19-52 (342)
12 PTZ00062 glutaredoxin; Provisi 44.4 13 0.00027 34.1 1.5 20 299-318 107-129 (204)
13 PF10275 Peptidase_C65: Peptid 43.9 12 0.00025 33.9 1.2 13 96-108 45-57 (244)
14 smart00165 UBA Ubiquitin assoc 43.8 28 0.00061 22.8 2.7 25 182-206 2-26 (37)
15 PF14723 SSFA2_C: Sperm-specif 43.8 51 0.0011 30.8 5.2 83 56-148 53-150 (179)
16 KOG3818 DNA polymerase epsilon 42.7 28 0.00061 36.7 3.8 74 116-223 17-91 (525)
17 PRK14987 gluconate operon tran 42.2 20 0.00043 32.0 2.3 33 124-156 19-52 (331)
18 PRK09492 treR trehalose repres 42.2 69 0.0015 28.2 5.7 68 123-194 17-94 (315)
19 TIGR03553 F420_FbiB_CTERM F420 41.5 23 0.0005 30.1 2.5 42 123-168 5-48 (194)
20 COG2345 Predicted transcriptio 41.1 26 0.00057 32.9 3.0 34 62-95 41-77 (218)
21 cd02062 Nitro_FMN_reductase Pr 38.7 18 0.00039 27.7 1.3 42 123-168 3-46 (122)
22 PRK10824 glutaredoxin-4; Provi 38.7 19 0.00041 30.4 1.5 18 301-318 11-31 (115)
23 TIGR00365 monothiol glutaredox 38.3 21 0.00046 28.3 1.8 18 301-318 8-28 (97)
24 cd04704 PLA2_bee_venom_like PL 38.2 11 0.00025 31.1 0.2 18 310-327 2-21 (97)
25 PF04355 SmpA_OmlA: SmpA / Oml 37.2 44 0.00096 24.7 3.2 58 186-244 9-68 (71)
26 KOG3288 OTU-like cysteine prot 37.1 30 0.00065 34.3 2.8 34 97-130 115-149 (307)
27 KOG3991 Uncharacterized conser 36.6 24 0.00052 34.4 2.1 57 257-329 199-255 (256)
28 cd00194 UBA Ubiquitin Associat 34.7 46 0.00099 21.8 2.6 24 182-205 2-25 (38)
29 cd01320 ADA Adenosine deaminas 34.3 1.6E+02 0.0035 27.1 6.9 43 104-148 282-324 (325)
30 PRK12334 nucleoside triphospha 34.2 50 0.0011 32.1 3.8 59 65-135 203-261 (277)
31 PF00627 UBA: UBA/TS-N domain; 33.9 54 0.0012 21.9 2.9 23 182-204 3-25 (37)
32 cd02151 NADPH_oxidoreductase_2 33.6 33 0.00072 28.4 2.2 43 122-168 6-50 (162)
33 PRK10014 DNA-binding transcrip 33.4 45 0.00097 29.8 3.1 33 124-156 20-53 (342)
34 cd02135 Arsenite_oxidase Nitro 33.3 32 0.00069 27.8 2.0 42 123-168 6-49 (160)
35 TIGR02405 trehalos_R_Ecol treh 33.2 45 0.00097 29.7 3.1 67 124-194 15-91 (311)
36 KOG3325 Membrane coat complex 32.8 82 0.0018 29.5 4.8 81 235-315 67-158 (183)
37 PF09876 DUF2103: Predicted me 31.9 52 0.0011 28.1 3.1 26 164-189 75-100 (103)
38 cd03028 GRX_PICOT_like Glutare 31.1 33 0.00072 26.5 1.7 18 301-318 4-24 (90)
39 cd02136 Nitroreductase Nitrore 31.1 38 0.00083 28.1 2.2 43 122-168 6-50 (178)
40 KOG3131 Uncharacterized conser 29.4 26 0.00057 34.5 1.1 14 288-301 155-168 (281)
41 COG1609 PurR Transcriptional r 29.3 50 0.0011 31.1 2.9 67 124-194 14-90 (333)
42 PF08856 DUF1826: Protein of u 29.2 39 0.00085 30.8 2.1 26 307-336 159-184 (196)
43 cd02140 Nitroreductase_4 Nitro 29.0 30 0.00065 29.7 1.3 43 123-169 7-53 (192)
44 PRK10727 DNA-binding transcrip 28.7 51 0.0011 29.7 2.7 34 124-157 15-49 (343)
45 PF13137 DUF3983: Protein of u 28.3 1E+02 0.0022 22.2 3.6 27 120-153 3-29 (34)
46 PF09179 TilS: TilS substrate 28.3 1.1E+02 0.0024 21.9 3.9 48 119-167 10-64 (69)
47 PF03965 Penicillinase_R: Peni 27.4 2.8E+02 0.0061 22.3 6.5 19 61-79 36-54 (115)
48 PRK10423 transcriptional repre 26.6 61 0.0013 28.7 2.8 34 124-157 12-46 (327)
49 COG3681 L-cysteine desulfidase 26.5 77 0.0017 32.7 3.8 69 97-167 155-227 (433)
50 PRK10401 DNA-binding transcrip 25.8 72 0.0016 28.8 3.2 35 123-157 14-49 (346)
51 PRK13777 transcriptional regul 25.7 1.4E+02 0.003 27.1 4.9 87 56-157 68-159 (185)
52 COG1846 MarR Transcriptional r 24.8 1.9E+02 0.004 21.5 4.7 58 64-122 54-113 (126)
53 TIGR01481 ccpA catabolite cont 24.3 71 0.0015 28.4 2.8 34 124-157 15-49 (329)
54 TIGR00444 mazG MazG family pro 24.1 74 0.0016 30.2 3.0 36 99-135 184-219 (248)
55 PRK10703 DNA-binding transcrip 23.3 77 0.0017 28.4 2.8 35 123-157 14-49 (341)
56 PRK12333 nucleoside triphospha 21.9 84 0.0018 29.6 2.9 36 99-135 165-200 (204)
57 PF02829 3H: 3H domain; Inter 21.9 1.9E+02 0.0042 24.1 4.7 51 124-193 46-96 (98)
58 PRK11041 DNA-binding transcrip 21.2 2E+02 0.0042 25.2 4.9 55 136-194 3-67 (309)
59 PRK06474 hypothetical protein; 20.7 5.8E+02 0.013 22.6 7.7 108 62-191 43-154 (178)
60 PF07499 RuvA_C: RuvA, C-termi 20.6 1.3E+02 0.0028 21.4 3.0 24 180-203 2-25 (47)
61 PF12650 DUF3784: Domain of un 20.1 65 0.0014 25.4 1.6 19 129-147 21-39 (97)
62 cd02150 NADPH_oxidoreductase_1 20.1 90 0.002 25.9 2.5 41 123-167 6-48 (166)
No 1
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=98.95 E-value=2.3e-09 Score=83.81 Aligned_cols=33 Identities=33% Similarity=0.598 Sum_probs=29.9
Q ss_pred CCCCchhHHHHHHhc----cCCCChHHHHHHHHHHHH
Q 019215 99 ADGNCLFTASQKAMT----ARDVDARELRRRTVRRFL 131 (344)
Q Consensus 99 ~dGnCLFtA~~~am~----~~~~~~relR~r~vrrF~ 131 (344)
.||||||.|+..+|. ....+..+||+++++...
