Query 032766
Match_columns 134
No_of_seqs 118 out of 840
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 05:41:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032766.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032766hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2606 OTU (ovarian tumor)-li 99.9 2.5E-22 5.5E-27 161.1 4.1 91 1-93 195-299 (302)
2 KOG3288 OTU-like cysteine prot 99.8 1.9E-21 4E-26 153.8 4.8 125 1-129 144-276 (307)
3 PF02338 OTU: OTU-like cystein 99.6 1.5E-15 3.2E-20 106.8 3.7 77 2-86 33-121 (121)
4 KOG3991 Uncharacterized conser 99.5 4.7E-14 1E-18 110.4 5.8 90 2-92 163-256 (256)
5 PF10275 Peptidase_C65: Peptid 99.4 2.2E-13 4.8E-18 107.3 7.4 90 1-91 145-244 (244)
6 COG5539 Predicted cysteine pro 99.1 7E-12 1.5E-16 101.0 -0.5 125 1-129 143-275 (306)
7 KOG2605 OTU (ovarian tumor)-li 98.6 1.3E-08 2.9E-13 85.1 2.7 90 1-92 251-344 (371)
8 COG5539 Predicted cysteine pro 98.4 1.1E-07 2.3E-12 77.0 2.7 83 4-89 212-304 (306)
9 KOG2605 OTU (ovarian tumor)-li 81.8 0.48 1E-05 40.1 0.2 46 13-60 2-47 (371)
10 TIGR02934 nifT_nitrog probable 81.1 0.12 2.7E-06 33.5 -2.8 35 6-41 5-40 (67)
11 PF06988 NifT: NifT/FixU prote 71.9 0.05 1.1E-06 35.0 -6.4 35 6-41 5-40 (64)
12 PF05415 Peptidase_C36: Beet n 71.1 7.3 0.00016 26.9 3.6 47 22-71 35-83 (104)
13 PRK10963 hypothetical protein; 61.7 5.6 0.00012 31.0 1.9 35 2-43 8-42 (223)
14 PF04340 DUF484: Protein of un 48.7 8.2 0.00018 29.8 0.8 34 2-42 11-44 (225)
15 PF05381 Peptidase_C21: Tymovi 41.5 1.2E+02 0.0025 21.3 5.7 45 41-88 48-94 (104)
16 COG3159 Uncharacterized protei 39.0 14 0.0003 29.2 0.7 15 2-16 9-23 (218)
17 KOG4015 Fatty acid-binding pro 38.9 1.1E+02 0.0024 22.3 5.4 39 21-66 15-53 (133)
18 KOG3325 Membrane coat complex 30.0 60 0.0013 24.7 2.9 23 35-57 92-114 (183)
19 COG3426 Butyrate kinase [Energ 28.3 44 0.00095 28.0 2.0 27 22-48 315-341 (358)
20 COG5562 Phage envelope protein 27.4 40 0.00086 24.8 1.5 18 19-36 87-104 (137)
21 PF05952 ComX: Bacillus compet 26.9 17 0.00037 22.8 -0.4 19 2-20 5-23 (57)
22 PF01381 HTH_3: Helix-turn-hel 26.1 66 0.0014 18.5 2.1 29 25-53 24-52 (55)
23 KOG4100 Uncharacterized conser 24.2 18 0.00039 26.0 -0.8 29 9-40 49-81 (125)
24 COG0773 MurC UDP-N-acetylmuram 23.6 1.1E+02 0.0024 26.8 3.8 82 9-90 187-273 (459)
25 PF10588 NADH-G_4Fe-4S_3: NADH 23.5 43 0.00093 19.2 0.9 17 37-53 22-38 (41)
26 COG4479 Uncharacterized protei 22.0 37 0.00081 22.3 0.5 30 2-31 44-73 (74)
27 PF00941 FAD_binding_5: FAD bi 21.7 54 0.0012 24.2 1.3 32 29-60 101-139 (171)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=2.5e-22 Score=161.09 Aligned_cols=91 Identities=31% Similarity=0.552 Sum_probs=78.7
Q ss_pred ChHHHHHhCccccccccCCC--------CCHHHHHHhhcCCCccCCHHHHHHHHhhcCccEEEEEcCCCceEEeecccCC
Q 032766 1 MVVQYIVKNRETFEPFIEDD--------VPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHE 72 (134)
Q Consensus 1 ~vv~ym~~n~d~f~~Fi~~~--------~~~~~Y~~~m~~~g~WGg~iEL~Als~~~~v~I~V~~~~~~~~~i~~~~~~~ 72 (134)
++|+|||+|.++|.||+.+. ++|++||+.|++++.|||+|||.|||.+|++||.||+.++|+..+++ +..
