Query 030263
Match_columns 180
No_of_seqs 221 out of 446
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 11:04:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030263.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030263hhsearch_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 1.1E-30 2.3E-35 221.7 4.1 106 74-179 139-263 (307)
2 KOG3288 OTU-like cysteine prot 99.9 4.3E-24 9.3E-29 181.6 5.3 86 1-93 219-304 (307)
3 KOG2606 OTU (ovarian tumor)-li 99.6 2.8E-15 6E-20 129.9 5.2 70 75-145 191-269 (302)
4 COG5539 Predicted cysteine pro 99.4 4.6E-14 1E-18 122.1 1.6 72 74-145 138-210 (306)
5 COG5539 Predicted cysteine pro 99.0 1.1E-10 2.5E-15 101.2 2.5 85 2-93 219-303 (306)
6 PF02338 OTU: OTU-like cystein 99.0 4.7E-10 1E-14 84.0 3.4 63 74-143 27-90 (121)
7 PF10275 Peptidase_C65: Peptid 97.0 0.002 4.3E-08 54.4 6.2 65 74-138 140-208 (244)
8 KOG3991 Uncharacterized conser 95.7 0.016 3.6E-07 49.5 4.5 71 75-145 158-230 (256)
9 KOG2605 OTU (ovarian tumor)-li 80.3 2 4.4E-05 39.2 3.7 51 75-126 247-297 (371)
10 PF01188 MR_MLE: Mandelate rac 40.7 28 0.0006 23.2 2.4 32 100-132 35-66 (67)
11 PHA00616 hypothetical protein 35.1 26 0.00057 22.5 1.5 30 66-96 3-32 (44)
12 TIGR02934 nifT_nitrog probable 33.0 12 0.00025 26.3 -0.4 22 98-119 20-41 (67)
13 KOG2586 Pyridoxamine-phosphate 32.4 31 0.00067 29.4 1.9 37 70-116 153-189 (228)
14 PRK05111 acetylornithine deace 30.2 55 0.0012 28.5 3.2 13 2-15 74-86 (383)
15 PRK13007 succinyl-diaminopimel 29.7 99 0.0021 26.5 4.7 48 2-52 64-111 (352)
16 PF06679 DUF1180: Protein of u 29.6 44 0.00096 27.2 2.3 21 146-166 141-161 (163)
17 PF06988 NifT: NifT/FixU prote 28.7 2.7 5.8E-05 29.2 -4.2 22 98-119 20-41 (64)
18 PRK13009 succinyl-diaminopimel 27.8 3.3E+02 0.0072 23.5 7.7 13 2-15 61-73 (375)
19 cd00022 BIR Baculoviral inhibi 27.1 28 0.00061 23.2 0.7 28 54-82 25-52 (69)
20 cd00814 MetRS_core catalytic c 26.8 1.5E+02 0.0033 25.7 5.4 31 42-72 99-129 (319)
21 PF07967 zf-C3HC: C3HC zinc fi 25.4 25 0.00055 26.9 0.2 24 54-77 33-56 (133)
22 KOG1247 Methionyl-tRNA synthet 25.4 44 0.00095 31.7 1.7 62 4-75 86-147 (567)
23 TIGR01902 dapE-lys-deAc N-acet 24.9 1.2E+02 0.0027 25.9 4.4 25 2-30 53-77 (336)
24 PF05129 Elf1: Transcription e 24.8 48 0.0011 23.7 1.6 33 60-107 42-74 (81)
25 COG4604 CeuD ABC-type enteroch 24.6 63 0.0014 27.9 2.4 28 116-143 223-250 (252)
26 PRK06915 acetylornithine deace 24.1 1.2E+02 0.0027 26.9 4.4 13 2-15 96-108 (422)
27 PF05415 Peptidase_C36: Beet n 23.6 72 0.0016 23.9 2.3 32 99-133 35-68 (104)
28 TIGR01246 dapE_proteo succinyl 23.5 4.4E+02 0.0096 22.7 7.7 13 2-15 58-70 (370)
29 COG3426 Butyrate kinase [Energ 22.2 59 0.0013 29.4 1.9 25 100-124 316-340 (358)
30 smart00238 BIR Baculoviral inh 21.7 42 0.00091 22.4 0.7 32 53-85 26-57 (71)
31 PRK12301 bssS biofilm formatio 21.1 74 0.0016 23.2 1.9 36 9-53 24-66 (84)
32 COG5554 NifU Nitrogen fixation 20.8 16 0.00035 25.3 -1.5 21 98-118 19-39 (69)
33 PRK10963 hypothetical protein; 20.7 87 0.0019 26.1 2.5 37 77-119 5-41 (223)
34 cd02426 Pol_gamma_b_Cterm C-te 20.7 1.9E+02 0.004 22.0 4.2 31 24-56 28-58 (128)
35 PF00096 zf-C2H2: Zinc finger, 20.0 95 0.0021 15.9 1.8 17 66-82 2-18 (23)