T Consensus 2 gDGnClF~Avs~~l~~~~~~~~~~~~~lR~~~~~~l~ 38 (121)
T PF02338_consen 2 GDGNCLFRAVSDQLYGDGGGSEDNHQELRKAVVDYLR 38 (121)
T ss_dssp SSTTHHHHHHHHHHCTT-SSSTTTHHHHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 699999999999998 778899999999987766
No 2
>COG0278 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=70.09 E-value=2.3 Score=36.58 Aligned_cols=15 Identities=60% Similarity=0.924 Sum_probs=12.9
Q ss_pred CCCCCCEEEEeeccc
Q 019215 301 DICEPPIFLFMKGTG 315 (344)
Q Consensus 301 ei~~~P~FLfMkgTg 315 (344)
+|.+.|+.||||||-
T Consensus 11 ~i~~n~VvLFMKGtp 25 (105)
T COG0278 11 QIKENPVVLFMKGTP 25 (105)
T ss_pred HhhcCceEEEecCCC
Confidence 467899999999994
No 3
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=68.15 E-value=2 Score=34.70 Aligned_cols=54 Identities=26% Similarity=0.375 Sum_probs=43.8
Q ss_pred ccchhhhHHHHHHHHHhhhhhhHHHHHHhhhcceecCCCcccchhhcccCCCCCceeeEEe
Q 019215 175 KEDRVGLDSAIDELVQLGMQREMAAESIYKERCIPVSDGPSWAKYMLISGSHDDEYDIITL 235 (344)
Q Consensus 175 k~dr~~Ldaai~Elv~~Gmqre~AAEsIYkErc~~V~dg~SwakYMsisGS~~de~diItL 235 (344)
...|.+..++.++|...|..--+-|+. .+.++.+|..||.++=..=..+|.|-+
T Consensus 12 ~~N~~~f~~~a~~L~~~G~~vvnPa~~-------~~~~~~~~~~ym~~~l~~L~~cD~i~~ 65 (92)
T PF14359_consen 12 DYNRPAFNAAAKRLRAKGYEVVNPAEL-------GIPEGLSWEEYMRICLAMLSDCDAIYM 65 (92)
T ss_pred chHHHHHHHHHHHHHHCCCEEeCchhh-------CCCCCCCHHHHHHHHHHHHHhCCEEEE
Confidence 345789999999999999998888887 678889999999997655556676654
No 4
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=64.41 E-value=10 Score=37.50 Aligned_cols=36 Identities=31% Similarity=0.391 Sum_probs=32.6
Q ss_pred ccccchhhhhhhhhhhcceEEEEEecCCcccccCCC
Q 019215 254 AAFGDDIAIECLATEFNREIYVVQAHGSDAMVDEEN 289 (344)
Q Consensus 254 aAfGDDiaIE~LATefkReIyVVqahg~damvdeen 289 (344)
++||-+|=|-+|+-=|+-.|-|.|+-|+...+.||-
T Consensus 236 ~~WGgelEL~AlShvL~~PI~Vy~~~~p~~~~geey 271 (302)
T KOG2606|consen 236 AAWGGELELKALSHVLQVPIEVYQADGPILEYGEEY 271 (302)
T ss_pred ccccchHHHHHHHHhhccCeEEeecCCCceeechhh
Confidence 589999999999999999999999998888777664
No 5
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=58.22 E-value=12 Score=27.06 Aligned_cols=33 Identities=36% Similarity=0.540 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccC
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPD 156 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~Pd 156 (344)
.-||-|.+..-..++++-|++|.++++.+ |.|+
T Consensus 13 ~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 13 KSTVSRVLNGPPRVSEETRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB-SS
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 45899999999999999999999999876 6663
No 6
>KOG2943 consensus Predicted glyoxalase [Carbohydrate transport and metabolism]
Probab=53.87 E-value=9 Score=37.68 Aligned_cols=43 Identities=30% Similarity=0.614 Sum_probs=35.7
Q ss_pred hhhcceecCCCc---ccchhhcccCCCCCceeeEEeeeccceeeEeec
Q 019215 203 YKERCIPVSDGP---SWAKYMLISGSHDDEYDIITLQYTEDGLLSVDE 247 (344)
Q Consensus 203 YkErc~~V~dg~---SwakYMsisGS~~de~diItLqYteeGLLsVDe 247 (344)
++|-|.+-+||+ -|.|=|.=-| ++|+|++|-|+|. -|.=+-|.
T Consensus 49 f~egc~aacngpyd~kwSktmvGyG-pEdshFViELTYN-YgV~~Yel 94 (299)
T KOG2943|consen 49 FEEGCEAACNGPYDGKWSKTMVGYG-PEDSHFVIELTYN-YGVSKYEL 94 (299)
T ss_pred hhhhhhhhcCCCcccchhhhheecC-CCcccEEEEEEec-cCccceec
Confidence 688999999995 6999898777 8999999999996 36656665
No 7
>PLN03093 Protein SENSITIVITY TO RED LIGHT REDUCED 1; Provisional
Probab=52.21 E-value=7.4 Score=37.93 Aligned_cols=13 Identities=31% Similarity=0.741 Sum_probs=11.6
Q ss_pred CCeEEeecCCCCC
Q 019215 288 ENCVFFLPHRPRS 300 (344)
Q Consensus 288 encvFFLPHrPR~ 300 (344)
++-+|||||||..
T Consensus 170 ~pTLFYMPHCp~~ 182 (273)
T PLN03093 170 KPTLFFMPHCEAE 182 (273)
T ss_pred CCeEEEeCCCCHH
Confidence 6899999999965
No 8
>PRK09358 adenosine deaminase; Provisional
Probab=50.68 E-value=1.3e+02 Score=28.18 Aligned_cols=86 Identities=7% Similarity=0.071 Sum_probs=56.8
Q ss_pred HHHHHHhhcCccccCCCCCC-------------------cceEEEeccCcccCCCCCchhHHHHHHhccCCCChHHHHHH
Q 019215 65 RHLERLHSKGVLWKHPEDQS-------------------RSIVFKLSHGGEVSADGNCLFTASQKAMTARDVDARELRRR 125 (344)
Q Consensus 65 ~~L~rl~~~GV~wk~p~~~~-------------------~~~vf~L~hggeV~~dGnCLFtA~~~am~~~~~~~relR~r 125 (344)
+.+++|.++|+...+-.+|. ..+...|.--+....+.| ||.-++.+...-.++..+|++-
T Consensus 234 ~~~~~l~~~gi~v~~cP~Sn~~l~~~~~~~~~pi~~l~~~Gv~v~lgTD~~~~~~~~-l~~e~~~~~~~~~l~~~el~~l 312 (340)
T PRK09358 234 ALMARLADRRIPLEVCPTSNVQTGAVPSLAEHPLKTLLDAGVRVTINTDDPLVFGTT-LTEEYEALAEAFGLSDEDLAQL 312 (340)
T ss_pred HHHHHHHHcCCeEEECCCccccccccCCcccChHHHHHHCCCEEEECCCCCcccCCC-HHHHHHHHHHHhCCCHHHHHHH
Confidence 46888999999875433221 112223322233233333 7777777776548999999888
Q ss_pred HHHHHHHHhccCChhhHHHHHHHHHhcc
Q 019215 126 TVRRFLEDLGSVGEGQREMINDAIRHMY 153 (344)
Q Consensus 126 ~vrrF~~~~~s~~~ee~e~Id~aIrhlY 153 (344)
+..-|..-|. +.++|+.+-+.|++.+
T Consensus 313 ~~nai~~sf~--~~~~k~~l~~~~~~~~ 338 (340)
T PRK09358 313 ARNALEAAFL--SEEEKAALLAEVDAWL 338 (340)
T ss_pred HHHHHHHHCC--CHHHHHHHHHHHHHHh
Confidence 8777766665 8999999999987654
No 9
>PF05826 Phospholip_A2_2: Phospholipase A2; InterPro: IPR001211 Phospholipase A2 (3.1.1.4 from EC) (PLA2) is a small lipolytic enzyme that releases fatty acids from the second carbon group of glycerol. It is involved in a number of physiologically important cellular processes, such as the liberation of arachidonic acid from membrane phospholipids []. It plays a pivotal role in the biosynthesis of prostaglandin and other mediators of inflammation. PLA2 has four to seven disulphide bonds and binds a calcium ion that is essential for activity. Within the active enzyme, the alpha amino group is involved in a conserved hydrogen-bonding network linking the N-terminal region to the active site. The side chains of two conserved residues, His and Asp, participate in the catalytic network. Many PLA2's are widely distributed in snakes, lizards, bees and mammals. In mammals there are at least four forms: pancreatic, membrane-associated as well as two less well characterised forms. The venom of most snakes contains multiple forms of PLA2. Some of them are presynaptic neurotoxins which inhibit neuromuscular transmission by blocking acetylcholine release from the nerve termini. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Api m 1.; GO: 0004623 phospholipase A2 activity, 0005509 calcium ion binding, 0016042 lipid catabolic process; PDB: 1POC_A.
Probab=50.67 E-value=6.8 Score=32.26 Aligned_cols=17 Identities=53% Similarity=1.210 Sum_probs=10.1
Q ss_pred eecccccCCC--CCCcccc
Q 019215 311 MKGTGWCGAG--ADHYEPL 327 (344)
Q Consensus 311 MkgTgWcgaG--aDHYEPl 327 (344)
|-||=|||.| |..|+.|
T Consensus 2 ~pGT~WCG~gn~a~~~~dl 20 (99)
T PF05826_consen 2 YPGTKWCGPGNIAKNYSDL 20 (99)
T ss_dssp -TT-SSSBSS---SSTT--
T ss_pred CCCCcccCCCCCccCcccc
Confidence 6799999999 5566654
No 10
>PHA02938 hypothetical protein; Provisional
Probab=49.84 E-value=39 Score=34.14 Aligned_cols=58 Identities=22% Similarity=0.377 Sum_probs=39.5
Q ss_pred hhHHHHHHhccCCCChHHHHHHHHHHHHHHhccCChhhHHHHHHHHHhccccCCCCcceee
Q 019215 104 LFTASQKAMTARDVDARELRRRTVRRFLEDLGSVGEGQREMINDAIRHMYSPDLKNGWGIH 164 (344)
Q Consensus 104 LFtA~~~am~~~~~~~relR~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY~PdLk~GWGVh 164 (344)
||.-+++-.--+.....||=+|++.+|+.+|+.- -++-.....+-+++|+ .+.||.+-
T Consensus 156 LhklL~kEa~~rgtT~seLVrrAIeefLqkYG~n-~eeIKkL~E~akdl~y--~~~g~kv~ 213 (361)
T PHA02938 156 LHKLLEKEAIKRGTTASELVRRAIEEFLKKYGNN-YEEIKKLYETAKDLFY--EKGPWKGR 213 (361)
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhccc-HHHHHHHHHhhhhhcc--cccCCcee
Confidence 6777776666668999999999999999999944 2222222233334443 57888764
No 11
>PRK09526 lacI lac repressor; Reviewed
Probab=45.62 E-value=19 Score=32.04 Aligned_cols=33 Identities=30% Similarity=0.530 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccC
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPD 156 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~Pd 156 (344)
.-||.|.+.....++++-|++|.++++.| |.|+
T Consensus 19 ~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn 52 (342)
T PRK09526 19 YQTVSRVLNQASHVSAKTREKVEAAMAELNYVPN 52 (342)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence 46899999999999999999999999888 8886
No 12
>PTZ00062 glutaredoxin; Provisional
Probab=44.44 E-value=13 Score=34.10 Aligned_cols=20 Identities=40% Similarity=0.713 Sum_probs=15.6
Q ss_pred CCCCCCCCEEEEeeccc---ccC
Q 019215 299 RSDICEPPIFLFMKGTG---WCG 318 (344)
Q Consensus 299 R~ei~~~P~FLfMkgTg---Wcg 318 (344)
..-|...|++||||||- ||+
T Consensus 107 ~~li~~~~Vvvf~Kg~~~~p~C~ 129 (204)
T PTZ00062 107 ERLIRNHKILLFMKGSKTFPFCR 129 (204)
T ss_pred HHHHhcCCEEEEEccCCCCCCCh
Confidence 33477899999999975 566
No 13
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=43.86 E-value=12 Score=33.89 Aligned_cols=13 Identities=46% Similarity=0.953 Sum_probs=0.0
Q ss_pred ccCCCCCchhHHH
Q 019215 96 EVSADGNCLFTAS 108 (344)
Q Consensus 96 eV~~dGnCLFtA~ 108 (344)
.|-.||||.|+|.