T Consensus 195 ~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~~p~~~~ge--ey~ 272 (302)
T KOG2606|consen 195 ETADYMREHVEDFLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQADGPILEYGE--EYG 272 (302)
T ss_pred HHHHHHHHHHHHhhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecCCCceeech--hhC
Confidence 47999999999999998753 35999999999999999999999999999999999999988777652 112
Q ss_pred -CcEEEEEEcC-----CCccceeecCC
Q 032766 73 -ARMIHLSYHD-----GEHYNGVRLKE 93 (134)
Q Consensus 73 -~~~i~L~y~~-----g~HYdsv~~~~ 93 (134)
.++|.|+||. |+||||+.+..
T Consensus 273 kd~pL~lvY~rH~y~LGeHYNS~~~~~ 299 (302)
T KOG2606|consen 273 KDKPLILVYHRHAYGLGEHYNSVTPLK 299 (302)
T ss_pred CCCCeeeehHHhHHHHHhhhccccccc
Confidence 3789999984 99999998753
No 2
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.84 E-value=1.9e-21 Score=153.84 Aligned_cols=125 Identities=24% Similarity=0.351 Sum_probs=102.8
Q ss_pred ChHHHHHhCccccccccCCCCCHHHHHHhhcCCCccCCHHHHHHHHhhcCccEEEEEcCCCceEEeecccC--CCcEEEE
Q 032766 1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYH--EARMIHL 78 (134)
Q Consensus 1 ~vv~ym~~n~d~f~~Fi~~~~~~~~Y~~~m~~~g~WGg~iEL~Als~~~~v~I~V~~~~~~~~~i~~~~~~--~~~~i~L 78 (134)
|+|+...+||+.|..-|.| .+-.+||.||+++.+|||.|||..||..|++.|+|++.+. .+|..|++. ....+.|
T Consensus 144 iiA~~Vasnp~~yn~AiLg-K~n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiqt--~rid~fged~~~~~rv~l 220 (307)
T KOG3288|consen 144 IIAQEVASNPDKYNDAILG-KPNKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQT--VRIDRFGEDKNFDNRVLL 220 (307)
T ss_pred HHHHHHhcChhhhhHHHhC-CCcHHHHHHHccccccCceEEeeeehhhhceeEEEEecce--eeehhcCCCCCCCceEEE
Confidence 5788899999999999998 7999999999999999999999999999999999999876 567777654 3567888
Q ss_pred EEcCCCccceeecCCCCCCCCCcce------EeehhhhHHhhhhhhhccccccchhh
Q 032766 79 SYHDGEHYNGVRLKEDSCIGSARPI------IIKVFIITLFSFRDRLFYYYNFVNFF 129 (134)
Q Consensus 79 ~y~~g~HYdsv~~~~~~~~~p~~~~------~~~~~~~~l~~~~~~~~~~~~~~~f~ 129 (134)
.| +|.|||++....-.++.+..++ .+......|.+.+++.+|||||.+|-
T Consensus 221 ly-dGIHYD~l~m~~~~~~~~~~tifp~~dd~v~~~alqLa~~~k~~r~ytdt~~ft 276 (307)
T KOG3288|consen 221 LY-DGIHYDPLAMNEFKPTDVDNTIFPVSDDTVLTQALQLASELKRTRYYTDTAKFT 276 (307)
T ss_pred Ee-cccccChhhhccCCccCCcccccccccchHHHHHHHHHHHHHhcceeccccceE
Confidence 88 8999999986553333333333 23344678888899999999999983
No 3
>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=99.57 E-value=1.5e-15 Score=106.75 Aligned_cols=77 Identities=39% Similarity=0.652 Sum_probs=64.1
Q ss_pred hHHHHH-hCccccccccCCCCCHHHHHHhhcCCCccCCHHHHHHHHhhcCccEEEEEcCCCce--EEeec----ccCCCc
Q 032766 2 VVQYIV-KNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRW--YIRNF----DYHEAR 74 (134)
Q Consensus 2 vv~ym~-~n~d~f~~Fi~~~~~~~~Y~~~m~~~g~WGg~iEL~Als~~~~v~I~V~~~~~~~~--~i~~~----~~~~~~ 74 (134)
||+||+ +|++.|++|++++ +|+++|+|||++||+|+|.+|+++|.|++...+.. .+... +....+
T Consensus 33 ~~~~l~~~~~~~~~~~~~~~--------~~~~~~~Wg~~~el~a~a~~~~~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~ 104 (121)
T PF02338_consen 33 VVDYLRDKNRDKFEEFLEGD--------KMSKPGTWGGEIELQALANVLNRPIIVYSSSDGDNVVFIKFTGKYPPLESPP 104 (121)
T ss_dssp HHHHHHTHTTTHHHHHHHHH--------HHTSTTSHEEHHHHHHHHHHHTSEEEEECETTTBEEEEEEESCEESTTTTTT
T ss_pred HHHHHHHhccchhhhhhhhh--------hhccccccCcHHHHHHHHHHhCCeEEEEEcCCCCccceeeecCccccCCCCC
Confidence 789999 9999999999872 99999999999999999999999999998865433 22211 133567
Q ss_pred EEEEEEcC-----CCcc
Q 032766 75 MIHLSYHD-----GEHY 86 (134)
Q Consensus 75 ~i~L~y~~-----g~HY 86 (134)
+|.|+|+. ++||
T Consensus 105 ~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 105 PICLCYHGHLYYTGNHY 121 (121)
T ss_dssp SEEEEEETEEEEETTEE
T ss_pred eEEEEEcCCccCCCCCC
Confidence 89999988 9998
No 4
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.48 E-value=4.7e-14 Score=110.35 Aligned_cols=90 Identities=22% Similarity=0.330 Sum_probs=77.8
Q ss_pred hHHHHHhCccccccccCCCCCHHHHHHh-hcCCCccCCHHHHHHHHhhcCccEEEEEcCCCce---EEeecccCCCcEEE
Q 032766 2 VVQYIVKNRETFEPFIEDDVPFDEYCQS-METDGTWAGHMELQAASLVTHSNICIHRHMSPRW---YIRNFDYHEARMIH 77 (134)
Q Consensus 2 vv~ym~~n~d~f~~Fi~~~~~~~~Y~~~-m~~~g~WGg~iEL~Als~~~~v~I~V~~~~~~~~---~i~~~~~~~~~~i~ 77 (134)
++.+|++|+|+|+|||+++++.++||++ ++....-.|||+|.|||+++++.|+|..++.+.. .-..|++...+.|.
