Query 028661
Match_columns 206
No_of_seqs 223 out of 561
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 15:00:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028661.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028661hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3288 OTU-like cysteine prot 100.0 1.4E-36 3E-41 263.0 5.9 125 74-205 139-263 (307)
2 KOG3288 OTU-like cysteine prot 99.9 5.4E-24 1.2E-28 184.9 5.3 85 1-92 219-303 (307)
3 KOG2606 OTU (ovarian tumor)-li 99.8 7.2E-21 1.6E-25 168.0 6.2 94 74-173 190-298 (302)
4 COG5539 Predicted cysteine pro 99.7 6.8E-18 1.5E-22 148.9 0.7 123 74-204 138-261 (306)
5 PF02338 OTU: OTU-like cystein 99.3 1.2E-12 2.6E-17 100.4 5.4 85 74-167 27-121 (121)
6 COG5539 Predicted cysteine pro 99.0 2.9E-10 6.3E-15 100.9 2.7 85 2-93 219-303 (306)
7 PF10275 Peptidase_C65: Peptid 98.5 5.9E-07 1.3E-11 77.7 8.8 94 74-171 140-243 (244)
8 KOG3991 Uncharacterized conser 98.4 1E-06 2.2E-11 76.4 7.2 96 75-172 158-255 (256)
9 KOG2605 OTU (ovarian tumor)-li 94.0 0.061 1.3E-06 50.1 4.0 61 74-135 246-309 (371)
10 PF01188 MR_MLE: Mandelate rac 37.8 46 0.00099 22.7 3.2 32 100-132 35-66 (67)
11 PHA00616 hypothetical protein 35.0 26 0.00057 23.1 1.5 29 66-95 3-31 (44)
12 PF06988 NifT: NifT/FixU prote 29.0 3.2 6.9E-05 29.5 -3.9 30 90-119 12-41 (64)
13 KOG1247 Methionyl-tRNA synthet 28.6 33 0.00072 33.2 1.6 62 4-75 86-147 (567)
14 KOG2989 Uncharacterized conser 25.7 42 0.00091 29.9 1.6 20 53-72 28-48 (253)
15 TIGR02934 nifT_nitrog probable 25.6 21 0.00045 25.6 -0.2 22 97-118 19-40 (67)
16 PF07967 zf-C3HC: C3HC zinc fi 24.7 26 0.00056 27.5 0.1 24 54-77 33-56 (133)
17 PF06107 DUF951: Bacterial pro 23.3 39 0.00085 23.5 0.8 16 61-76 28-43 (57)
18 COG3426 Butyrate kinase [Energ 23.3 51 0.0011 30.4 1.7 25 100-124 316-340 (358)
19 PRK05111 acetylornithine deace 22.6 88 0.0019 28.0 3.2 13 2-15 74-86 (383)
20 PF00096 zf-C2H2: Zinc finger, 20.6 70 0.0015 16.8 1.4 19 66-84 2-20 (23)
21 cd00022 BIR Baculoviral inhibi 20.5 38 0.00082 23.1 0.3 25 54-79 25-49 (69)
No 1
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.4e-36 Score=263.01 Aligned_cols=125 Identities=46% Similarity=0.831 Sum_probs=117.7
Q ss_pred chhHHHHHHHHHhccccccccccCCChHHHhhhcCCCCccchHHHHHHHHHHhCCeeEEEEcCCCCeeeeCCCccccccc
Q 028661 74 VIGQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLYGQCSHFQEKK 153 (206)
Q Consensus 74 l~lR~~vA~~I~~np~~f~~~~L~~~~~eYc~~I~~~~~WGG~iEL~aLs~~~~~~I~v~~~~~~~~~~~ge~~~~~~~~ 153 (206)
.+||+++|+.+++||+.||+||||+|+.|||.||+++++|||+|||+|||++|+++|.|+|+++.|+++||| +++
T Consensus 139 ~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiqt~rid~fge-----d~~ 213 (307)
T KOG3288|consen 139 YELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQTVRIDRFGE-----DKN 213 (307)
T ss_pred HHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccccccCceEEeeeehhhhceeEEEEecceeeehhcCC-----CCC