T Consensus 45 ~vRGDGNCFYRAf 57 (244)
T PF10275_consen 45 RVRGDGNCFYRAF 57 (244)
T ss_dssp -B-SSSTHHHHHH
T ss_pred eecCCccHHHHHH
No 14
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=43.78 E-value=28 Score=22.78 Aligned_cols=25 Identities=28% Similarity=0.565 Sum_probs=21.3
Q ss_pred HHHHHHHHHhhhhhhHHHHHHhhhc
Q 019215 182 DSAIDELVQLGMQREMAAESIYKER 206 (344)
Q Consensus 182 daai~Elv~~Gmqre~AAEsIYkEr 206 (344)
+.+|+.|++.|++++.|.+++++-.
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~~ 26 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAAN 26 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhC
Confidence 5689999999999999998887643
No 15
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=43.78 E-value=51 Score=30.79 Aligned_cols=83 Identities=20% Similarity=0.275 Sum_probs=55.4
Q ss_pred eccchHHHHHHHHHHhhcCccccCCCCCCcceEEEeccCcccCCCCCchhHHHHHHhccCCCChHHHHHHHHHHHHHH--
Q 019215 56 VIGLEEQQRRHLERLHSKGVLWKHPEDQSRSIVFKLSHGGEVSADGNCLFTASQKAMTARDVDARELRRRTVRRFLED-- 133 (344)
Q Consensus 56 V~gld~qqr~~L~rl~~~GV~wk~p~~~~~~~vf~L~hggeV~~dGnCLFtA~~~am~~~~~~~relR~r~vrrF~~~-- 133 (344)
-+-+|.|.||.|+-|.. -.|.-. -|.+-+|++..++.-+--.+++...++ .+.-=+..+|...-|+++
T Consensus 53 ~~~~EmQlrrvLhdir~--t~q~l~-------q~~~~~g~~~~~~~~~~~~sv~~L~~~-T~~Elq~mr~~ln~FR~qm~ 122 (179)
T PF14723_consen 53 PSSTEMQLRRVLHDIRD--TLQNLS-------QYPVMRGSDLNADPYSTQRSVRELYSC-TVQELQQMRRSLNSFREQMM 122 (179)
T ss_pred ccCHHHHHHHHHHHHHH--HHHHhc-------cccccccccccccccccchhHHHHhhh-hHHHHHHHHHHHHHHHHHHH
Confidence 56689999999999864 344442 455667888877775544455555444 333445566677777664
Q ss_pred -------------hccCChhhHHHHHHH
Q 019215 134 -------------LGSVGEGQREMINDA 148 (344)
Q Consensus 134 -------------~~s~~~ee~e~Id~a 148 (344)
|..+++|||+..++-
T Consensus 123 dlE~~l~~QQalvy~hMSeeER~EaeQL 150 (179)
T PF14723_consen 123 DLELHLMRQQALVYRHMSEEEREEAEQL 150 (179)
T ss_pred HHHHHHHHhHHHHHhcCCHHHHHHHHHH
Confidence 677889999888763
No 16
>KOG3818 consensus DNA polymerase epsilon, subunit B [Replication, recombination and repair]
Probab=42.73 E-value=28 Score=36.74 Aligned_cols=74 Identities=22% Similarity=0.302 Sum_probs=56.1
Q ss_pred CCChHHHHHHHHHHHHHHhccCChhhHH-HHHHHHHhccccCCCCcceeeEEEEEEeeeeccchhhhHHHHHHHHHhhhh
Q 019215 116 DVDARELRRRTVRRFLEDLGSVGEGQRE-MINDAIRHMYSPDLKNGWGIHVVQEVKLLAKKEDRVGLDSAIDELVQLGMQ 194 (344)
Q Consensus 116 ~~~~relR~r~vrrF~~~~~s~~~ee~e-~Id~aIrhlY~PdLk~GWGVhvVQevKlLA~k~dr~~Ldaai~Elv~~Gmq 194 (344)
+.-..-+|..+++-..|....-+.+||+ -|++.| .++|+.||..+-..|.+++++++|+-..|
T Consensus 17 k~~G~l~R~~~ik~L~e~~~~~~~~er~~~i~~i~--------------e~iq~q~l~s~~~~r~~~~~avq~~~~sg-- 80 (525)
T KOG3818|consen 17 KLCGHLWRSEAIKLLVELALDWKKEERKKWINKII--------------ELIQKQKLNSPHEEREAIEAAVQECSSSG-- 80 (525)
T ss_pred hhhhHHHHHhHHHHHHHHHhhhHHHHhhhhHHHHH--------------HHHHhhccCCchhhHHHHHHHHHHhhhcc--
Confidence 3445667888888777777666666665 466644 34688899999999999999999999999
Q ss_pred hhHHHHHHhhhcceecCCCcccchhhccc
Q 019215 195 REMAAESIYKERCIPVSDGPSWAKYMLIS 223 (344)
Q Consensus 195 re~AAEsIYkErc~~V~dg~SwakYMsis 223 (344)
...|.||..|-
T Consensus 81 ------------------~~~~e~~F~vi 91 (525)
T KOG3818|consen 81 ------------------TQDAEKYFNVI 91 (525)
T ss_pred ------------------cccHHHHHhhc
Confidence 55677777774
No 17
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=42.22 E-value=20 Score=32.04 Aligned_cols=33 Identities=33% Similarity=0.533 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccC
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPD 156 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~Pd 156 (344)
.-||.|-+.....++++-|++|.++++.| |.|.
T Consensus 19 ~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn 52 (331)
T PRK14987 19 KMTVSRFLRNPEQVSVALRGKIAAALDELGYIPN 52 (331)
T ss_pred HHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCcc
Confidence 46899999888899999999999999988 8885
No 18
>PRK09492 treR trehalose repressor; Provisional
Probab=42.21 E-value=69 Score=28.23 Aligned_cols=68 Identities=19% Similarity=0.382 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHhccCChhhHHHHHHHHHhc-cccC-----CCCcceeeEEEEEEeeeecc----chhhhHHHHHHHHHhh
Q 019215 123 RRRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPD-----LKNGWGIHVVQEVKLLAKKE----DRVGLDSAIDELVQLG 192 (344)
Q Consensus 123 R~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~Pd-----Lk~GWGVhvVQevKlLA~k~----dr~~Ldaai~Elv~~G 192 (344)
-.-||.|.+..-..++++.|++|.++++.| |.|. |+.+=. ..+-++.+.- -...+....+++.+.|
T Consensus 17 S~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~----~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~g 92 (315)
T PRK09492 17 GKSTVSRVLNNESGVSEETRERVEAVINQHGFSPSKSARAMRGQSD----KVVGIIVSRLDSLSENQAVRTMLPAFYEQG 92 (315)
T ss_pred CHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCC----CeEEEEecCCcCcccHHHHHHHHHHHHHcC
Confidence 356899999988889999999999999876 8885 333321 1233333321 2345566667777778
Q ss_pred hh
Q 019215 193 MQ 194 (344)
Q Consensus 193 mq 194 (344)
|+
T Consensus 93 y~ 94 (315)
T PRK09492 93 YD 94 (315)
T ss_pred Ce
Confidence 76
No 19
>TIGR03553 F420_FbiB_CTERM F420 biosynthesis protein FbiB, C-terminal domain. Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5-6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems likely that the C-terminal domain of FbiB, modeled by this alignment, is involved in additional glutamate ligation.
Probab=41.48 E-value=23 Score=30.07 Aligned_cols=42 Identities=26% Similarity=0.288 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhccCChhhHHHHHHHHHhccccCC--CCcceeeEEEE
Q 019215 123 RRRTVRRFLEDLGSVGEGQREMINDAIRHMYSPDL--KNGWGIHVVQE 168 (344)
Q Consensus 123 R~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY~PdL--k~GWGVhvVQe 168 (344)
.||++|+|... .++.|+.+.|=++-+. +|+= .-.|.+.|||.