T Consensus 163 tS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~fpe~s~P~I~ 242 (256)
T KOG3991|consen 163 TSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDFPEASAPEIY 242 (256)
T ss_pred HHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcCccccCceEE
Confidence 6789999999999999999999999995 8888899999999999999999999999875322 22356677889999
Q ss_pred EEEcCCCccceeecC
Q 032766 78 LSYHDGEHYNGVRLK 92 (134)
Q Consensus 78 L~y~~g~HYdsv~~~ 92 (134)
|.|..| |||.+++.
T Consensus 243 LLYrpG-HYdilY~~ 256 (256)
T KOG3991|consen 243 LLYRPG-HYDILYKK 256 (256)
T ss_pred EEecCC-ccccccCC
Confidence 999765 99999874
No 5
>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=99.45 E-value=2.2e-13 Score=107.26 Aligned_cols=90 Identities=23% Similarity=0.403 Sum_probs=69.0
Q ss_pred ChHHHHHhCccccccccCCC--CCHHHHHH-hhcCCCccCCHHHHHHHHhhcCccEEEEEcCCC----ceEEeecc---c
Q 032766 1 MVVQYIVKNRETFEPFIEDD--VPFDEYCQ-SMETDGTWAGHMELQAASLVTHSNICIHRHMSP----RWYIRNFD---Y 70 (134)
Q Consensus 1 ~vv~ym~~n~d~f~~Fi~~~--~~~~~Y~~-~m~~~g~WGg~iEL~Als~~~~v~I~V~~~~~~----~~~i~~~~---~ 70 (134)
+++.||+.|+++|+||+++. .++++||+ .++..+.-+||+.+.|||++++++|.|+..++. ......++ +
T Consensus 145 lts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~~~~~~~~~~~~~~~~~ 224 (244)
T PF10275_consen 145 LTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRSVEGDEVNRHEFPPDNE 224 (244)
T ss_dssp HHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSSGCSTTSEEEEES-SST
T ss_pred HHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCCCCCCccccccCCCccC
Confidence 36889999999999999975 79999997 599999999999999999999999999988743 22333443 3
Q ss_pred CCCcEEEEEEcCCCccceeec
Q 032766 71 HEARMIHLSYHDGEHYNGVRL 91 (134)
Q Consensus 71 ~~~~~i~L~y~~g~HYdsv~~ 91 (134)
+..+.|+|.|.+| |||.++|
T Consensus 225 ~~~~~i~LLyrpg-HYdIly~ 244 (244)
T PF10275_consen 225 SQEPQITLLYRPG-HYDILYP 244 (244)
T ss_dssp TSS-SEEEEEETB-EEEEEEE
T ss_pred CCCCEEEEEEcCC-ccccccC
Confidence 4578899999877 9999986
No 6
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=99.12 E-value=7e-12 Score=100.97 Aligned_cols=125 Identities=16% Similarity=0.162 Sum_probs=96.3
Q ss_pred ChHHHHHhCccccccccCCCCCHHHHHHhhcCCCccC-CHHHHHHHHhhcCccEEEEEcCCCceEEeeccc-CCCcEEEE
Q 032766 1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWA-GHMELQAASLVTHSNICIHRHMSPRWYIRNFDY-HEARMIHL 78 (134)
Q Consensus 1 ~vv~ym~~n~d~f~~Fi~~~~~~~~Y~~~m~~~g~WG-g~iEL~Als~~~~v~I~V~~~~~~~~~i~~~~~-~~~~~i~L 78 (134)
+|+..+.+|||.|.+.+.+ .+--.||.|+.++..|| |++|+.++|..+++.|+|++.+... +..++. .....+.+
T Consensus 143 ~vs~Ev~snPDl~n~~i~~-~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~--~dr~~~~~~~q~~~i 219 (306)
T COG5539 143 VVSLEVLSNPDLYNPAILE-IDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDS--EDRYNSHPYVQRISI 219 (306)
T ss_pred HHHHHHhhCccccchhhcC-cchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhH--HhhccCChhhhhhhh
Confidence 3677888999999999998 78999999999999999 9999999999999999999998532 222222 22345677
Q ss_pred EEcCCCccceeecC----CCCCCC--CCcceEeehhhhHHhhhhhhhccccccchhh
Q 032766 79 SYHDGEHYNGVRLK----EDSCIG--SARPIIIKVFIITLFSFRDRLFYYYNFVNFF 129 (134)
Q Consensus 79 ~y~~g~HYdsv~~~----~~~~~~--p~~~~~~~~~~~~l~~~~~~~~~~~~~~~f~ 129 (134)
.| .|.|||...-. ++-.+. +...-.+......|.+.++.-+|||||..|-
T Consensus 220 ~f-~g~hfD~~t~~m~~~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~~~~ 275 (306)
T COG5539 220 LF-TGIHFDEETLAMVLWDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTASPS 275 (306)
T ss_pred hh-cccccchhhhhcchHHHHHhhhcccccccchHHHHHHHHHhcCceEEeecCCce
Confidence 77 78999998732 222221 1111126778899999999999999998763
No 7