No 1
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=1.1e-30 Score=221.74 Aligned_cols=106 Identities=44% Similarity=0.728 Sum_probs=94.6
Q ss_pred cchhHHHHHHHHhccccccccccCCChHHHHHhcCCCCCcccHHHHHHHHhHhCceEEEEEcCCCceeeeec--------
Q 030263 74 VIGQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLYGQ-------- 145 (180)
Q Consensus 74 l~lr~~vA~~I~~~p~~y~~~~L~~~~~eYc~~I~~~~~WGG~IEL~iLS~~~~~~I~v~d~~~~~~~~fge-------- 145 (180)
.+||+++|+.+++||+.||+|+|||++.|||.||++.++|||+|||+|||++|+++|+|+|++++|+++|||
T Consensus 139 ~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiqt~rid~fged~~~~~rv 218 (307)
T KOG3288|consen 139 YELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQTVRIDRFGEDKNFDNRV 218 (307)
T ss_pred HHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccccccCceEEeeeehhhhceeEEEEecceeeehhcCCCCCCCceE
Confidence 479999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -----------ccCCCCCCCCCCeeeeeCCCCCChhHHHHHHhhh
Q 030263 146 -----------ISAFEGAPVEFDQSSVPVRKDRTIGPAEELAFET 179 (180)
Q Consensus 146 -----------~~~~~~~~~~~d~t~f~~~d~~~~~~~l~~a~~l 179 (180)
+....-.|.+.|.|+||.+|+.++..++++|.+|
T Consensus 219 ~llydGIHYD~l~m~~~~~~~~~~tifp~~dd~v~~~alqLa~~~ 263 (307)
T KOG3288|consen 219 LLLYDGIHYDPLAMNEFKPTDVDNTIFPVSDDTVLTQALQLASEL 263 (307)
T ss_pred EEEecccccChhhhccCCccCCcccccccccchHHHHHHHHHHHH
Confidence 1111225678899999999987777788877764
No 2
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=4.3e-24 Score=181.59 Aligned_cols=86 Identities=47% Similarity=0.746 Sum_probs=77.1
Q ss_pred CeeecccccceeeccCCCCCCCCCCeeeeeCCCCCccchHHHHHHHHHHHHHhcCCCcccccceeeecccccccchhHHH
Q 030263 1 MLIYDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIGQKAI 80 (180)
Q Consensus 1 ~liYsGIHYD~l~l~~~~~~~~~~d~t~F~~~d~~~l~~~~~~A~~L~~~lk~~~~~Tdt~~F~l~C~~C~~~l~lr~~v 80 (180)
+|||||||||+|++++. .|.+.|-|+||.+|+.+ +..|++||+++|++||||||++|+|||++|+.++.|++.+
T Consensus 219 ~llydGIHYD~l~m~~~--~~~~~~~tifp~~dd~v----~~~alqLa~~~k~~r~ytdt~~ftlRC~~Cq~glvGq~ea 292 (307)
T KOG3288|consen 219 LLLYDGIHYDPLAMNEF--KPTDVDNTIFPVSDDTV----LTQALQLASELKRTRYYTDTAKFTLRCMVCQMGLVGQKEA 292 (307)
T ss_pred EEEecccccChhhhccC--CccCCcccccccccchH----HHHHHHHHHHHHhcceeccccceEEEeeecccceeeHHHH
Confidence 58999999999999976 56778999999999755 4899999999999999999999999999999999999755
Q ss_pred HHHHHhccccccc
Q 030263 81 AATVASDTVKHSE 93 (180)
Q Consensus 81 A~~I~~~p~~y~~ 93 (180)
+ .|+..++|-|-
T Consensus 293 ~-eHA~~TGH~nF 304 (307)
T KOG3288|consen 293 A-EHAKATGHVNF 304 (307)
T ss_pred H-HHHHhcCCCcc
Confidence 5 49999999763
No 3
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.56 E-value=2.8e-15 Score=129.85 Aligned_cols=70 Identities=20% Similarity=0.349 Sum_probs=64.5
Q ss_pred chhHHHHHHHHhccccccccccC------C---ChHHHHHhcCCCCCcccHHHHHHHHhHhCceEEEEEcCCCceeeeec
Q 030263 75 IGQKAIAATVASDTVKHSEAFIG------K---SNQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLYGQ 145 (180)
Q Consensus 75 ~lr~~vA~~I~~~p~~y~~~~L~------~---~~~eYc~~I~~~~~WGG~IEL~iLS~~~~~~I~v~d~~~~~~~~fge 145 (180)
.||...|+|+++|-++|-|+++. . ++++||+.|++|..|||+|||.|||+.|++||.||+.. +.+..|||