Confidence 479999999999999999999999999999999999999999999999999999999999999999999999 888
Q ss_pred CCCeEEEEecCcccccccccccCCCCCCCCeeeeeCCCCCChhHHHHHHhhh
Q 028661 154 YSERVMLIYDELHYDAVAISAFEGAPVEFDQSSVPVRKDRTIGPAEELAFET 205 (206)
Q Consensus 154 ~~~~i~L~Y~G~HYdsl~~~~~~~~~~~~d~t~f~~~~~~~~~~~~~~a~~l 205 (206)
|.+|++|+|+|+|||+|.+++. .|.+.|.|+||.+|+.++..++++|.+|
T Consensus 214 ~~~rv~llydGIHYD~l~m~~~--~~~~~~~tifp~~dd~v~~~alqLa~~~ 263 (307)
T KOG3288|consen 214 FDNRVLLLYDGIHYDPLAMNEF--KPTDVDNTIFPVSDDTVLTQALQLASEL 263 (307)
T ss_pred CCceEEEEecccccChhhhccC--CccCCcccccccccchHHHHHHHHHHHH
Confidence 9999999999999999999876 6888999999999987777777777664
No 2
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=5.4e-24 Score=184.86 Aligned_cols=85 Identities=48% Similarity=0.782 Sum_probs=77.5
Q ss_pred CEeecccccceeeecCCCCCCCCCCeeeeeCCCCCccchHHHHHHHHHHHHhhcCcccccccceeeeeeccccchhHHHH
Q 028661 1 MLIYDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIGQKAI 80 (206)
Q Consensus 1 ~liYsGIHYD~l~l~~~~~~~~~~d~tiF~~~d~~~~~~~~~~A~~L~~~lk~~~~~Tdt~~F~LrC~~C~~~l~lR~~v 80 (206)
+|||||||||+|++++. .|.+.|-|+||.+|+.+ +..|++||+++|++||||||++|+|||++|+++|.|++.
T Consensus 219 ~llydGIHYD~l~m~~~--~~~~~~~tifp~~dd~v----~~~alqLa~~~k~~r~ytdt~~ftlRC~~Cq~glvGq~e- 291 (307)
T KOG3288|consen 219 LLLYDGIHYDPLAMNEF--KPTDVDNTIFPVSDDTV----LTQALQLASELKRTRYYTDTAKFTLRCMVCQMGLVGQKE- 291 (307)
T ss_pred EEEecccccChhhhccC--CccCCcccccccccchH----HHHHHHHHHHHHhcceeccccceEEEeeecccceeeHHH-
Confidence 58999999999999976 56778999999999754 489999999999999999999999999999999999997
Q ss_pred HHHHHhcccccc
Q 028661 81 AATVASDTVKHS 92 (206)
Q Consensus 81 A~~I~~np~~f~ 92 (206)
|..|++.++|-|
T Consensus 292 a~eHA~~TGH~n 303 (307)
T KOG3288|consen 292 AAEHAKATGHVN 303 (307)
T ss_pred HHHHHHhcCCCc
Confidence 669999999965
No 3
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.82 E-value=7.2e-21 Score=168.02 Aligned_cols=94 Identities=21% Similarity=0.366 Sum_probs=81.2
Q ss_pred chhHHHHHHHHHhccccccccccC------CC---hHHHhhhcCCCCccchHHHHHHHHHHhCCeeEEEEcCCCCeeeeC
Q 028661 74 VIGQKAIAATVASDTVKHSEAFIG------KS---NQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLYG 144 (206)
Q Consensus 74 l~lR~~vA~~I~~np~~f~~~~L~------~~---~~eYc~~I~~~~~WGG~iEL~aLs~~~~~~I~v~~~~~~~~~~~g 144 (206)
-.||...|+|+++|.++|-|+++. .+ |++||+.|++|+.|||+|||.|||++|++||.||+.+ +.+..||
T Consensus 190 ~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~-~p~~~~g 268 (302)
T KOG2606|consen 190 QKLREETADYMREHVEDFLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQAD-GPILEYG 268 (302)
T ss_pred HHHHHHHHHHHHHHHHHhhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecC-CCceeec
Confidence 479999999999999999996652 23 9999999999999999999999999999999999986 6678999
Q ss_pred CCcccccccCCCeEEEEec------Cccccccccc
Q 028661 145 QCSHFQEKKYSERVMLIYD------ELHYDAVAIS 173 (206)
Q Consensus 145 e~~~~~~~~~~~~i~L~Y~------G~HYdsl~~~ 173 (206)
+ +.+..++++|+|+ |+||||+...