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.65 E-value=1.3e-08 Score=85.09 Aligned_cols=90 Identities=21% Similarity=0.299 Sum_probs=68.5
Q ss_pred ChHHHHHhCccccccccCCCCCHHHHHHhhcCCCccCCHHHHHHHHh---hcCccEEEEEcCCCceEE-eecccCCCcEE
Q 032766 1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASL---VTHSNICIHRHMSPRWYI-RNFDYHEARMI 76 (134)
Q Consensus 1 ~vv~ym~~n~d~f~~Fi~~~~~~~~Y~~~m~~~g~WGg~iEL~Als~---~~~v~I~V~~~~~~~~~i-~~~~~~~~~~i 76 (134)
++++++..+++.|+.|+.. +|.+|+.+|++++.||+|+|+||+|. ....++.+.+...+.+.- .+-.+.+...+
T Consensus 251 ~~~dq~~~e~~~~~~~vt~--~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~ 328 (371)
T KOG2605|consen 251 ECVDQLKKERDFYEDYVTE--DFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNITSFKDTCYIQTPPAIEESVKME 328 (371)
T ss_pred HHHHHHhhccccccccccc--chhhcccccccCCCCcchHHHhhhhhhhhhccccceeecccccceeccCcccccchhhh
Confidence 5789999999999999996 79999999999999999999999995 445555555554433321 12122344457
Q ss_pred EEEEcCCCccceeecC
Q 032766 77 HLSYHDGEHYNGVRLK 92 (134)
Q Consensus 77 ~L~y~~g~HYdsv~~~ 92 (134)
++.++.-.||+.++.-
T Consensus 329 ~~n~~~~~h~~~~~~~ 344 (371)
T KOG2605|consen 329 KYNFWVEVHYNTARHS 344 (371)
T ss_pred hhcccchhhhhhcccc
Confidence 7777788999999874
No 8
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.44 E-value=1.1e-07 Score=76.99 Aligned_cols=83 Identities=18% Similarity=0.146 Sum_probs=62.8
Q ss_pred HHHHhCccccccccCCC-----CCHHHHHHhhcCCCccCCHHHHHHHHhhcCccEEEEEcCCCceEEeecccCCCcEEEE
Q 032766 4 QYIVKNRETFEPFIEDD-----VPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHL 78 (134)
Q Consensus 4 ~ym~~n~d~f~~Fi~~~-----~~~~~Y~~~m~~~g~WGg~iEL~Als~~~~v~I~V~~~~~~~~~i~~~~~~~~~~i~L 78 (134)
.|..++.+.|.++.-+. .+|++||..|+-+..||+.+|++|||..|++++.++...++.+.-.+.+-. ...-+
T Consensus 212 ~~~q~~~i~f~g~hfD~~t~~m~~~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~~~~ik~n~c~~~--~~~e~ 289 (306)
T COG5539 212 PYVQRISILFTGIHFDEETLAMVLWDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTASPSIKCNICGTG--FVGEK 289 (306)
T ss_pred hhhhhhhhhhcccccchhhhhcchHHHHHhhhcccccccchHHHHHHHHHhcCceEEeecCCceEEeeccccc--cchhh
Confidence 45677888899887653 379999999999999999999999999999999999988765554432211 11222
Q ss_pred E-----EcCCCcccee
Q 032766 79 S-----YHDGEHYNGV 89 (134)
Q Consensus 79 ~-----y~~g~HYdsv 89 (134)
. |-.| |||++
T Consensus 290 ~~~~Ha~a~G-H~n~~ 304 (306)
T COG5539 290 DYYAHALATG-HYNFG 304 (306)
T ss_pred HHHHHHHhhc-Ccccc
Confidence 2 3347 99987
No 9
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=81.81 E-value=0.48 Score=40.13 Aligned_cols=46 Identities=24% Similarity=0.231 Sum_probs=41.3
Q ss_pred cccccCCCCCHHHHHHhhcCCCccCCHHHHHHHHhhcCccEEEEEcCC
Q 032766 13 FEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMS 60 (134)
Q Consensus 13 f~~Fi~~~~~~~~Y~~~m~~~g~WGg~iEL~Als~~~~v~I~V~~~~~ 60 (134)
|.+++.+ +|+.|+.-+.++.+-|+.+||.+++.+++.+.+.+...+
T Consensus 2 ~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~~~s~~~r~~~~~~~~~g 47 (371)
T KOG2605|consen 2 FREEVSG--DFDWYLWDLGKTKTLGTILELGAMSHVYRRNVIDYEPFG 47 (371)
T ss_pred CccccCc--hHHHHhhcCCCCcccccchhhhhccccccCCCCCcCCcc
Confidence 5567776 799999999999999999999999999999999988754
No 10
>TIGR02934 nifT_nitrog probable nitrogen fixation protein FixT. This largely uncharacterized protein family is assigned a role in nitrogen fixation by two criteria. First, its gene occurs, generally, among genes essential for expression of active nitrogenase. Second, its phylogenetic profile closely matches that of nitrogen-fixing bacteria. However, mutational studies in Klebsiella pneumoniae failed to demonstrate any phenotype for deletion or overexpression of the protein.