T Consensus 191 kLR~~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~-~p~~~~ge 269 (302)
T KOG2606|consen 191 KLREETADYMREHVEDFLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQAD-GPILEYGE 269 (302)
T ss_pred HHHHHHHHHHHHHHHHhhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecC-CCceeech
Confidence 79999999999999999997763 2 39999999999999999999999999999999999975 66999997
No 4
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=99.41 E-value=4.6e-14 Score=122.11 Aligned_cols=72 Identities=24% Similarity=0.399 Sum_probs=70.1
Q ss_pred cchhHHHHHHHHhccccccccccCCChHHHHHhcCCCCCcc-cHHHHHHHHhHhCceEEEEEcCCCceeeeec
Q 030263 74 VIGQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWG-GAIELSILADYYGSEIAAYDIQTTRCDLYGQ 145 (180)
Q Consensus 74 l~lr~~vA~~I~~~p~~y~~~~L~~~~~eYc~~I~~~~~WG-G~IEL~iLS~~~~~~I~v~d~~~~~~~~fge 145 (180)
-+||.+++..+.++|+.|++++++.|.-+||.||.++++|| |.||+.|||+.|+++|+|+|+..++.++||+
T Consensus 138 ~~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~ 210 (306)
T COG5539 138 AKLREVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNS 210 (306)
T ss_pred HHHHHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccC
Confidence 47999999999999999999999999999999999999999 9999999999999999999999899999998
No 5
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=99.02 E-value=1.1e-10 Score=101.21 Aligned_cols=85 Identities=20% Similarity=0.310 Sum_probs=65.6
Q ss_pred eeecccccceeeccCCCCCCCCCCeeeeeCCCCCccchHHHHHHHHHHHHHhcCCCcccccceeeecccccccchhHHHH
Q 030263 2 LIYDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVIGQKAIA 81 (180)
Q Consensus 2 liYsGIHYD~l~l~~~~~~~~~~d~t~F~~~d~~~l~~~~~~A~~L~~~lk~~~~~Tdt~~F~l~C~~C~~~l~lr~~vA 81 (180)
++|+|||||..++...+- ...++.-.|+.++- +.-.+++||+-|+..+|+|||+++.++|+.||.+++|.+.+.
T Consensus 219 i~f~g~hfD~~t~~m~~~-dt~~ne~~~~a~~g-----~~~ei~qLas~lk~~~~~~nT~~~~ik~n~c~~~~~~e~~~~ 292 (306)
T COG5539 219 ILFTGIHFDEETLAMVLW-DTYVNEVLFDASDG-----ITIEIQQLASLLKNPHYYTNTASPSIKCNICGTGFVGEKDYY 292 (306)
T ss_pred hhhcccccchhhhhcchH-HHHHhhhccccccc-----chHHHHHHHHHhcCceEEeecCCceEEeeccccccchhhHHH
Confidence 479999999998653220 11123344444443 236899999999999999999999999999999999997555
Q ss_pred HHHHhccccccc
Q 030263 82 ATVASDTVKHSE 93 (180)
Q Consensus 82 ~~I~~~p~~y~~ 93 (180)
+ |+--+||||-
T Consensus 293 ~-Ha~a~GH~n~ 303 (306)
T COG5539 293 A-HALATGHYNF 303 (306)
T ss_pred H-HHHhhcCccc
Confidence 5 9999999985
No 6
>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=98.96 E-value=4.7e-10 Score=83.98 Aligned_cols=63 Identities=25% Similarity=0.392 Sum_probs=55.9
Q ss_pred cchhHHHHHHHH-hccccccccccCCChHHHHHhcCCCCCcccHHHHHHHHhHhCceEEEEEcCCCceeee
Q 030263 74 VIGQKAIAATVA-SDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLY 143 (180)
Q Consensus 74 l~lr~~vA~~I~-~~p~~y~~~~L~~~~~eYc~~I~~~~~WGG~IEL~iLS~~~~~~I~v~d~~~~~~~~f 143 (180)
.++|+.++++++ .+++.|.+++.+. +++++..|||++||.|||+.|+++|.|++..+++...+
T Consensus 27 ~~lR~~~~~~l~~~~~~~~~~~~~~~-------~~~~~~~Wg~~~el~a~a~~~~~~I~v~~~~~~~~~~~ 90 (121)
T PF02338_consen 27 QELRKAVVDYLRDKNRDKFEEFLEGD-------KMSKPGTWGGEIELQALANVLNRPIIVYSSSDGDNVVF 90 (121)
T ss_dssp HHHHHHHHHHHHTHTTTHHHHHHHHH-------HHTSTTSHEEHHHHHHHHHHHTSEEEEECETTTBEEEE