T Consensus 269 e-----ey~kd~pL~lvY~rH~y~LGeHYNS~~~~ 298 (302)
T KOG2606|consen 269 E-----EYGKDKPLILVYHRHAYGLGEHYNSVTPL 298 (302)
T ss_pred h-----hhCCCCCeeeehHHhHHHHHhhhcccccc
Confidence 8 3222478999995 8999999764
No 4
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=99.67 E-value=6.8e-18 Score=148.91 Aligned_cols=123 Identities=20% Similarity=0.328 Sum_probs=101.4
Q ss_pred chhHHHHHHHHHhccccccccccCCChHHHhhhcCCCCccc-hHHHHHHHHHHhCCeeEEEEcCCCCeeeeCCCcccccc
Q 028661 74 VIGQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWG-GAIELSILADYYGSEIAAYDIQTTRCDLYGQCSHFQEK 152 (206)
Q Consensus 74 l~lR~~vA~~I~~np~~f~~~~L~~~~~eYc~~I~~~~~WG-G~iEL~aLs~~~~~~I~v~~~~~~~~~~~ge~~~~~~~ 152 (206)
-+||.+||-.+.+||+.|++++++.|.-.||.||+++.+|| |.||+.+||+.++++|.|+|+..++.++||+ .
T Consensus 138 ~~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~-----~- 211 (306)
T COG5539 138 AKLREVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNS-----H- 211 (306)
T ss_pred HHHHHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccC-----C-
Confidence 47999999999999999999999999999999999999999 9999999999999999999999889999998 3
Q ss_pred cCCCeEEEEecCcccccccccccCCCCCCCCeeeeeCCCCCChhHHHHHHhh
Q 028661 153 KYSERVMLIYDELHYDAVAISAFEGAPVEFDQSSVPVRKDRTIGPAEELAFE 204 (206)
Q Consensus 153 ~~~~~i~L~Y~G~HYdsl~~~~~~~~~~~~d~t~f~~~~~~~~~~~~~~a~~ 204 (206)
.|..++.+.|.|+|||...+...+ -....+...|+.++-.. -.++++|.-
T Consensus 212 ~~~q~~~i~f~g~hfD~~t~~m~~-~dt~~ne~~~~a~~g~~-~ei~qLas~ 261 (306)
T COG5539 212 PYVQRISILFTGIHFDEETLAMVL-WDTYVNEVLFDASDGIT-IEIQQLASL 261 (306)
T ss_pred hhhhhhhhhhcccccchhhhhcch-HHHHHhhhcccccccch-HHHHHHHHH
Confidence 367889999999999999854321 01223445565555422 456666654
No 5
>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=99.34 E-value=1.2e-12 Score=100.43 Aligned_cols=85 Identities=24% Similarity=0.366 Sum_probs=66.3
Q ss_pred chhHHHHHHHHH-hccccccccccCCChHHHhhhcCCCCccchHHHHHHHHHHhCCeeEEEEcCCCCeeee---CCCccc
Q 028661 74 VIGQKAIAATVA-SDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLY---GQCSHF 149 (206)
Q Consensus 74 l~lR~~vA~~I~-~np~~f~~~~L~~~~~eYc~~I~~~~~WGG~iEL~aLs~~~~~~I~v~~~~~~~~~~~---ge~~~~ 149 (206)
.++|+.++++++ .+++.|.+.+.+. +|+++..|||++||.|||++|+++|.||+...++...+ +.. .