T Consensus 5 ~RRSvR~f~~~--~V~~e~l~~il~aA~~--APS~~n~Qpw~fvvv~~ 48 (194)
T TIGR03553 5 LRRSVRRFSDD--PVDPDAVRAAVAAALT--APAPHHTRPVRFVWVED 48 (194)
T ss_pred hccccccCCCC--CCCHHHHHHHHHHHHh--CCCCCCCCCeEEEEEeC
Confidence 57899999743 5677777776666654 6664 45788888873
No 20
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=41.06 E-value=26 Score=32.94 Aligned_cols=34 Identities=26% Similarity=0.494 Sum_probs=28.4
Q ss_pred HHHHHHHHHhhcC---ccccCCCCCCcceEEEeccCc
Q 019215 62 QQRRHLERLHSKG---VLWKHPEDQSRSIVFKLSHGG 95 (344)
Q Consensus 62 qqr~~L~rl~~~G---V~wk~p~~~~~~~vf~L~hgg 95 (344)
.-|+||+.|+++| +.|+++..+-|...|+|.=-|
T Consensus 41 avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g 77 (218)
T COG2345 41 AVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKG 77 (218)
T ss_pred HHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccc
Confidence 4699999999999 568888778899999997443
No 21
>cd02062 Nitro_FMN_reductase Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase.
Probab=38.73 E-value=18 Score=27.69 Aligned_cols=42 Identities=38% Similarity=0.604 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhccCChhhHHHHHHHHHhccccCCC--CcceeeEEEE
Q 019215 123 RRRTVRRFLEDLGSVGEGQREMINDAIRHMYSPDLK--NGWGIHVVQE 168 (344)
Q Consensus 123 R~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY~PdLk--~GWGVhvVQe 168 (344)
.||++|+|... ..++++.+.|-++.+ ++|+-. ..|.+.++.+
T Consensus 3 ~RrS~R~f~~~--~i~~~~l~~l~~~~~--~aPs~~n~qp~~~~~v~~ 46 (122)
T cd02062 3 KRRSVRKFTDE--PVPEEVLEKILEAAR--YAPSGGNLQPWRFVVVYG 46 (122)
T ss_pred cceecccCCCC--CCCHHHHHHHHHHHH--hCCCcCCCCCEEEEEEeC
Confidence 47899999765 788888888888776 566654 6798888843
No 22
>PRK10824 glutaredoxin-4; Provisional
Probab=38.70 E-value=19 Score=30.44 Aligned_cols=18 Identities=56% Similarity=1.102 Sum_probs=14.6
Q ss_pred CCCCCCEEEEeeccc---ccC
Q 019215 301 DICEPPIFLFMKGTG---WCG 318 (344)
Q Consensus 301 ei~~~P~FLfMkgTg---Wcg 318 (344)
-|.+.|+.+|||||- ||+
T Consensus 11 ~I~~~~Vvvf~Kg~~~~p~Cp 31 (115)
T PRK10824 11 QIAENPILLYMKGSPKLPSCG 31 (115)
T ss_pred HHhcCCEEEEECCCCCCCCCc
Confidence 367899999999974 675
No 23
>TIGR00365 monothiol glutaredoxin, Grx4 family. The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation.
Probab=38.33 E-value=21 Score=28.30 Aligned_cols=18 Identities=56% Similarity=1.019 Sum_probs=14.8
Q ss_pred CCCCCCEEEEeecc---cccC
Q 019215 301 DICEPPIFLFMKGT---GWCG 318 (344)
Q Consensus 301 ei~~~P~FLfMkgT---gWcg 318 (344)
-|.+.|+.+||||| -||+
T Consensus 8 ~i~~~~Vvvf~kg~~~~~~Cp 28 (97)
T TIGR00365 8 QIKENPVVLYMKGTPQFPQCG 28 (97)
T ss_pred HhccCCEEEEEccCCCCCCCc
Confidence 36789999999998 6775
No 24
>cd04704 PLA2_bee_venom_like PLA2_bee_venom_like: A sub-family of Phospholipase A2, similar to bee venom PLA2. PLA2 is a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. Enzymatically active PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids; secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers. Bee venom PLA2 has fewer conserved disulfide bridges than most canonical PLA2s.
Probab=38.16 E-value=11 Score=31.06 Aligned_cols=18 Identities=50% Similarity=1.186 Sum_probs=13.3
Q ss_pred EeecccccCCC--CCCcccc
Q 019215 310 FMKGTGWCGAG--ADHYEPL 327 (344)
Q Consensus 310 fMkgTgWcgaG--aDHYEPl 327 (344)
.|-||=|||+| |..|+.|
T Consensus 2 ~~pGTkWCG~Gn~a~~~~dl 21 (97)
T cd04704 2 IVPGTKWCGPGNIATNYSDL 21 (97)
T ss_pred ccCCCeecCCCCCCCCcccc
Confidence 46799999998 4556544
No 25
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=37.24 E-value=44 Score=24.70 Aligned_cols=58 Identities=14% Similarity=0.260 Sum_probs=37.2
Q ss_pred HHHHHhhhhhhHHHHHHhhhcceecCCCcccchhhcccCC--CCCceeeEEeeeccceeeE
Q 019215 186 DELVQLGMQREMAAESIYKERCIPVSDGPSWAKYMLISGS--HDDEYDIITLQYTEDGLLS 244 (344)
Q Consensus 186 ~Elv~~Gmqre~AAEsIYkErc~~V~dg~SwakYMsisGS--~~de~diItLqYteeGLLs 244 (344)
-.-++.||+++.-...+=+=.-....+...|- |..-.-. ...+...+.|.|.++|+++
T Consensus 9 ~~~i~~GmTk~qV~~lLG~P~~~~~~~~~~W~-Y~~~~~~~~~~~~~~~l~V~Fd~~~~v~ 68 (71)
T PF04355_consen 9 LAQIKPGMTKDQVRALLGSPSLRDPFDPNRWY-YVYSKRRGNGANEQRQLKVYFDDDGVVK 68 (71)
T ss_dssp HTTT-TTSBHHHHHHHHTS-SEE-CTTSSEEE-EEEEETTCSSSSCEEEEEEEECTTSBEE
T ss_pred HHhhcCCCCHHHHHHhcCCCCccccccCCEEE-EEEEEecCCCccEEEEEEEEEcCCCEEE
Confidence 34467899998876655433333445666898 5443332 3566899999999999886
No 26
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=37.05 E-value=30 Score=34.35 Aligned_cols=34 Identities=29% Similarity=0.397 Sum_probs=22.8
Q ss_pred cCCCCCchhHHHHHHhccCCC-ChHHHHHHHHHHH
Q 019215 97 VSADGNCLFTASQKAMTARDV-DARELRRRTVRRF 130 (344)
Q Consensus 97 V~~dGnCLFtA~~~am~~~~~-~~relR~r~vrrF 130 (344)
|-+|..|||+|+.--|....- .+.|||+-.-+.-
T Consensus 115 vp~DNSCLF~ai~yv~~k~~~~~~~elR~iiA~~V 149 (307)
T KOG3288|consen 115 VPDDNSCLFTAIAYVIFKQVSNRPYELREIIAQEV 149 (307)
T ss_pred ccCCcchhhhhhhhhhcCccCCCcHHHHHHHHHHH
Confidence 677888999999888855222 2346776655443
No 27
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.58 E-value=24 Score=34.36 Aligned_cols=57 Identities=25% Similarity=0.444 Sum_probs=43.0
Q ss_pred cchhhhhhhhhhhcceEEEEEecCCcccccCCCeEEeecCCCCCCCCCCCEEEEeecccccCCCCCCcccccc
Q 019215 257 GDDIAIECLATEFNREIYVVQAHGSDAMVDEENCVFFLPHRPRSDICEPPIFLFMKGTGWCGAGADHYEPLIA 329 (344)
Q Consensus 257 GDDiaIE~LATefkReIyVVqahg~damvdeencvFFLPHrPR~ei~~~P~FLfMkgTgWcgaGaDHYEPlia 329 (344)
-|-|.|-+|+++-.=-|=|+=+--+++ + -+-|.|-.|...|-+.|+-| +| ||+||..
T Consensus 199 sdhi~I~ALs~Al~i~irVey~dr~~~-----~---~~~hH~fpe~s~P~I~LLYr-pG-------HYdilY~ 255 (256)
T KOG3991|consen 199 SDHIHITALSQALGIRIRVEYVDRGSG-----D---TVNHHDFPEASAPEIYLLYR-PG-------HYDILYK 255 (256)
T ss_pred cCceeHHHHHhhhCceEEEEEecCCCC-----C---CCCCCcCccccCceEEEEec-CC-------ccccccC
Confidence 367999999999998888886653322 2 34577777888888999987 45 9999864
No 28
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=34.71 E-value=46 Score=21.81 Aligned_cols=24 Identities=21% Similarity=0.547 Sum_probs=19.9
Q ss_pred HHHHHHHHHhhhhhhHHHHHHhhh
Q 019215 182 DSAIDELVQLGMQREMAAESIYKE 205 (344)
Q Consensus 182 daai~Elv~~Gmqre~AAEsIYkE 205 (344)
+.+|+.|++.|++++.+.++...-
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 568999999999998888877653
No 29
>cd01320 ADA Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in the purine pathway. Low, as well as high levels of ADA activity have been linked to several diseases.