T ss_pred HHHHHHHHHHHHHhccchhhhhhhhh-------hhccccccCcHHHHHHHHHHhCCeEEEEEcCCCCccce
Confidence 489999999999 9999999966544 99999999999999999999999999998877765444
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=96.96 E-value=0.002 Score=54.39 Aligned_cols=65 Identities=14% Similarity=0.184 Sum_probs=51.2
Q ss_pred cchhHHHHHHHHhccccccccccC---CChHHHH-HhcCCCCCcccHHHHHHHHhHhCceEEEEEcCCC
Q 030263 74 VIGQKAIAATVASDTVKHSEAFIG---KSNQDYC-SWIQDPEKWGGAIELSILADYYGSEIAAYDIQTT 138 (180)
Q Consensus 74 l~lr~~vA~~I~~~p~~y~~~~L~---~~~~eYc-~~I~~~~~WGG~IEL~iLS~~~~~~I~v~d~~~~ 138 (180)
.-+|-..+.+++.|++.|.+++.| .++++|| +.|+....=.+.|.+.|||++++++|.|+-...+
T Consensus 140 ~flRLlts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~ 208 (244)
T PF10275_consen 140 IFLRLLTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRS 208 (244)
T ss_dssp HHHHHHHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSS
T ss_pred HHHHHHHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCC
Confidence 368888999999999999996666 8899999 6777777788999999999999999999877643
No 8
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.67 E-value=0.016 Score=49.53 Aligned_cols=71 Identities=11% Similarity=0.085 Sum_probs=57.7
Q ss_pred chhHHHHHHHHhccccccccccC-CChHHHHHh-cCCCCCcccHHHHHHHHhHhCceEEEEEcCCCceeeeec
Q 030263 75 IGQKAIAATVASDTVKHSEAFIG-KSNQDYCSW-IQDPEKWGGAIELSILADYYGSEIAAYDIQTTRCDLYGQ 145 (180)
Q Consensus 75 ~lr~~vA~~I~~~p~~y~~~~L~-~~~~eYc~~-I~~~~~WGG~IEL~iLS~~~~~~I~v~d~~~~~~~~fge 145 (180)
-+|-..+..++++++.|-|++=| +++++||.. ++--..=-+.|+|-|||+++++.|.|..+.-+.....|.
T Consensus 158 ylRLvtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~h 230 (256)
T KOG3991|consen 158 YLRLVTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNH 230 (256)
T ss_pred HHHHHHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCC
Confidence 58888999999999999996665 899999975 444444578999999999999999999876555555553
No 9
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=80.34 E-value=2 Score=39.17 Aligned_cols=51 Identities=14% Similarity=0.194 Sum_probs=45.4
Q ss_pred chhHHHHHHHHhccccccccccCCChHHHHHhcCCCCCcccHHHHHHHHhHh
Q 030263 75 IGQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIELSILADYY 126 (180)
Q Consensus 75 ~lr~~vA~~I~~~p~~y~~~~L~~~~~eYc~~I~~~~~WGG~IEL~iLS~~~ 126 (180)
.-|+++.++...+.++|+. +.-+.+..|.+.-+....||-.||+++.|..+
T Consensus 247 ~~~~~~~dq~~~e~~~~~~-~vt~~~~~y~k~kr~~~~~gnhie~Qa~a~~~ 297 (371)
T KOG2605|consen 247 HNRRECVDQLKKERDFYED-YVTEDFTSYIKRKRADGEPGNHIEQQAAADIY 297 (371)
T ss_pred HHHHHHHHHHhhccccccc-ccccchhhcccccccCCCCcchHHHhhhhhhh
Confidence 5677888989889999988 66789999999999999999999999999733
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=40.67 E-value=28 Score=23.24 Aligned_cols=32 Identities=31% Similarity=0.401 Sum_probs=24.7
Q ss_pred hHHHHHhcCCCCCcccHHHHHHHHhHhCceEEE
Q 030263 100 NQDYCSWIQDPEKWGGAIELSILADYYGSEIAA 132 (180)
Q Consensus 100 ~~eYc~~I~~~~~WGG~IEL~iLS~~~~~~I~v 132 (180)
.++| .||+.|-....--++..|++...+||++
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 7888777777778888999999999974
No 11
>PHA00616 hypothetical protein