T Consensus 27 ~~lR~~~~~~l~~~~~~~~~~~~~~~-------~~~~~~~Wg~~~el~a~a~~~~~~I~v~~~~~~~~~~~~~~~~~--~ 97 (121)
T PF02338_consen 27 QELRKAVVDYLRDKNRDKFEEFLEGD-------KMSKPGTWGGEIELQALANVLNRPIIVYSSSDGDNVVFIKFTGK--Y 97 (121)
T ss_dssp HHHHHHHHHHHHTHTTTHHHHHHHHH-------HHTSTTSHEEHHHHHHHHHHHTSEEEEECETTTBEEEEEEESCE--E
T ss_pred HHHHHHHHHHHHHhccchhhhhhhhh-------hhccccccCcHHHHHHHHHHhCCeEEEEEcCCCCccceeeecCc--c
Confidence 489999999999 9999998844434 99999999999999999999999999998876653222 210 0
Q ss_pred ccccCCCeEEEEec------Cccc
Q 028661 150 QEKKYSERVMLIYD------ELHY 167 (206)
Q Consensus 150 ~~~~~~~~i~L~Y~------G~HY 167 (206)
......+.+.+.|+ |+||
T Consensus 98 ~~~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 98 PPLESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp STTTTTTSEEEEEETEEEEETTEE
T ss_pred ccCCCCCeEEEEEcCCccCCCCCC
Confidence 01234567888887 6898
No 6
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.96 E-value=2.9e-10 Score=100.87 Aligned_cols=85 Identities=19% Similarity=0.298 Sum_probs=65.2
Q ss_pred EeecccccceeeecCCCCCCCCCCeeeeeCCCCCccchHHHHHHHHHHHHhhcCcccccccceeeeeeccccchhHHHHH
Q 028661 2 LIYDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIGQKAIA 81 (206)
Q Consensus 2 liYsGIHYD~l~l~~~~~~~~~~d~tiF~~~d~~~~~~~~~~A~~L~~~lk~~~~~Tdt~~F~LrC~~C~~~l~lR~~vA 81 (206)
++|+|||||..++.-.+- ...++.-.|+.++- +...+++||+-|+..+|+|||++|.+||+.|+++++|.+. +
T Consensus 219 i~f~g~hfD~~t~~m~~~-dt~~ne~~~~a~~g-----~~~ei~qLas~lk~~~~~~nT~~~~ik~n~c~~~~~~e~~-~ 291 (306)
T COG5539 219 ILFTGIHFDEETLAMVLW-DTYVNEVLFDASDG-----ITIEIQQLASLLKNPHYYTNTASPSIKCNICGTGFVGEKD-Y 291 (306)
T ss_pred hhhcccccchhhhhcchH-HHHHhhhccccccc-----chHHHHHHHHHhcCceEEeecCCceEEeeccccccchhhH-H
Confidence 479999999998653220 01122334444442 3368999999999999999999999999999999999996 4
Q ss_pred HHHHhccccccc
Q 028661 82 ATVASDTVKHSE 93 (206)
Q Consensus 82 ~~I~~np~~f~~ 93 (206)
-.|+--+|||+.