Probab=81.08 E-value=0.12 Score=33.48 Aligned_cols=35 Identities=23% Similarity=0.526 Sum_probs=28.0
Q ss_pred HHhCccc-cccccCCCCCHHHHHHhhcCCCccCCHHH
Q 032766 6 IVKNRET-FEPFIEDDVPFDEYCQSMETDGTWAGHME 41 (134)
Q Consensus 6 m~~n~d~-f~~Fi~~~~~~~~Y~~~m~~~g~WGg~iE 41 (134)
||+|.+- +..||.- .+.|+=+-.|++++.|||.+.
T Consensus 5 iR~~~~g~l~~YvpK-KDLEE~Vv~~e~~~~WGG~v~ 40 (67)
T TIGR02934 5 IRRNRAGELSAYVPK-KDLEEVIVSVEKEELWGGWVT 40 (67)
T ss_pred EEeCCCCCEEEEEEC-CcchhheeeeecCccccCEEE
Confidence 3566665 7788887 789999999999999999653
No 11
>PF06988 NifT: NifT/FixU protein; InterPro: IPR009727 This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation [].; GO: 0009399 nitrogen fixation; PDB: 2JN4_A.
Probab=71.87 E-value=0.05 Score=35.03 Aligned_cols=35 Identities=26% Similarity=0.472 Sum_probs=24.1
Q ss_pred HHhCcc-ccccccCCCCCHHHHHHhhcCCCccCCHHH
Q 032766 6 IVKNRE-TFEPFIEDDVPFDEYCQSMETDGTWAGHME 41 (134)
Q Consensus 6 m~~n~d-~f~~Fi~~~~~~~~Y~~~m~~~g~WGg~iE 41 (134)
||+|.+ .+.-||.- .+.|+=+-.|++++.|||.++
T Consensus 5 iR~~~~G~ls~YVpK-KDLEE~Vv~~E~~~~wGG~v~ 40 (64)
T PF06988_consen 5 IRKNGAGGLSAYVPK-KDLEEPVVSMEKPELWGGEVT 40 (64)
T ss_dssp EEE-SS--EEEEETT-TTEEEEEEEESSSSS-SSEEE
T ss_pred EEeCCCcCEEEEEeC-CccccceeeeeccCccCCEEE
Confidence 355555 67777776 678887888889999999653
No 12
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 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 group of cysteine peptidases correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=71.14 E-value=7.3 Score=26.87 Aligned_cols=47 Identities=9% Similarity=0.100 Sum_probs=32.6
Q ss_pred CHHHHHHhhcC--CCccCCHHHHHHHHhhcCccEEEEEcCCCceEEeecccC
Q 032766 22 PFDEYCQSMET--DGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYH 71 (134)
Q Consensus 22 ~~~~Y~~~m~~--~g~WGg~iEL~Als~~~~v~I~V~~~~~~~~~i~~~~~~ 71 (134)
..+.||.|.++ +.+|-|-+ .+|..+++.|.|--....+..+..+.++
T Consensus 35 ~i~~y~~W~r~~~~STW~DC~---mFA~~LkVsm~vkV~~~~~~~l~~~~d~ 83 (104)
T PF05415_consen 35 TIKKYHTWLRKKRPSTWDDCR---MFADALKVSMQVKVLSDKPYDLLYFVDG 83 (104)
T ss_pred HHHHHHHHHhcCCCCcHHHHH---HHHHhheeEEEEEEcCCCCceeeEeecC
Confidence 57899998765 78997765 8999999999875443333444334443
No 13
>PRK10963 hypothetical protein; Provisional
Probab=61.69 E-value=5.6 Score=30.98 Aligned_cols=35 Identities=23% Similarity=0.353 Sum_probs=25.4
Q ss_pred hHHHHHhCccccccccCCCCCHHHHHHhhcCCCccCCHHHHH
Q 032766 2 VVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQ 43 (134)
Q Consensus 2 vv~ym~~n~d~f~~Fi~~~~~~~~Y~~~m~~~g~WGg~iEL~ 43 (134)
|++|+++|||+|...- +-++.|+-+...||.|-|+