Probab=34.33 E-value=1.6e+02 Score=27.09 Aligned_cols=43 Identities=12% Similarity=0.071 Sum_probs=31.9
Q ss_pred hhHHHHHHhccCCCChHHHHHHHHHHHHHHhccCChhhHHHHHHH
Q 019215 104 LFTASQKAMTARDVDARELRRRTVRRFLEDLGSVGEGQREMINDA 148 (344)
Q Consensus 104 LFtA~~~am~~~~~~~relR~r~vrrF~~~~~s~~~ee~e~Id~a 148 (344)
++.-++.+...-.+++.||++-+..-+..-|. +.++|+++.+.
T Consensus 282 ~~~e~~~~~~~~~l~~~el~~~~~na~~~~f~--~~~~k~~~~~~ 324 (325)
T cd01320 282 LTDEYELLAEAFGLTEEELKKLARNAVEASFL--SEEEKAELLKR 324 (325)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHhCC--CHHHHHHHHhh
Confidence 56666666654489999999988777766665 89999887654
No 30
>PRK12334 nucleoside triphosphate pyrophosphohydrolase; Reviewed
Probab=34.15 E-value=50 Score=32.15 Aligned_cols=59 Identities=24% Similarity=0.259 Sum_probs=46.3
Q ss_pred HHHHHHhhcCccccCCCCCCcceEEEeccCcccCCCCCchhHHHHHHhccCCCChHHHHHHHHHHHHHHhc
Q 019215 65 RHLERLHSKGVLWKHPEDQSRSIVFKLSHGGEVSADGNCLFTASQKAMTARDVDARELRRRTVRRFLEDLG 135 (344)
Q Consensus 65 ~~L~rl~~~GV~wk~p~~~~~~~vf~L~hggeV~~dGnCLFtA~~~am~~~~~~~relR~r~vrrF~~~~~ 135 (344)
+...|...-|..|..... + -.-..-|++||+-+..|-.. ++||+.-=++++++|...|.
T Consensus 203 ki~~ra~~~Gf~~~~~~~-----~------~~e~e~GdlLf~lv~~ar~~-~idpE~aLr~a~~kf~~rf~ 261 (277)
T PRK12334 203 KVLSRARKAGLPVPLAPA-----E------DSEDELGALLLALVAVAVAA-GVDAEAALRAAVRDFRDRIR 261 (277)
T ss_pred HHHHHHHhcCCCCCCccc-----h------hhHHHHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHHHH
Confidence 455667777999977542 1 11236799999999988877 99999999999999999997
No 31
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=33.85 E-value=54 Score=21.94 Aligned_cols=23 Identities=26% Similarity=0.596 Sum_probs=18.0
Q ss_pred HHHHHHHHHhhhhhhHHHHHHhh
Q 019215 182 DSAIDELVQLGMQREMAAESIYK 204 (344)
Q Consensus 182 daai~Elv~~Gmqre~AAEsIYk 204 (344)
+..|+.|++.|++++.|-+....
T Consensus 3 ~~~v~~L~~mGf~~~~~~~AL~~ 25 (37)
T PF00627_consen 3 EEKVQQLMEMGFSREQAREALRA 25 (37)
T ss_dssp HHHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 46899999999999988777643
No 32
>cd02151 NADPH_oxidoreductase_2 NAD(P)H:flavin oxidoreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=33.60 E-value=33 Score=28.35 Aligned_cols=43 Identities=23% Similarity=0.486 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhccCChhhHHHHHHHHHhccccCCC--CcceeeEEEE
Q 019215 122 LRRRTVRRFLEDLGSVGEGQREMINDAIRHMYSPDLK--NGWGIHVVQE 168 (344)
Q Consensus 122 lR~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY~PdLk--~GWGVhvVQe 168 (344)
..||++|+|.+ ..++.++.+.|-++.+ ++|+-. --|.+.||+.
T Consensus 6 ~~RrSvR~f~~--~~v~~e~l~~il~aa~--~aPs~~n~Qp~~f~vv~~ 50 (162)
T cd02151 6 KKRRSIRKFTD--EPVEKEKVDALLKAAL--RAPSSRNRRPWEFIVVTD 50 (162)
T ss_pred HhhchhhcCCC--CCCCHHHHHHHHHHHH--hCcCCCCCCCeEEEEECC
Confidence 35889999965 3677777777777765 788866 4688888874
No 33
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=33.43 E-value=45 Score=29.77 Aligned_cols=33 Identities=24% Similarity=0.385 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccC
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPD 156 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~Pd 156 (344)
+.||.|-+..-+.++++-|++|.++++.| |.|+
T Consensus 20 ~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~ 53 (342)
T PRK10014 20 VSTVSLVLSGKGRISTATGERVNQAIEELGFVRN 53 (342)
T ss_pred HHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence 56888889888889999999999999988 9995
No 34
>cd02135 Arsenite_oxidase Nitroreductase-like family which includes NADH oxidase and arsenite oxidiase. NADH oxidase catalyses the oxidation of NAD(P)H and accepts a wide broad range of compounds as electron acceptors, such as nitrocompound. Arsenite oxidase in a beta-proteobacterial strain is able to oxidize arsenite to arsenate.
Probab=33.31 E-value=32 Score=27.78 Aligned_cols=42 Identities=24% Similarity=0.400 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhccCChhhHHHHHHHHHhccccCCC--CcceeeEEEE
Q 019215 123 RRRTVRRFLEDLGSVGEGQREMINDAIRHMYSPDLK--NGWGIHVVQE 168 (344)
Q Consensus 123 R~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY~PdLk--~GWGVhvVQe 168 (344)
.||+||+|.+. .++.|+.+.|-++.+ ++|+-. -.|-+.||+.
T Consensus 6 ~RrSvR~f~~~--~v~~e~l~~il~aA~--~APs~~n~Qpw~f~vv~~ 49 (160)
T cd02135 6 TRRSIKKLTLP--APDREQLEQILEAAA--RAPDHGKLEPWRFIVIRG 49 (160)
T ss_pred hcccchhcCCC--CCCHHHHHHHHHHHH--hCCCcCCccCeEEEEEec
Confidence 47899999753 566666666655654 678865 4788888864
No 35
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=33.20 E-value=45 Score=29.72 Aligned_cols=67 Identities=18% Similarity=0.357 Sum_probs=44.8
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccCC-----CCcceeeEEEEEEeeeecc----chhhhHHHHHHHHHhhh
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPDL-----KNGWGIHVVQEVKLLAKKE----DRVGLDSAIDELVQLGM 193 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~PdL-----k~GWGVhvVQevKlLA~k~----dr~~Ldaai~Elv~~Gm 193 (344)
+-||.|.+.....++++.|++|.++++.| |.|.. +.|-- -.+-++.+.- -...++...+++.+.||
T Consensus 15 ~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~----~~Ig~i~~~~~~~~~~~~~~~i~~~~~~~gy 90 (311)
T TIGR02405 15 KSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPSKSARAMRGGSD----KVVAVIVSRLDSPSENLAVSGMLPVFYTAGY 90 (311)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCC----CEEEEEeCCcccccHHHHHHHHHHHHHHCCC
Confidence 56899999988889999999999999776 88863 33321 0133333321 12345566666777777
Q ss_pred h
Q 019215 194 Q 194 (344)
Q Consensus 194 q 194 (344)
+
T Consensus 91 ~ 91 (311)
T TIGR02405 91 D 91 (311)
T ss_pred e
Confidence 6
No 36
>KOG3325 consensus Membrane coat complex Retromer, subunit VPS29/PEP11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.82 E-value=82 Score=29.46 Aligned_cols=81 Identities=22% Similarity=0.397 Sum_probs=58.4
Q ss_pred eeeccceeeEeecCC----CCc-cccccchhhhhhhhhhhcceEEEEEecCCcccccCCCeEEeecCCCCCCCC------
Q 019215 235 LQYTEDGLLSVDENR----EGH-AAAFGDDIAIECLATEFNREIYVVQAHGSDAMVDEENCVFFLPHRPRSDIC------ 303 (344)
Q Consensus 235 LqYteeGLLsVDenr----eg~-aaAfGDDiaIE~LATefkReIyVVqahg~damvdeencvFFLPHrPR~ei~------ 303 (344)
+.|.+.+.++|-.=+ .|| -+.|||--+++.||.++.-+|.+-=--=.=.-.+-|||.|.=|-+-.|--.
T Consensus 67 ~~yP~~kvvtvGqfkIG~chGhqViP~gd~~sL~~LaRqldvDILl~G~Th~f~Aye~eg~ffvnPGSaTGAfn~~~t~~ 146 (183)
T KOG3325|consen 67 LKYPENKVVTVGQFKIGLCHGHQVIPWGDPESLALLARQLDVDILLTGHTHKFEAYEHEGKFFVNPGSATGAFNVSDTDI 146 (183)
T ss_pred ccCCccceEEeccEEEEeecCcEeecCCCHHHHHHHHHhcCCcEEEeCCceeEEEEEeCCcEEeCCCcccCCCcccccCC
Confidence 888888888876433 343 568999999999999999999764110011234459999999988777532
Q ss_pred CCCEEEEeeccc
Q 019215 304 EPPIFLFMKGTG 315 (344)
Q Consensus 304 ~~P~FLfMkgTg 315 (344)
-.|-|.+|-=.|
T Consensus 147 ~~PSFvLmDiqg 158 (183)
T KOG3325|consen 147 IVPSFVLMDIQG 158 (183)
T ss_pred CCCceEEEEecC
Confidence 379999996544
No 37
>PF09876 DUF2103: Predicted metal-binding protein (DUF2103); InterPro: IPR018664 This family of various putative metal binding prokaryotic proteins has no known function.