T Consensus 292 ~~Ha~a~GH~n~ 303 (306)
T COG5539 292 YAHALATGHYNF 303 (306)
T ss_pred HHHHHhhcCccc
Confidence 488888999974
No 7
>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=98.49 E-value=5.9e-07 Score=77.70 Aligned_cols=94 Identities=16% Similarity=0.227 Sum_probs=66.7
Q ss_pred chhHHHHHHHHHhccccccccccC---CChHHHhh-hcCCCCccchHHHHHHHHHHhCCeeEEEEcCCC---C---eeee
Q 028661 74 VIGQKAIAATVASDTVKHSEAFIG---KSNQDYCS-WIQDPEKWGGAIELSILADYYGSEIAAYDIQTT---R---CDLY 143 (206)
Q Consensus 74 l~lR~~vA~~I~~np~~f~~~~L~---~~~~eYc~-~I~~~~~WGG~iEL~aLs~~~~~~I~v~~~~~~---~---~~~~ 143 (206)
.-+|-..+.+++.|++.|.+++.+ .++++||+ .|.....=.++|.+.|||++++++|.|+-.+.+ . ...|
T Consensus 140 ~flRLlts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~~~~~~~~~~~~ 219 (244)
T PF10275_consen 140 IFLRLLTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRSVEGDEVNRHEF 219 (244)
T ss_dssp HHHHHHHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSSGCSTTSEEEEE
T ss_pred HHHHHHHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCCCCCCccccccC
Confidence 469988999999999999885545 78999996 666666888999999999999999999987743 1 1233
Q ss_pred CCCcccccccCCCeEEEEecCccccccc
Q 028661 144 GQCSHFQEKKYSERVMLIYDELHYDAVA 171 (206)
Q Consensus 144 ge~~~~~~~~~~~~i~L~Y~G~HYdsl~ 171 (206)
.+. ..+...+|.|+|-.-|||.++
T Consensus 220 ~~~----~~~~~~~i~LLyrpgHYdIly 243 (244)
T PF10275_consen 220 PPD----NESQEPQITLLYRPGHYDILY 243 (244)
T ss_dssp S-S----STTSS-SEEEEEETBEEEEEE
T ss_pred CCc----cCCCCCEEEEEEcCCcccccc
Confidence 220 012246799999988999886
No 8
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.37 E-value=1e-06 Score=76.43 Aligned_cols=96 Identities=16% Similarity=0.197 Sum_probs=77.5
Q ss_pred hhHHHHHHHHHhccccccccccC-CChHHHhhhcCCCC-ccchHHHHHHHHHHhCCeeEEEEcCCCCeeeeCCCcccccc
Q 028661 75 IGQKAIAATVASDTVKHSEAFIG-KSNQDYCSWIQDPE-KWGGAIELSILADYYGSEIAAYDIQTTRCDLYGQCSHFQEK 152 (206)
Q Consensus 75 ~lR~~vA~~I~~np~~f~~~~L~-~~~~eYc~~I~~~~-~WGG~iEL~aLs~~~~~~I~v~~~~~~~~~~~ge~~~~~~~ 152 (206)
-+|-..+..|++|++.|.|++-| +++.+||..-..|. .-.++|+|.|||+++++.|.|..++.+....+|.. .|. .
T Consensus 158 ylRLvtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH-~fp-e 235 (256)
T KOG3991|consen 158 YLRLVTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNHH-DFP-E 235 (256)
T ss_pred HHHHHHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCCC-cCc-c
Confidence 58999999999999999994444 89999999877776 77899999999999999999998876655555531 010 1
Q ss_pred cCCCeEEEEecCcccccccc
Q 028661 153 KYSERVMLIYDELHYDAVAI 172 (206)
Q Consensus 153 ~~~~~i~L~Y~G~HYdsl~~ 172 (206)
+...+|.|+|---|||.|+.
T Consensus 236 ~s~P~I~LLYrpGHYdilY~ 255 (256)
T KOG3991|consen 236 ASAPEIYLLYRPGHYDILYK 255 (256)
T ss_pred ccCceEEEEecCCccccccC
Confidence 23467999999999999874
No 9
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=94.03 E-value=0.061 Score=50.08 Aligned_cols=61 Identities=10% Similarity=0.090 Sum_probs=50.4
Q ss_pred chhHHHHHHHHHhccccccccccCCChHHHhhhcCCCCccchHHHHHHHHH---HhCCeeEEEEc
Q 028661 74 VIGQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILAD---YYGSEIAAYDI 135 (206)
Q Consensus 74 l~lR~~vA~~I~~np~~f~~~~L~~~~~eYc~~I~~~~~WGG~iEL~aLs~---~~~~~I~v~~~ 135 (206)
...|+.+.++...+++.|+. +.-+.+..|.+..+....||-+||++++|. ....++.+-..