T Consensus 8 V~~yL~~~PdFf~~h~-------~Ll~~L~lph~~~gaVSL~ 42 (223)
T PRK10963 8 VVDYLLQNPDFFIRNA-------RLVEQMRVPHPVRGTVSLV 42 (223)
T ss_pred HHHHHHHCchHHhhCH-------HHHHhccCCCCCCCeecHH
Confidence 7899999999988653 4566777776677655443
No 14
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=48.74 E-value=8.2 Score=29.85 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=1.7
Q ss_pred hHHHHHhCccccccccCCCCCHHHHHHhhcCCCccCCHHHH
Q 032766 2 VVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMEL 42 (134)
Q Consensus 2 vv~ym~~n~d~f~~Fi~~~~~~~~Y~~~m~~~g~WGg~iEL 42 (134)
|++|+++|||+|..+-+ =+..|+-+..=||-+-|
T Consensus 11 V~~yL~~~PdFf~~~~~-------ll~~l~~ph~~~~avSL 44 (225)
T PF04340_consen 11 VAAYLRQHPDFFERHPE-------LLAELRLPHPSGGAVSL 44 (225)
T ss_dssp -------------------------------------HHHH
T ss_pred HHHHHHhCcHHHHhCHH-------HHHHcCCCCCCCCcccH
Confidence 78999999999987643 23444444444554443
No 15
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 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 entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=41.53 E-value=1.2e+02 Score=21.33 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=32.4
Q ss_pred HHHHHHhhcCccEEEEEcCCCceEEeecccCCCcEEEEEEcCC--Cccce
Q 032766 41 ELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDG--EHYNG 88 (134)
Q Consensus 41 EL~Als~~~~v~I~V~~~~~~~~~i~~~~~~~~~~i~L~y~~g--~HYds 88 (134)
.|.|||..|+....|+...+ .+.++. .+....+.|.+.+| .||..
T Consensus 48 hltaLa~~~~~~~~~hs~~~-~~~~Gi--~~as~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 48 HLTALAYRYHFQCTFHSDHG-VLHYGI--KDASTVFTITHTPGPPGHFSL 94 (104)
T ss_pred HHHHHHHHHheEEEEEcCCc-eEEeec--CCCceEEEEEeCCCCCCcccc
Confidence 46799999999999988664 233332 23456788888776 69988
No 16
>COG3159 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.97 E-value=14 Score=29.23 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=13.6
Q ss_pred hHHHHHhCccccccc
Q 032766 2 VVQYIVKNRETFEPF 16 (134)
Q Consensus 2 vv~ym~~n~d~f~~F 16 (134)
|++|++.||++|..+
T Consensus 9 VadyL~~hPeFf~~h 23 (218)
T COG3159 9 VADYLRQHPEFFIQH 23 (218)
T ss_pred HHHHHHhCcHHHHhC
Confidence 789999999999975
No 17
>KOG4015 consensus Fatty acid-binding protein FABP [Lipid transport and metabolism]
Probab=38.88 E-value=1.1e+02 Score=22.30 Aligned_cols=39 Identities=13% Similarity=0.212 Sum_probs=28.4
Q ss_pred CCHHHHHHhhcCCCccCCHHHHHHHHhhcCccEEEEEcCCCceEEe
Q 032766 21 VPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIR 66 (134)
Q Consensus 21 ~~~~~Y~~~m~~~g~WGg~iEL~Als~~~~v~I~V~~~~~~~~~i~ 66 (134)
+.||+|+..+ |=.+.+.-+|.+.+ |+..+..++..+.+.