Probab=35.05 E-value=26 Score=22.52 Aligned_cols=30 Identities=10% Similarity=-0.037 Sum_probs=22.8
Q ss_pred eecccccccchhHHHHHHHHhcccccccccc
Q 030263 66 CYGVCQIGVIGQKAIAATVASDTVKHSEAFI 96 (180)
Q Consensus 66 ~C~~C~~~l~lr~~vA~~I~~~p~~y~~~~L 96 (180)
+|.-||..+.-.+....-++.++++ +++.+
T Consensus 3 qC~~CG~~F~~~s~l~~H~r~~hg~-~~~~~ 32 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHLLSVHKQ-NKLTL 32 (44)
T ss_pred ccchhhHHHhhHHHHHHHHHHhcCC-Cccce
Confidence 6999999987777777778888777 55443
No 12
>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=33.02 E-value=12 Score=26.29 Aligned_cols=22 Identities=27% Similarity=0.542 Sum_probs=17.9
Q ss_pred CChHHHHHhcCCCCCcccHHHH
Q 030263 98 KSNQDYCSWIQDPEKWGGAIEL 119 (180)
Q Consensus 98 ~~~~eYc~~I~~~~~WGG~IEL 119 (180)
++.+|=+-.++++..|||.+-|
T Consensus 20 KDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 20 KDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred CcchhheeeeecCccccCEEEE
Confidence 6788888889999999996533
No 13
>KOG2586 consensus Pyridoxamine-phosphate oxidase [Coenzyme transport and metabolism]
Probab=32.38 E-value=31 Score=29.41 Aligned_cols=37 Identities=16% Similarity=0.265 Sum_probs=21.2
Q ss_pred cccccchhHHHHHHHHhccccccccccCCChHHHHHhcCCCCCcccH
Q 030263 70 CQIGVIGQKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGA 116 (180)
Q Consensus 70 C~~~l~lr~~vA~~I~~~p~~y~~~~L~~~~~eYc~~I~~~~~WGG~ 116 (180)
|+.....|..-+..-.+.+++|-.. +-|..|++|||-
T Consensus 153 qs~vI~~re~l~k~~e~l~~~~~~~----------~~IpkP~swgg~ 189 (228)
T KOG2586|consen 153 QSEVIPDREELEKKDEELTELFGDE----------QSIPKPDSWGGY 189 (228)
T ss_pred CCCccCCHHHHHHHHHHHHHHhccc----------ccccCCCcccce
Confidence 3334455554444444444444431 468889999993
No 14
>PRK05111 acetylornithine deacetylase; Provisional
Probab=30.16 E-value=55 Score=28.52 Aligned_cols=13 Identities=31% Similarity=0.669 Sum_probs=9.7
Q ss_pred eeecccccceeecc
Q 030263 2 LIYDGLHYDALAIS 15 (180)
Q Consensus 2 liYsGIHYD~l~l~ 15 (180)
|++.| |||+++..
T Consensus 74 il~~~-H~Dvvp~~ 86 (383)
T PRK05111 74 LLLAG-HTDTVPFD 86 (383)
T ss_pred EEEEe-eeceecCC
Confidence 45666 99999764
No 15
>PRK13007 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=29.71 E-value=99 Score=26.53 Aligned_cols=48 Identities=10% Similarity=0.221 Sum_probs=24.4
Q ss_pred eeecccccceeeccCCCCCCCCCCeeeeeCCCCCccchHHHHHHHHHHHHH
Q 030263 2 LIYDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQ 52 (180)
Q Consensus 2 liYsGIHYD~l~l~~~~~~~~~~d~t~F~~~d~~~l~~~~~~A~~L~~~lk 52 (180)
|+++| |||+++... +-.+...|-.++-..-.+. ...+..++.+++.++
T Consensus 64 i~l~~-H~Dtvp~~~-~~~~~~~~g~i~GrG~~D~-Kg~~a~~l~a~~~l~ 111 (352)
T PRK13007 64 VVLAG-HLDTVPVAD-NLPSRREGDRLYGCGASDM-KSGLAVMLHLAATLA 111 (352)
T ss_pred EEEEc-cccccCCCC-CCCcceeCCEEEccCcccc-cHHHHHHHHHHHHhh
Confidence 56777 999998652 1112233556775322111 122345555555563
No 16
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=29.59 E-value=44 Score=27.16 Aligned_cols=21 Identities=10% Similarity=0.156 Sum_probs=16.1
Q ss_pred ccCCCCCCCCCCeeeeeCCCC
Q 030263 146 ISAFEGAPVEFDQSSVPVRKD 166 (180)
Q Consensus 146 ~~~~~~~~~~~d~t~f~~~d~ 166 (180)
+.|.....+|+|.|||+.+-.