T Consensus 246 ~~~~~~~~dq~~~e~~~~~~-~vt~~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~~~~ 309 (371)
T KOG2605|consen 246 DHNRRECVDQLKKERDFYED-YVTEDFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNITSF 309 (371)
T ss_pred HHHHHHHHHHHhhccccccc-ccccchhhcccccccCCCCcchHHHhhhhhhhhhccccceeecc
Confidence 35788899999999999977 778899999999999999999999999996 44444444433
No 10
>PF01188 MR_MLE: Mandelate racemase / muconate lactonizing enzyme, C-terminal domain; InterPro: IPR013342 Mandelate racemase 5.1.2.2 from EC (MR) and muconate lactonising enzyme 5.5.1.1 from EC (MLE) are two bacterial enzymes involved in aromatic acid catabolism. They catalyse mechanistically distinct reactions yet they are related at the level of their primary, quaternary (homooctamer) and tertiary structures [, ]. A number of other proteins also seem to be evolutionary related to these two enzymes. These include, various plasmid-encoded chloromuconate cycloisomerases 5.5.1.7 from EC, Escherichia coli protein rspA [], E. coli bifunctional DGOA protein, E. coli hypothetical proteins ycjG, yfaW and yidU and a hypothetical protein from Streptomyces ambofaciens []. This entry represents the C-terminal region of these proteins.; PDB: 3QLD_B 3CYJ_C 2QDD_B 3FVD_A 3H7V_A 2OZT_A 3NXL_A 1JDF_D 1JCT_B 1EC9_C ....
Probab=37.84 E-value=46 Score=22.72 Aligned_cols=32 Identities=31% Similarity=0.401 Sum_probs=23.9
Q ss_pred hHHHhhhcCCCCccchHHHHHHHHHHhCCeeEE
Q 028661 100 NQDYCSWIQDPEKWGGAIELSILADYYGSEIAA 132 (206)
Q Consensus 100 ~~eYc~~I~~~~~WGG~iEL~aLs~~~~~~I~v 132 (206)
+++| .||++|-....--++..|++..++||.+
T Consensus 35 l~~~-~~iEeP~~~~d~~~~~~l~~~~~~pia~ 66 (67)
T PF01188_consen 35 LEDY-EWIEEPLPPDDLDGLAELRQQTSVPIAA 66 (67)
T ss_dssp HGGG-SEEESSSSTTSHHHHHHHHHHCSSEEEE
T ss_pred cChh-heeecCCCCCCHHHHHHHHHhCCCCEEe
Confidence 3445 7777777766667888889999999864
No 11
>PHA00616 hypothetical protein
Probab=34.97 E-value=26 Score=23.06 Aligned_cols=29 Identities=10% Similarity=-0.071 Sum_probs=22.9
Q ss_pred eeeeccccchhHHHHHHHHHhccccccccc
Q 028661 66 CYGVCQIGVIGQKAIAATVASDTVKHSEAF 95 (206)
Q Consensus 66 rC~~C~~~l~lR~~vA~~I~~np~~f~~~~ 95 (206)
+|.-||..+.=.+.....+++++++ ++..