T Consensus 15 ENFdeymk~l------GV~~~~Rk~a~~~k-p~~~i~~~G~~~~~~ 53 (133)
T KOG4015|consen 15 ENFDEYLKAL------GVGWATRKIAKLAK-PVLEITQDGDKFTIK 53 (133)
T ss_pred cCHHHHHHhc------CCcHhHHHHHhhcC-CeEEEEEcCCEEEEE
Confidence 5899999987 34456677777777 777777777666665
No 18
>KOG3325 consensus Membrane coat complex Retromer, subunit VPS29/PEP11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.00 E-value=60 Score=24.66 Aligned_cols=23 Identities=13% Similarity=0.221 Sum_probs=21.0
Q ss_pred ccCCHHHHHHHHhhcCccEEEEE
Q 032766 35 TWAGHMELQAASLVTHSNICIHR 57 (134)
Q Consensus 35 ~WGg~iEL~Als~~~~v~I~V~~ 57 (134)
-|||..-|.+|++-++++|-+.-
T Consensus 92 P~gd~~sL~~LaRqldvDILl~G 114 (183)
T KOG3325|consen 92 PWGDPESLALLARQLDVDILLTG 114 (183)
T ss_pred cCCCHHHHHHHHHhcCCcEEEeC
Confidence 49999999999999999998864
No 19
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=28.34 E-value=44 Score=27.99 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=23.4
Q ss_pred CHHHHHHhhcCCCccCCHHHHHHHHhh
Q 032766 22 PFDEYCQSMETDGTWAGHMELQAASLV 48 (134)
Q Consensus 22 ~~~~Y~~~m~~~g~WGg~iEL~Als~~ 48 (134)
-.++|++|+.+-=.+.|+.||.|||+-
T Consensus 315 ~I~~~v~~iapv~v~PGE~EleALA~G 341 (358)
T COG3426 315 AIEDRVSWIAPVIVYPGEDELEALAEG 341 (358)
T ss_pred HHHHHHhhhcceEecCCchHHHHHHhh
Confidence 357888999988899999999999974
No 20
>COG5562 Phage envelope protein [General function prediction only]
Probab=27.40 E-value=40 Score=24.81 Aligned_cols=18 Identities=22% Similarity=0.831 Sum_probs=14.9
Q ss_pred CCCCHHHHHHhhcCCCcc
Q 032766 19 DDVPFDEYCQSMETDGTW 36 (134)
Q Consensus 19 ~~~~~~~Y~~~m~~~g~W 36 (134)
|.-+|++||+.|.+.|+.
T Consensus 87 GqttF~ef~~~la~AGVf 104 (137)
T COG5562 87 GQTTFEEFCSALAEAGVF 104 (137)
T ss_pred CCccHHHHHHHHHhCCeE
Confidence 346999999999888865
No 21
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=26.94 E-value=17 Score=22.76 Aligned_cols=19 Identities=37% Similarity=0.711 Sum_probs=16.5
Q ss_pred hHHHHHhCccccccccCCC
Q 032766 2 VVQYIVKNRETFEPFIEDD 20 (134)
Q Consensus 2 vv~ym~~n~d~f~~Fi~~~ 20 (134)
+++|+.+||+-.+...+|.
T Consensus 5 iV~YLv~nPevl~kl~~g~ 23 (57)
T PF05952_consen 5 IVNYLVQNPEVLEKLKEGE 23 (57)
T ss_pred HHHHHHHChHHHHHHHcCC
Confidence 6899999999998888774
No 22
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=26.13 E-value=66 Score=18.48 Aligned_cols=29 Identities=7% Similarity=-0.081 Sum_probs=22.7
Q ss_pred HHHHhhcCCCccCCHHHHHHHHhhcCccE
Q 032766 25 EYCQSMETDGTWAGHMELQAASLVTHSNI 53 (134)
Q Consensus 25 ~Y~~~m~~~g~WGg~iEL~Als~~~~v~I 53 (134)
.++.++.+....=..-.+.++|++|++++
T Consensus 24 ~~i~~~~~g~~~~~~~~~~~ia~~l~~~~ 52 (55)
T PF01381_consen 24 STISRIENGKRNPSLDTLKKIAKALGVSP 52 (55)
T ss_dssp HHHHHHHTTSSTSBHHHHHHHHHHHTSEH
T ss_pred chhHHHhcCCCCCCHHHHHHHHHHHCCCH
Confidence 56666666667777888999999999874
No 23
>KOG4100 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.16 E-value=18 Score=25.99 Aligned_cols=29 Identities=21% Similarity=0.625 Sum_probs=20.4
Q ss_pred CccccccccCCCCCHHHHHHhhcC----CCccCCHH
Q 032766 9 NRETFEPFIEDDVPFDEYCQSMET----DGTWAGHM 40 (134)
Q Consensus 9 n~d~f~~Fi~~~~~~~~Y~~~m~~----~g~WGg~i 40 (134)
||++-.+|+. +|+.||..+++ .|+|-|++
T Consensus 49 np~~~~~Flt---eW~~Ya~~l~qql~~~g~~K~~~ 81 (125)
T KOG4100|consen 49 NPLEAQGFLT---EWERYAVALSQQLSSAGKWKGEI 81 (125)
T ss_pred ChHHHHHHHH---HHHHHHHHHHHHhhhcCcccccc
Confidence 4555566876 59999987765 68886553
No 24
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=23.62 E-value=1.1e+02 Score=26.78 Aligned_cols=82 Identities=12% Similarity=0.150 Sum_probs=47.9
Q ss_pred CccccccccCCCCCHHHHHHhhcCCC---ccCCHHHHHH-HHhhcCccEEEEEcCC-CceEEeecccCCCcEEEEEEcCC
Q 032766 9 NRETFEPFIEDDVPFDEYCQSMETDG---TWAGHMELQA-ASLVTHSNICIHRHMS-PRWYIRNFDYHEARMIHLSYHDG 83 (134)
Q Consensus 9 n~d~f~~Fi~~~~~~~~Y~~~m~~~g---~WGg~iEL~A-ls~~~~v~I~V~~~~~-~~~~i~~~~~~~~~~i~L~y~~g 83 (134)
|.|.|..|-.-...|.+|++++.+-| .+|+..+|+. +++..++++.-+-.+. ..|++........+..+-.+..|
T Consensus 187 H~D~y~~~~~i~~~F~~f~~~vp~~G~~v~~~dd~~l~~l~~~~~~~~v~tyG~~~~ad~~a~ni~~~~~~~~F~V~~~g 266 (459)
T COG0773 187 HLDYYGDLEAIKQAFHHFVRNVPFYGRAVVCGDDPNLRELLSRGCWSPVVTYGFDDEADWRAENIRQDGSGTTFDVLFRG 266 (459)
T ss_pred hhhhhCCHHHHHHHHHHHHHhCCccceEEEECCCHHHHHHHhcccCCcEEeecCCCcCcEEEEEeEEeccccEEEEEEcC
Confidence 44555533211147899999998773 5799999999 5656677666664442 35666554333232223333455
Q ss_pred Cccceee
Q 032766 84 EHYNGVR 90 (134)
Q Consensus 84 ~HYdsv~ 90 (134)
+.|-.+.