Probab=31.94 E-value=52 Score=28.07 Aligned_cols=26 Identities=35% Similarity=0.303 Sum_probs=23.3
Q ss_pred eEEEEEEeeeeccchhhhHHHHHHHH
Q 019215 164 HVVQEVKLLAKKEDRVGLDSAIDELV 189 (344)
Q Consensus 164 hvVQevKlLA~k~dr~~Ldaai~Elv 189 (344)
.-|||+.++-..++|+..+..+++|-
T Consensus 75 ~SvQEvfVVT~~~~~e~~~~i~~~Ln 100 (103)
T PF09876_consen 75 SSVQEVFVVTTLSDRELGERIIEELN 100 (103)
T ss_pred CeeEEEEEEeeCCcHHHHHHHHHHHH
Confidence 46999999999999999999998884
No 38
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=31.12 E-value=33 Score=26.47 Aligned_cols=18 Identities=61% Similarity=0.984 Sum_probs=14.0
Q ss_pred CCCCCCEEEEeecc---cccC
Q 019215 301 DICEPPIFLFMKGT---GWCG 318 (344)
Q Consensus 301 ei~~~P~FLfMkgT---gWcg 318 (344)
.|.+.|+.+||||| -||.
T Consensus 4 ~i~~~~vvvf~k~~~~~~~Cp 24 (90)
T cd03028 4 LIKENPVVLFMKGTPEEPRCG 24 (90)
T ss_pred hhccCCEEEEEcCCCCCCCCc
Confidence 46788999999986 3564
No 39
>cd02136 Nitroreductase Nitroreductase family. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source of reducing equivalents in an obligatory two-election transfer mechanism. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=31.06 E-value=38 Score=28.07 Aligned_cols=43 Identities=33% Similarity=0.400 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhccCChhhHHHHHHHHHhccccCCC--CcceeeEEEE
Q 019215 122 LRRRTVRRFLEDLGSVGEGQREMINDAIRHMYSPDLK--NGWGIHVVQE 168 (344)
Q Consensus 122 lR~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY~PdLk--~GWGVhvVQe 168 (344)
..||+||+|.+. .++.++.+.|-++.+ ++|+-. -.|-+.+|+.
T Consensus 6 ~~RrSvR~f~~~--~v~~e~l~~il~~a~--~aPs~~n~q~~~f~vv~~ 50 (178)
T cd02136 6 KSRHSVRAFLPD--PVPRETIEEILAAAQ--RAPSGCNTQPWQVYVVTG 50 (178)
T ss_pred hhchhhhcCCCC--CCCHHHHHHHHHHHH--hCccccCCCCEEEEEECc
Confidence 368999999974 788888888888876 456654 5677766643
No 40
>KOG3131 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.36 E-value=26 Score=34.46 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=11.5
Q ss_pred CCeEEeecCCCCCC
Q 019215 288 ENCVFFLPHRPRSD 301 (344)
Q Consensus 288 encvFFLPHrPR~e 301 (344)
..-+|||||||-.=
T Consensus 155 kpTLyylPHcp~~L 168 (281)
T KOG3131|consen 155 KPTLYYLPHCPYAL 168 (281)
T ss_pred ceeeEecCCCchHH
Confidence 56799999999753
No 41
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=29.27 E-value=50 Score=31.08 Aligned_cols=67 Identities=25% Similarity=0.337 Sum_probs=45.5
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccC-----CCCcceeeEEEEEEeeee----ccchhhhHHHHHHHHHhhh
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPD-----LKNGWGIHVVQEVKLLAK----KEDRVGLDSAIDELVQLGM 193 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~Pd-----Lk~GWGVhvVQevKlLA~----k~dr~~Ldaai~Elv~~Gm 193 (344)
.-||-|.+..-..+|+|-|++|.++|+.| |-|+ |+.| --+-+-++.+ .---..+...-+++.+.|+
T Consensus 14 ~sTVSrvln~~~~Vs~eTr~kV~~a~~elgY~pN~~Ar~L~~~----~s~~Ig~i~p~~~~~~~~~i~~gi~~~~~~~gy 89 (333)
T COG1609 14 KATVSRVLNGSPYVSEETREKVLAAIKELGYRPNAVARSLRTG----RTKTIGLVVPDITNPFFAEILKGIEEAAREAGY 89 (333)
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHhC----CCCEEEEEeCCCCCchHHHHHHHHHHHHHHcCC
Confidence 46899999999999999999999999976 7776 4444 2233445444 2223344444455666666
Q ss_pred h
Q 019215 194 Q 194 (344)
Q Consensus 194 q 194 (344)
+
T Consensus 90 ~ 90 (333)
T COG1609 90 S 90 (333)
T ss_pred E
Confidence 4
No 42
>PF08856 DUF1826: Protein of unknown function (DUF1826); InterPro: IPR014955 These proteins are functionally uncharacterised.
Probab=29.17 E-value=39 Score=30.82 Aligned_cols=26 Identities=23% Similarity=0.345 Sum_probs=19.3
Q ss_pred EEEEeecccccCCCCCCccccccccccccc
Q 019215 307 IFLFMKGTGWCGAGADHYEPLIANACSVIS 336 (344)
Q Consensus 307 ~FLfMkgTgWcgaGaDHYEPlia~~~~~vs 336 (344)
-+.||||++|-|. -.+=|-|+||.++
T Consensus 159 ~vallKG~~w~g~----~~~glvHRSP~~~ 184 (196)
T PF08856_consen 159 DVALLKGERWPGN----EGAGLVHRSPPIS 184 (196)
T ss_pred CEEEEccCCCCCC----CCCceeeCCCCCC
Confidence 4789999999873 3345667777777
No 43
>cd02140 Nitroreductase_4 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=28.95 E-value=30 Score=29.67 Aligned_cols=43 Identities=14% Similarity=0.112 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHhccCChhhHHHHHHHHH-h-ccccCCCC--cceeeEEEEE
Q 019215 123 RRRTVRRFLEDLGSVGEGQREMINDAIR-H-MYSPDLKN--GWGIHVVQEV 169 (344)
Q Consensus 123 R~r~vrrF~~~~~s~~~ee~e~Id~aIr-h-lY~PdLk~--GWGVhvVQev 169 (344)
.||.||+|... .+..+|.|++.|. - +++|+=+| -|-+.||+.-
T Consensus 7 ~RRSiR~f~~~----~~V~~e~l~~ileaA~~~APS~~N~QPW~f~Vv~~~ 53 (192)
T cd02140 7 ARRSIYALGKN----LPVSDDEIEEIVKEAVKHSPSSFNSQSSRAVILFGE 53 (192)
T ss_pred hCeehhccCCC----CCCCHHHHHHHHHHHHHhCCCCCCCCCeEEEEEECh
Confidence 46788887521 3577888888887 5 69999765 6888888754
No 44
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=28.70 E-value=51 Score=29.71 Aligned_cols=34 Identities=24% Similarity=0.443 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccCC
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPDL 157 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~PdL 157 (344)
.-||-|.+..-+.++++-|++|.++++.| |.|..
T Consensus 15 ~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn~ 49 (343)
T PRK10727 15 VATVSRVINNSPKASEASRLAVHSAMESLSYHPNA 49 (343)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence 56899999888889999999999999887 88865
No 45
>PF13137 DUF3983: Protein of unknown function (DUF3983)
Probab=28.35 E-value=1e+02 Score=22.20 Aligned_cols=27 Identities=15% Similarity=0.409 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHhccCChhhHHHHHHHHHhcc
Q 019215 120 RELRRRTVRRFLEDLGSVGEGQREMINDAIRHMY 153 (344)
Q Consensus 120 relR~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY 153 (344)
+.+|..+.||+-+. |++.+++|-||+|
T Consensus 3 kkikKai~rR~k~v-------eK~rv~kAWRNiF 29 (34)
T PF13137_consen 3 KKIKKAIARRAKAV-------EKYRVDKAWRNIF 29 (34)
T ss_pred hHHHHHHHHHHHHH-------HHHHHHHHHHHHH
Confidence 45777888887665 8999999999987
No 46
>PF09179 TilS: TilS substrate binding domain; InterPro: IPR015262 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the substrate-binding domain of lysidine-tRNA(Ile) synthetase, which ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a PP-loop motif involved in ATP binding. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) versus AUG (Met) and UGA (stop) versus UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This domain is found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain architecture of this protein is variable; some, including characterised proteins of Escherichia coli and Bacillus subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family. It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer). The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, E. coli NtrL, and B. subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain. The HUP domain class (after HIGH-signature proteins, UspA, and PP-ATPase) groups together PP-loop ATPases, the nucleotide-binding domains of class I aminoacyl-tRNA synthetases, UspA protein (USPA domains), photolyases, and electron transport flavoproteins (ETFP). The HUP domain is a distinct class of alpha/beta domain[]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016879 ligase activity, forming carbon-nitrogen bonds, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 1NI5_A 3A2K_A.