T Consensus 3 qC~~CG~~F~~~s~l~~H~r~~hg~-~~~~ 31 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHLLSVHKQ-NKLT 31 (44)
T ss_pred ccchhhHHHhhHHHHHHHHHHhcCC-Cccc
Confidence 6999999988777788888888877 5533
No 12
>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=28.96 E-value=3.2 Score=29.52 Aligned_cols=30 Identities=27% Similarity=0.438 Sum_probs=19.4
Q ss_pred cccccccCCChHHHhhhcCCCCccchHHHH
Q 028661 90 KHSEAFIGKSNQDYCSWIQDPEKWGGAIEL 119 (206)
Q Consensus 90 ~f~~~~L~~~~~eYc~~I~~~~~WGG~iEL 119 (206)
.+.-.+-=++++|=+-.++++..|||.+.|
T Consensus 12 ~ls~YVpKKDLEE~Vv~~E~~~~wGG~v~L 41 (64)
T PF06988_consen 12 GLSAYVPKKDLEEPVVSMEKPELWGGEVTL 41 (64)
T ss_dssp -EEEEETTTTEEEEEEEESSSSS-SSEEEE
T ss_pred CEEEEEeCCccccceeeeeccCccCCEEEE
Confidence 443323346777777888899999997654
No 13
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=28.59 E-value=33 Score=33.16 Aligned_cols=62 Identities=16% Similarity=0.210 Sum_probs=40.5
Q ss_pred ecccccceeeecCCCCCCCCCCeeeeeCCCCCccchHHHHHHHHHHHHhhcCcccccccceeeeeeccccch
Q 028661 4 YDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVI 75 (206)
Q Consensus 4 YsGIHYD~l~l~~~~~~~~~~d~tiF~~~d~~~~~~~~~~A~~L~~~lk~~~~~Tdt~~F~LrC~~C~~~l~ 75 (206)
|.||||++--.-. -++|.--+-+.+..+ ..++.+-.++.+++|+.-.+-=.|.|.+|+.-|.
T Consensus 86 yh~ihk~vy~Wf~-----IdfD~fgrtTT~~qT-----~i~Q~iF~kl~~ng~~se~tv~qLyC~vc~~fla 147 (567)
T KOG1247|consen 86 YHGIHKVVYDWFK-----IDFDEFGRTTTKTQT-----EICQDIFSKLYDNGYLSEQTVKQLYCEVCDTFLA 147 (567)
T ss_pred cchhHHHHHHhhc-----ccccccCcccCcchh-----HHHHHHhhchhhcCCcccceeeeEEehhhccccc
Confidence 7899988764421 112322222333332 4677888888889998888888899998887553
No 14
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.72 E-value=42 Score=29.86 Aligned_cols=20 Identities=15% Similarity=0.207 Sum_probs=13.5
Q ss_pred hcCcc-cccccceeeeeeccc
Q 028661 53 RKKTY-TDTANFTLCYGVCQI 72 (206)
Q Consensus 53 ~~~~~-Tdt~~F~LrC~~C~~ 72 (206)
.++++ -=.+-|++||+.|+-
T Consensus 28 ~~q~~~Rlm~Pf~~rC~tCge 48 (253)
T KOG2989|consen 28 NRQLKIRLMTPFRLRCNTCGE 48 (253)
T ss_pred hhhcceeecccceeecccccc
Confidence 33344 344579999999973
No 15
>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=25.65 E-value=21 Score=25.61 Aligned_cols=22 Identities=23% Similarity=0.465 Sum_probs=18.1
Q ss_pred CCChHHHhhhcCCCCccchHHH
Q 028661 97 GKSNQDYCSWIQDPEKWGGAIE 118 (206)
Q Consensus 97 ~~~~~eYc~~I~~~~~WGG~iE 118 (206)
=++++|=+-.+.++..|||.+-
T Consensus 19 KKDLEE~Vv~~e~~~~WGG~v~ 40 (67)
T TIGR02934 19 KKDLEEVIVSVEKEELWGGWVT 40 (67)
T ss_pred CCcchhheeeeecCccccCEEE
Confidence 4678888888999999999653
No 16
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=24.66 E-value=26 Score=27.51 Aligned_cols=24 Identities=8% Similarity=0.112 Sum_probs=21.1
Q ss_pred cCcccccccceeeeeeccccchhH
Q 028661 54 KKTYTDTANFTLCYGVCQIGVIGQ 77 (206)
Q Consensus 54 ~~~~Tdt~~F~LrC~~C~~~l~lR 77 (206)
++-.++++..+|+|..|+..+.+.