T Consensus 141 m~pL~~ddedeD~TvFd~~~~ 161 (163)
T PF06679_consen 141 MAPLEEDDEDEDSTVFDANHP 161 (163)
T ss_pred ecccCCCccccccceeeeccc
Confidence 667766677889999987653
No 17
>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=28.73 E-value=2.7 Score=29.25 Aligned_cols=22 Identities=32% Similarity=0.696 Sum_probs=15.9
Q ss_pred CChHHHHHhcCCCCCcccHHHH
Q 030263 98 KSNQDYCSWIQDPEKWGGAIEL 119 (180)
Q Consensus 98 ~~~~eYc~~I~~~~~WGG~IEL 119 (180)
++.+|=+-.++++..|||.+.|
T Consensus 20 KDLEE~Vv~~E~~~~wGG~v~L 41 (64)
T PF06988_consen 20 KDLEEPVVSMEKPELWGGEVTL 41 (64)
T ss_dssp TTEEEEEEEESSSSS-SSEEEE
T ss_pred CccccceeeeeccCccCCEEEE
Confidence 5666666778899999997655
No 18
>PRK13009 succinyl-diaminopimelate desuccinylase; Reviewed
Probab=27.79 E-value=3.3e+02 Score=23.47 Aligned_cols=13 Identities=31% Similarity=0.593 Sum_probs=9.4
Q ss_pred eeecccccceeecc
Q 030263 2 LIYDGLHYDALAIS 15 (180)
Q Consensus 2 liYsGIHYD~l~l~ 15 (180)
|++.| |+|+++..
T Consensus 61 i~l~~-H~D~Vp~g 73 (375)
T PRK13009 61 LCFAG-HTDVVPPG 73 (375)
T ss_pred EEEEe-ecccCCCC
Confidence 45666 99999653
No 19
>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=27.05 E-value=28 Score=23.15 Aligned_cols=28 Identities=11% Similarity=-0.005 Sum_probs=18.1
Q ss_pred cCCCcccccceeeecccccccchhHHHHH
Q 030263 54 KKTYTDTANFTLCYGVCQIGVIGQKAIAA 82 (180)
Q Consensus 54 ~~~~Tdt~~F~l~C~~C~~~l~lr~~vA~ 82 (180)
-=||+.+ +..++|..|+..+...+...+
T Consensus 25 Gfyy~~~-~d~v~C~~C~~~~~~w~~~d~ 52 (69)
T cd00022 25 GFYYTGR-GDEVKCFFCGLELKNWEPGDD 52 (69)
T ss_pred CCeEcCC-CCEEEeCCCCCCccCCCCCCC
Confidence 3344433 567999999988876543333
No 20
>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.
Probab=26.83 E-value=1.5e+02 Score=25.69 Aligned_cols=31 Identities=10% Similarity=0.096 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhcCCCcccccceeeeccccc
Q 030263 42 DLALKLVKEQQRKKTYTDTANFTLCYGVCQI 72 (180)
Q Consensus 42 ~~A~~L~~~lk~~~~~Tdt~~F~l~C~~C~~ 72 (180)
..+.++.++|+++++..-...=..-|..|+.
T Consensus 99 ~~v~~i~~~L~ekG~iY~~~~~~~yc~~~~~ 129 (319)
T cd00814 99 EIVQEFFKKLYENGYIYEGEYEGLYCVSCER 129 (319)
T ss_pred HHHHHHHHHHHHCCCEEeeeeeeeECCCCCc
Confidence 5678889999999886433333446777764
No 21
>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=25.44 E-value=25 Score=26.88 Aligned_cols=24 Identities=8% Similarity=0.112 Sum_probs=21.3
Q ss_pred cCCCcccccceeeecccccccchh
Q 030263 54 KKTYTDTANFTLCYGVCQIGVIGQ 77 (180)
Q Consensus 54 ~~~~Tdt~~F~l~C~~C~~~l~lr 77 (180)
++-.++++..+++|-.|+..+...