Probab=28.26 E-value=1.1e+02 Score=21.95 Aligned_cols=48 Identities=23% Similarity=0.401 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHHhccCChhhHHHHHHHHHhcc------ccCCCC-cceeeEEE
Q 019215 119 ARELRRRTVRRFLEDLGSVGEGQREMINDAIRHMY------SPDLKN-GWGIHVVQ 167 (344)
Q Consensus 119 ~relR~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY------~PdLk~-GWGVhvVQ 167 (344)
+..+|++.+|+|++..+. ..-....+++.++.+- .|+|.. |+-|...|
T Consensus 10 ~~~~q~~lLR~wL~~~g~-~~ps~~~l~~i~~~l~~~~~~~~~~l~~~~~~vrr~~ 64 (69)
T PF09179_consen 10 PPARQRRLLRRWLRQLGL-PMPSQAHLEQILRQLIQAKPDAQPQLPWAGGEVRRYR 64 (69)
T ss_dssp -HHHHHHHHHHHHHHTT--T--HHHHHHHHHHHCCTS-CCCEEEECCTTEEEEECT
T ss_pred CHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHHhhhCCCCceEEEeCCEEEEEEC
Confidence 457899999999999975 6666777777777665 456664 66555443
No 47
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=27.37 E-value=2.8e+02 Score=22.31 Aligned_cols=19 Identities=32% Similarity=0.412 Sum_probs=15.4
Q ss_pred HHHHHHHHHHhhcCccccC
Q 019215 61 EQQRRHLERLHSKGVLWKH 79 (344)
Q Consensus 61 ~qqr~~L~rl~~~GV~wk~ 79 (344)
.--+..|.||.+||+.-..
T Consensus 36 sTv~t~L~rL~~Kg~l~~~ 54 (115)
T PF03965_consen 36 STVQTLLNRLVEKGFLTRE 54 (115)
T ss_dssp HHHHHHHHHHHHTTSEEEE
T ss_pred hHHHHHHHHHHhCCceeEe
Confidence 3457899999999998765
No 48
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=26.59 E-value=61 Score=28.65 Aligned_cols=34 Identities=24% Similarity=0.380 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccCC
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPDL 157 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~PdL 157 (344)
.-||.|-+.....++++-|++|.++++.| |.|..
T Consensus 12 ~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~ 46 (327)
T PRK10423 12 TSTVSHVINKDRFVSEAITAKVEAAIKELNYAPSA 46 (327)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCccH
Confidence 46899999888889999999999999877 88864
No 49
>COG3681 L-cysteine desulfidase [Amino acid transport and metabolism]
Probab=26.49 E-value=77 Score=32.73 Aligned_cols=69 Identities=22% Similarity=0.385 Sum_probs=53.1
Q ss_pred cCCCCCchhHHHHHHhccCCCChHHHH-HHHHHHHHHHhccCChhhHHHHHHHHH---hccccCCCCcceeeEEE
Q 019215 97 VSADGNCLFTASQKAMTARDVDARELR-RRTVRRFLEDLGSVGEGQREMINDAIR---HMYSPDLKNGWGIHVVQ 167 (344)
Q Consensus 97 V~~dGnCLFtA~~~am~~~~~~~relR-~r~vrrF~~~~~s~~~ee~e~Id~aIr---hlY~PdLk~GWGVhvVQ 167 (344)
++-++.-|||- ++-+.++.+|-..| +-+++.|++.-+....+--.-|-+.|| ++--|-|++-||+|.+-
T Consensus 155 i~~~~kvl~tq--~~n~g~~~s~l~~~k~ltlk~i~d~v~~ip~d~Ik~I~~~ir~N~als~egl~gk~g~~ig~ 227 (433)
T COG3681 155 IETHDKVLFTQ--QANEGEQESPLTVLKRLTLKEILDFVNEIPFDAIKFILDSIRLNCALSQEGLSGKWGLHIGA 227 (433)
T ss_pred EecCCceeeeh--hhccccccCcchhhhhccHHHHHHHHHhCCHHHHHHHHHHHHhcccccCccccCccccccch
Confidence 45566677763 44477777776555 557889999888888888888888887 57789999999999764
No 50
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=25.76 E-value=72 Score=28.79 Aligned_cols=35 Identities=29% Similarity=0.465 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhccCChhhHHHHHHHHHhc-cccCC
Q 019215 123 RRRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPDL 157 (344)
Q Consensus 123 R~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~PdL 157 (344)
-.-||.|-+.....++++-|++|-++++.| |.|..
T Consensus 14 S~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn~ 49 (346)
T PRK10401 14 SVATVSRVLNNSALVSADTREAVMKAVSELGYRPNA 49 (346)
T ss_pred CHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence 356899999888889999999999999776 88864
No 51
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=25.66 E-value=1.4e+02 Score=27.05 Aligned_cols=87 Identities=16% Similarity=0.165 Sum_probs=50.9
Q ss_pred eccchH-HHHHHHHHHhhcCccccCCC-CCCcceEEEeccCcccCCCCCchhHHHHHHhccCCCChHHHHHHHHHHHHH-
Q 019215 56 VIGLEE-QQRRHLERLHSKGVLWKHPE-DQSRSIVFKLSHGGEVSADGNCLFTASQKAMTARDVDARELRRRTVRRFLE- 132 (344)
Q Consensus 56 V~gld~-qqr~~L~rl~~~GV~wk~p~-~~~~~~vf~L~hggeV~~dGnCLFtA~~~am~~~~~~~relR~r~vrrF~~- 132 (344)
..+++. .--+.|.+|+++|..-.-++ +..+...-+|.=-|. =++.-+. ....++...+.+.|.+
T Consensus 68 ~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~------~l~~~l~-------~~~~~~e~~~~~~~s~~ 134 (185)
T PRK13777 68 FGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGE------ELLLETM-------EEYDPENNSVFNGALPL 134 (185)
T ss_pred HHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHH------HHHHHHH-------HHHHHHHHHHHhcccHH
Confidence 344553 33467999999999887655 233555555543332 1111111 1223344444444422
Q ss_pred --HhccCChhhHHHHHHHHHhccccCC
Q 019215 133 --DLGSVGEGQREMINDAIRHMYSPDL 157 (344)
Q Consensus 133 --~~~s~~~ee~e~Id~aIrhlY~PdL 157 (344)
.|+ ..+|.+.+-..|+|+|.+|.
T Consensus 135 ~~l~~--~~~e~~~l~~ll~~iy~~~~ 159 (185)
T PRK13777 135 RELYG--KFPEFIELMAIVRNIYGDDF 159 (185)
T ss_pred HHHhh--hhHHHHHHHHHHHHHhCcHH
Confidence 444 55999999999999999984
No 52
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=24.78 E-value=1.9e+02 Score=21.54 Aligned_cols=58 Identities=22% Similarity=0.317 Sum_probs=34.5
Q ss_pred HHHHHHHhhcCccccCCCCC-CcceEEEe-ccCcccCCCCCchhHHHHHHhccCCCChHHH
Q 019215 64 RRHLERLHSKGVLWKHPEDQ-SRSIVFKL-SHGGEVSADGNCLFTASQKAMTARDVDAREL 122 (344)
Q Consensus 64 r~~L~rl~~~GV~wk~p~~~-~~~~vf~L-~hggeV~~dGnCLFtA~~~am~~~~~~~rel 122 (344)
-+.|.+|+++|....-++.. .+.+.++| .-|.++...-.+.+......+-. .++..|+
T Consensus 54 t~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~~~~~~~~~~~~-~l~~~e~ 113 (126)
T COG1846 54 TRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLPAAQELLAEILA-GLSEEEL 113 (126)
T ss_pred HHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhccHHHHHHHHhcc-CCCHHHH
Confidence 36899999999988877733 34555554 34445554444544444444422 5555555
No 53
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=24.31 E-value=71 Score=28.36 Aligned_cols=34 Identities=24% Similarity=0.426 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhc-cccCC
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPDL 157 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~PdL 157 (344)
.-||-|.+.+-..++++-|++|.++++.| |.|+.
T Consensus 15 ~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~ 49 (329)
T TIGR01481 15 MATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPNA 49 (329)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence 46899999998899999999999999887 88854
No 54
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=24.14 E-value=74 Score=30.21 Aligned_cols=36 Identities=19% Similarity=0.244 Sum_probs=33.0
Q ss_pred CCCCchhHHHHHHhccCCCChHHHHHHHHHHHHHHhc
Q 019215 99 ADGNCLFTASQKAMTARDVDARELRRRTVRRFLEDLG 135 (344)
Q Consensus 99 ~dGnCLFtA~~~am~~~~~~~relR~r~vrrF~~~~~ 135 (344)
.-|+.||+-+..|-.. ++||++-=+++.++|...|.
T Consensus 184 ElGDlLFalvnlAr~~-giDpE~ALr~a~~KF~~Rf~ 219 (248)
T TIGR00444 184 EMGDLLFATVNLARHL-KTDAEIALQKANEKFERRFR 219 (248)
T ss_pred HHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHHHH
Confidence 5799999999998877 99999999999999999987
No 55
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=23.29 E-value=77 Score=28.36 Aligned_cols=35 Identities=29% Similarity=0.429 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhccCChhhHHHHHHHHHhc-cccCC
Q 019215 123 RRRTVRRFLEDLGSVGEGQREMINDAIRHM-YSPDL 157 (344)
Q Consensus 123 R~r~vrrF~~~~~s~~~ee~e~Id~aIrhl-Y~PdL 157 (344)
-+-||.|.+..-..+|++-|++|.++++-| |.|..