T Consensus 267 ~~~~~~~ 273 (459)
T COG0773 267 EELGEVK 273 (459)
T ss_pred ceeEEEE
Confidence 5555544
No 25
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=23.48 E-value=43 Score=19.18 Aligned_cols=17 Identities=24% Similarity=0.194 Sum_probs=11.7
Q ss_pred CCHHHHHHHHhhcCccE
Q 032766 37 AGHMELQAASLVTHSNI 53 (134)
Q Consensus 37 Gg~iEL~Als~~~~v~I 53 (134)
.|+-|||.++..+++.-
T Consensus 22 ~G~CeLQ~~~~~~gv~~ 38 (41)
T PF10588_consen 22 NGNCELQDLAYEYGVDE 38 (41)
T ss_dssp GGG-HHHHHHHHH-S--
T ss_pred CCCCHHHHHHHHhCCCc
Confidence 67889999999998763
No 26
>COG4479 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.02 E-value=37 Score=22.28 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=18.7
Q ss_pred hHHHHHhCccccccccCCCCCHHHHHHhhc
Q 032766 2 VVQYIVKNRETFEPFIEDDVPFDEYCQSME 31 (134)
Q Consensus 2 vv~ym~~n~d~f~~Fi~~~~~~~~Y~~~m~ 31 (134)
+.+||..|.++.-+--.=|+-|++|++.+.
T Consensus 44 is~YLE~~a~f~~~m~~FDeiwe~Yle~~~ 73 (74)
T COG4479 44 ISDYLETNADFLFNMSVFDEIWEEYLEHLK 73 (74)
T ss_pred HHHHHHhcCCcccchhhHHHHHHHHHHHhc
Confidence 567787777764432211257889988754
No 27
>PF00941 FAD_binding_5: FAD binding domain in molybdopterin dehydrogenase; InterPro: IPR002346 Oxidoreductases, that also bind molybdopterin, have essentially no similarity outside this common domain. They include aldehyde oxidase (1.2.3.1 from EC), that converts an aldehyde and water to an acid and hydrogen peroxide, and xanthine dehydrogenase (1.1.1.204 from EC), that converts xanthine to urate. These enzymes require molybdopterin and FAD as cofactors and have and two 2FE-2S clusters. Another enzyme that contains this domain is the Pseudomonas thermocarboxydovorans carbon monoxide oxygenase.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2E1Q_C 2CKJ_A 3EUB_K 3NS1_K 3NVV_B 1FO4_B 3AM9_A 3AX7_B 3BDJ_A 3ETR_B ....
Probab=21.66 E-value=54 Score=24.23 Aligned_cols=32 Identities=19% Similarity=0.221 Sum_probs=23.0
Q ss_pred hhcCCCccCCHHH-------HHHHHhhcCccEEEEEcCC
Q 032766 29 SMETDGTWAGHME-------LQAASLVTHSNICIHRHMS 60 (134)
Q Consensus 29 ~m~~~g~WGg~iE-------L~Als~~~~v~I~V~~~~~ 60 (134)
.+|+.|||||++. +..+-.+++-.+.|...++
T Consensus 101 ~IRn~aTiGGNl~~~~~~sD~~~~Llal~A~v~i~~~~g 139 (171)
T PF00941_consen 101 QIRNRATIGGNLCNASPASDLAPALLALDARVEIASPDG 139 (171)
T ss_dssp HHHTT-BHHHHHHHTBTT-SHHHHHHHTT-EEEEEETTE
T ss_pred hHeeeeeeccccccCcccccHHHHHHHhCcEEEEEcCCe
Confidence 5788999999994 4445567888888888765
Done!