T Consensus 33 ~~GW~~~~~d~l~C~~C~~~l~~~ 56 (133)
T PF07967_consen 33 RRGWICVSKDMLKCESCGARLCVK 56 (133)
T ss_pred HcCCCcCCCCEEEeCCCCCEEEEe
Confidence 588999999999999999887666
No 22
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.39 E-value=44 Score=31.67 Aligned_cols=62 Identities=16% Similarity=0.210 Sum_probs=39.0
Q ss_pred ecccccceeeccCCCCCCCCCCeeeeeCCCCCccchHHHHHHHHHHHHHhcCCCcccccceeeecccccccc
Q 030263 4 YDGLHYDALAISPFEGAPEEFDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKTYTDTANFTLCYGVCQIGVI 75 (180)
Q Consensus 4 YsGIHYD~l~l~~~~~~~~~~d~t~F~~~d~~~l~~~~~~A~~L~~~lk~~~~~Tdt~~F~l~C~~C~~~l~ 75 (180)
|.||||++--.-- -++|.--+-+.+..+ ..++.+-.++.+++|+.-.+-=.+.|.+|+.-|.
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 7899998764421 122322222333332 4677777888888888777777788888876543
No 23
>TIGR01902 dapE-lys-deAc N-acetyl-ornithine/N-acetyl-lysine deacetylase. This clade of mainly archaeal and related bacterial species contains two characterized enzymes, an deacetylase with specificity for both N-acetyl-ornithine and N-acetyl-lysine from Thermus which is found within a lysine biosynthesis operon, and a fusion protein with acetyl-glutamate kinase (an enzyme of ornithine biosynthesis) from Lactobacillus. It is possible that all of the sequences within this clade have dual specificity, or that a mix of specificities have evolved within this clade.
Probab=24.92 E-value=1.2e+02 Score=25.95 Aligned_cols=25 Identities=12% Similarity=0.131 Sum_probs=14.5
Q ss_pred eeecccccceeeccCCCCCCCCCCeeeee
Q 030263 2 LIYDGLHYDALAISPFEGAPEEFDQTIFP 30 (180)
Q Consensus 2 liYsGIHYD~l~l~~~~~~~~~~d~t~F~ 30 (180)
|+++| |||+++- .-.+...|-.+|-
T Consensus 53 i~~~~-H~D~vp~---~~~~~~~~g~i~G 77 (336)
T TIGR01902 53 ILLAG-HVDTVPG---YIPVKIEGGLLYG 77 (336)
T ss_pred EEEEc-cccccCC---CcccEEeCCEEEE
Confidence 56777 9999952 1112223457776
No 24
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=24.82 E-value=48 Score=23.66 Aligned_cols=33 Identities=18% Similarity=0.250 Sum_probs=19.8
Q ss_pred cccceeeecccccccchhHHHHHHHHhccccccccccCCChHHHHHhc
Q 030263 60 TANFTLCYGVCQIGVIGQKAIAATVASDTVKHSEAFIGKSNQDYCSWI 107 (180)
Q Consensus 60 t~~F~l~C~~C~~~l~lr~~vA~~I~~~p~~y~~~~L~~~~~eYc~~I 107 (180)
.....+.|..|+...+.+ . --|.+|++-|.+||
T Consensus 42 ~~~~~~~C~~Cg~~~~~~-------------i--~~L~epiDVY~~wi 74 (81)
T PF05129_consen 42 EGIGILSCRVCGESFQTK-------------I--NPLSEPIDVYSEWI 74 (81)
T ss_dssp TTEEEEEESSS--EEEEE-----------------SS--TTHHHHHHH
T ss_pred CCEEEEEecCCCCeEEEc-------------c--CccCcccchhHHHH
Confidence 456678898996544433 1 24668999999998
No 25
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=24.65 E-value=63 Score=27.92 Aligned_cols=28 Identities=25% Similarity=0.468 Sum_probs=23.2
Q ss_pred HHHHHHHHhHhCceEEEEEcCCCceeee
Q 030263 116 AIELSILADYYGSEIAAYDIQTTRCDLY 143 (180)
Q Consensus 116 ~IEL~iLS~~~~~~I~v~d~~~~~~~~f 143 (180)
=|.-.+|++.|+.+|.|.+++++++-.|
T Consensus 223 ii~~~~L~eiydm~i~v~~i~g~kIcvy 250 (252)
T COG4604 223 IIQPEILSEIYDMDIPVEEINGKKICVY 250 (252)
T ss_pred hcCHHHHHHHhcCCceeEEeCCcEEEEE
Confidence 3566799999999999999998876544
No 26
>PRK06915 acetylornithine deacetylase; Validated
Probab=24.11 E-value=1.2e+02 Score=26.88 Aligned_cols=13 Identities=31% Similarity=0.654 Sum_probs=9.9
Q ss_pred eeecccccceeecc
Q 030263 2 LIYDGLHYDALAIS 15 (180)
Q Consensus 2 liYsGIHYD~l~l~ 15 (180)
|+|.| |||+++..