T Consensus 33 ~~GW~~~~~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 33 RRGWICVSKDMLKCESCGARLCVK 56 (133)
T ss_pred HcCCCcCCCCEEEeCCCCCEEEEe
Confidence 588999999999999999877666
No 17
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=23.35 E-value=39 Score=23.50 Aligned_cols=16 Identities=13% Similarity=0.123 Sum_probs=12.7
Q ss_pred ccceeeeeeccccchh
Q 028661 61 ANFTLCYGVCQIGVIG 76 (206)
Q Consensus 61 ~~F~LrC~~C~~~l~l 76 (206)
+.|.|+|.-|+..+-+
T Consensus 28 aDikikC~gCg~~iml 43 (57)
T PF06107_consen 28 ADIKIKCLGCGRQIML 43 (57)
T ss_pred CcEEEEECCCCCEEEE
Confidence 4689999999986543
No 18
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=23.31 E-value=51 Score=30.40 Aligned_cols=25 Identities=36% Similarity=0.488 Sum_probs=21.4
Q ss_pred hHHHhhhcCCCCccchHHHHHHHHH
Q 028661 100 NQDYCSWIQDPEKWGGAIELSILAD 124 (206)
Q Consensus 100 ~~eYc~~I~~~~~WGG~iEL~aLs~ 124 (206)
+++|..||..=-..+|+.||.||+.
T Consensus 316 I~~~v~~iapv~v~PGE~EleALA~ 340 (358)
T COG3426 316 IEDRVSWIAPVIVYPGEDELEALAE 340 (358)
T ss_pred HHHHHhhhcceEecCCchHHHHHHh
Confidence 5778888888888899999999975
No 19
>PRK05111 acetylornithine deacetylase; Provisional
Probab=22.65 E-value=88 Score=27.98 Aligned_cols=13 Identities=31% Similarity=0.669 Sum_probs=9.7
Q ss_pred Eeecccccceeeec
Q 028661 2 LIYDGLHYDALAIS 15 (206)
Q Consensus 2 liYsGIHYD~l~l~ 15 (206)
|++.| |||+++..
T Consensus 74 il~~~-H~Dvvp~~ 86 (383)
T PRK05111 74 LLLAG-HTDTVPFD 86 (383)
T ss_pred EEEEe-eeceecCC
Confidence 45666 99999764
No 20
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=20.63 E-value=70 Score=16.82 Aligned_cols=19 Identities=5% Similarity=0.179 Sum_probs=12.9
Q ss_pred eeeeccccchhHHHHHHHH
Q 028661 66 CYGVCQIGVIGQKAIAATV 84 (206)
Q Consensus 66 rC~~C~~~l~lR~~vA~~I 84 (206)
+|..|++.+.-+......+
T Consensus 2 ~C~~C~~~f~~~~~l~~H~ 20 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHM 20 (23)
T ss_dssp EETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHH
Confidence 6889998877666544433
No 21
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=20.54 E-value=38 Score=23.09 Aligned_cols=25 Identities=12% Similarity=0.062 Sum_probs=17.0
Q ss_pred cCcccccccceeeeeeccccchhHHH
Q 028661 54 KKTYTDTANFTLCYGVCQIGVIGQKA 79 (206)
Q Consensus 54 ~~~~Tdt~~F~LrC~~C~~~l~lR~~ 79 (206)
-=||+.+ +..++|..|+..+...+.
T Consensus 25 Gfyy~~~-~d~v~C~~C~~~~~~w~~ 49 (69)
T cd00022 25 GFYYTGR-GDEVKCFFCGLELKNWEP 49 (69)
T ss_pred CCeEcCC-CCEEEeCCCCCCccCCCC
Confidence 3344433 678999999988765543
Done!