T Consensus 14 S~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~pn~ 49 (341)
T PRK10703 14 STTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSA 49 (341)
T ss_pred CHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence 457899999988889999999999999877 88853
No 56
>PRK12333 nucleoside triphosphate pyrophosphohydrolase; Reviewed
Probab=21.91 E-value=84 Score=29.57 Aligned_cols=36 Identities=14% Similarity=0.136 Sum_probs=32.3
Q ss_pred CCCCchhHHHHHHhccCCCChHHHHHHHHHHHHHHhc
Q 019215 99 ADGNCLFTASQKAMTARDVDARELRRRTVRRFLEDLG 135 (344)
Q Consensus 99 ~dGnCLFtA~~~am~~~~~~~relR~r~vrrF~~~~~ 135 (344)
.-|+.||+-+..|-.. ++||++-=+++.++|.+...
T Consensus 165 E~GDlLFalvn~aR~~-~idpE~ALr~an~Kf~~~~~ 200 (204)
T PRK12333 165 GVAEALWAVVAWARAE-GIDPEIALRERTEKACAQLP 200 (204)
T ss_pred cHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHhCc
Confidence 6899999999988877 99999999999999998765
No 57
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=21.86 E-value=1.9e+02 Score=24.10 Aligned_cols=51 Identities=27% Similarity=0.439 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhccCChhhHHHHHHHHHhccccCCCCcceeeEEEEEEeeeeccchhhhHHHHHHHHHhhh
Q 019215 124 RRTVRRFLEDLGSVGEGQREMINDAIRHMYSPDLKNGWGIHVVQEVKLLAKKEDRVGLDSAIDELVQLGM 193 (344)
Q Consensus 124 ~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY~PdLk~GWGVhvVQevKlLA~k~dr~~Ldaai~Elv~~Gm 193 (344)
++=|++|++.++..... .|| .|++|.-.|.|. -.+.+.|+..+++|-..|+
T Consensus 46 r~Dv~~Fi~~l~~~~~~----------~Ls--~LT~GvH~HtI~-------a~~~e~l~~I~~~L~~~G~ 96 (98)
T PF02829_consen 46 RRDVDKFIEKLEKSKAK----------PLS--SLTGGVHYHTIE-------APDEEDLDKIEEALKKKGF 96 (98)
T ss_dssp HHHHHHHHHHHHH--S------------ST--TGGGGEEEEEEE-------ESSHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHhccCCc----------chH--HhcCCEeeEEEE-------ECCHHHHHHHHHHHHHCCC
Confidence 45578999988843221 455 588998888764 3578899999999999986
No 58
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=21.25 E-value=2e+02 Score=25.19 Aligned_cols=55 Identities=16% Similarity=0.200 Sum_probs=34.5
Q ss_pred cCChhhHHHHHHHHHhc-cccC-----CCCcceeeEEEEEEeeeecc----chhhhHHHHHHHHHhhhh
Q 019215 136 SVGEGQREMINDAIRHM-YSPD-----LKNGWGIHVVQEVKLLAKKE----DRVGLDSAIDELVQLGMQ 194 (344)
Q Consensus 136 s~~~ee~e~Id~aIrhl-Y~Pd-----Lk~GWGVhvVQevKlLA~k~----dr~~Ldaai~Elv~~Gmq 194 (344)
.++++-||+|.++|+.| |.|+ |++|..- .+=++.+.. -...+....+++.+.|++
T Consensus 3 ~Vs~~Tr~rV~~~a~elgY~pn~~a~~l~~~~~~----~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~ 67 (309)
T PRK11041 3 KVSQATRQRVEQAVLEVGYSPQSLGRNLKRNESR----TILVIVPDICDPFFSEIIRGIEVTAAEHGYL 67 (309)
T ss_pred cCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCc----EEEEEeCCCcCccHHHHHHHHHHHHHHCCCE
Confidence 57899999999999766 8774 6666542 233444432 233444555556666764
No 59
>PRK06474 hypothetical protein; Provisional
Probab=20.70 E-value=5.8e+02 Score=22.63 Aligned_cols=108 Identities=13% Similarity=0.140 Sum_probs=57.1
Q ss_pred HHHHHHHHHhhcCccccCCCC---CCcceEEEeccCcccCCCCCchhHHHHHHhccCCCChHHHHHHHHHHHHHHhccCC
Q 019215 62 QQRRHLERLHSKGVLWKHPED---QSRSIVFKLSHGGEVSADGNCLFTASQKAMTARDVDARELRRRTVRRFLEDLGSVG 138 (344)
Q Consensus 62 qqr~~L~rl~~~GV~wk~p~~---~~~~~vf~L~hggeV~~dGnCLFtA~~~am~~~~~~~relR~r~vrrF~~~~~s~~ 138 (344)
.--|||+.|.+.|+.-.-+.. +..-..|++...+=-... .=++ ..++.+.++ .+.-|...|.
T Consensus 43 TvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~~~~-~~~~----------~~~~e~~~~-~~~~~~~~~~--- 107 (178)
T PRK06474 43 TLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAKIEG-SEWT----------GLSDDEKLN-YISYYQLSLL--- 107 (178)
T ss_pred HHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceeeeCH-HHHH----------HhCHHHHHH-HHHHHHHHHH---
Confidence 356899999999999876542 235578888765422211 0011 122322222 2222221111
Q ss_pred hhhHHHHHHHHHhc-cccCCCCcceeeEEEEEEeeeeccchhhhHHHHHHHHHh
Q 019215 139 EGQREMINDAIRHM-YSPDLKNGWGIHVVQEVKLLAKKEDRVGLDSAIDELVQL 191 (344)
Q Consensus 139 ~ee~e~Id~aIrhl-Y~PdLk~GWGVhvVQevKlLA~k~dr~~Ldaai~Elv~~ 191 (344)
+..++.++.+ -.+..+.|.| ++...|-...++...|...+.+|++.
T Consensus 108 ----~~~~~yl~~~~~~~~~~d~~~---~s~~~L~Lt~ee~~el~~el~~ll~~ 154 (178)
T PRK06474 108 ----QQYQSYLKSLEEQNSKEDKAT---FSVVELKLDEEEFEEFQSELNELMIK 154 (178)
T ss_pred ----HHHHHHHHhCcccchhccccc---eeeeeEecCHHHHHHHHHHHHHHHHH
Confidence 1112222221 0022334444 44667778888889999999998875
No 60
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=20.57 E-value=1.3e+02 Score=21.42 Aligned_cols=24 Identities=25% Similarity=0.555 Sum_probs=18.6
Q ss_pred hhHHHHHHHHHhhhhhhHHHHHHh
Q 019215 180 GLDSAIDELVQLGMQREMAAESIY 203 (344)
Q Consensus 180 ~Ldaai~Elv~~Gmqre~AAEsIY 203 (344)
.++.+++-|+.+||++.+|...|=
T Consensus 2 ~~~d~~~AL~~LGy~~~e~~~av~ 25 (47)
T PF07499_consen 2 ALEDALEALISLGYSKAEAQKAVS 25 (47)
T ss_dssp HHHHHHHHHHHTTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHH
Confidence 467889999999999998876553
No 61
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=20.14 E-value=65 Score=25.41 Aligned_cols=19 Identities=5% Similarity=0.258 Sum_probs=16.4
Q ss_pred HHHHHhccCChhhHHHHHH
Q 019215 129 RFLEDLGSVGEGQREMIND 147 (344)
Q Consensus 129 rF~~~~~s~~~ee~e~Id~ 147 (344)
.+.+-||.+|.|||+..|.
T Consensus 21 ~LIaGyntms~eEk~~~D~ 39 (97)
T PF12650_consen 21 FLIAGYNTMSKEEKEKYDK 39 (97)
T ss_pred cchhhcccCCHHHHHHhhH
Confidence 4578899999999999885
No 62
>cd02150 NADPH_oxidoreductase_1 NAD(P)H:flavin oxidoreductase-like family 1. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=20.09 E-value=90 Score=25.91 Aligned_cols=41 Identities=32% Similarity=0.485 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHhccCChhhHHHHHHHHHhccccCCCC--cceeeEEE
Q 019215 123 RRRTVRRFLEDLGSVGEGQREMINDAIRHMYSPDLKN--GWGIHVVQ 167 (344)
Q Consensus 123 R~r~vrrF~~~~~s~~~ee~e~Id~aIrhlY~PdLk~--GWGVhvVQ 167 (344)
.||++|.|.+ ...+.|+.+.|-++.+ ++|+=.+ .|.+.+|+
T Consensus 6 ~RrS~R~f~~--~~i~~e~l~~il~~a~--~aPs~~n~qp~~~~vv~ 48 (166)
T cd02150 6 TRRSVRKYTD--EPVSDELIEKILRAAM--AAPSAGNQQPWRFVVVR 48 (166)
T ss_pred hcchhhcCCC--CCCCHHHHHHHHHHHh--hCCCCCCCCCeEEEEEe
Confidence 4788999965 3678888888777775 5787654 78888884
Done!