T Consensus 96 l~l~~-H~Dtvp~~ 108 (422)
T PRK06915 96 MILNG-HIDVVPEG 108 (422)
T ss_pred EEEEe-eccccCCC
Confidence 46666 99999764
No 27
>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=23.59 E-value=72 Score=23.85 Aligned_cols=32 Identities=19% Similarity=0.585 Sum_probs=25.5
Q ss_pred ChHHHHHhcCC--CCCcccHHHHHHHHhHhCceEEEE
Q 030263 99 SNQDYCSWIQD--PEKWGGAIELSILADYYGSEIAAY 133 (180)
Q Consensus 99 ~~~eYc~~I~~--~~~WGG~IEL~iLS~~~~~~I~v~ 133 (180)
.++.||.|.++ +..|-- -..+++.+++.|.+=
T Consensus 35 ~i~~y~~W~r~~~~STW~D---C~mFA~~LkVsm~vk 68 (104)
T PF05415_consen 35 TIKKYHTWLRKKRPSTWDD---CRMFADALKVSMQVK 68 (104)
T ss_pred HHHHHHHHHhcCCCCcHHH---HHHHHHhheeEEEEE
Confidence 58899999984 567954 347899999998874
No 28
>TIGR01246 dapE_proteo succinyl-diaminopimelate desuccinylase, proteobacterial clade. This model describes a proteobacterial subset of succinyl-diaminopimelate desuccinylases. An experimentally confirmed Gram-positive lineage succinyl-diaminopimelate desuccinylase has been described for Corynebacterium glutamicum, and a neighbor-joining tree shows the seed members, SP:Q59284, and putative archaeal members such as TrEMBL:O58003 in a single clade. However, the archaeal members differ substantially, share a number of motifs with acetylornithine deacetylases rather than succinyl-diaminopimelate desuccinylases, and are not taken as trusted examples of succinyl-diaminopimelate desuccinylases. This model is limited to proteobacterial members for this reason.
Probab=23.47 E-value=4.4e+02 Score=22.73 Aligned_cols=13 Identities=31% Similarity=0.647 Sum_probs=10.0
Q ss_pred eeecccccceeecc
Q 030263 2 LIYDGLHYDALAIS 15 (180)
Q Consensus 2 liYsGIHYD~l~l~ 15 (180)
|++.| |+|+++..
T Consensus 58 i~~~~-H~DtVp~~ 70 (370)
T TIGR01246 58 LAFAG-HTDVVPAG 70 (370)
T ss_pred EEEEc-cccccCCC
Confidence 56667 99999764
No 29
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=22.20 E-value=59 Score=29.35 Aligned_cols=25 Identities=36% Similarity=0.488 Sum_probs=20.9
Q ss_pred hHHHHHhcCCCCCcccHHHHHHHHh
Q 030263 100 NQDYCSWIQDPEKWGGAIELSILAD 124 (180)
Q Consensus 100 ~~eYc~~I~~~~~WGG~IEL~iLS~ 124 (180)
..+|.+||..---..|+.||.+|+.
T Consensus 316 I~~~v~~iapv~v~PGE~EleALA~ 340 (358)
T COG3426 316 IEDRVSWIAPVIVYPGEDELEALAE 340 (358)
T ss_pred HHHHHhhhcceEecCCchHHHHHHh
Confidence 6677777777777899999999986
No 30
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=21.75 E-value=42 Score=22.42 Aligned_cols=32 Identities=9% Similarity=-0.127 Sum_probs=20.0
Q ss_pred hcCCCcccccceeeecccccccchhHHHHHHHH
Q 030263 53 RKKTYTDTANFTLCYGVCQIGVIGQKAIAATVA 85 (180)
Q Consensus 53 ~~~~~Tdt~~F~l~C~~C~~~l~lr~~vA~~I~ 85 (180)
.-=|||.+ +-.++|..|+..+......-+...
T Consensus 26 ~Gfyy~~~-~d~v~C~~C~~~l~~w~~~d~p~~ 57 (71)
T smart00238 26 AGFYYTGV-GDEVKCFFCGGELDNWEPGDDPWE 57 (71)
T ss_pred cCCeECCC-CCEEEeCCCCCCcCCCCCCCCHHH
Confidence 33445544 667999999988876643333333
No 31
>PRK12301 bssS biofilm formation regulatory protein BssS; Reviewed
Probab=21.11 E-value=74 Score=23.19 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=20.0
Q ss_pred cceeecc----CCCCCCCC---CCeeeeeCCCCCccchHHHHHHHHHHHHHh
Q 030263 9 YDALAIS----PFEGAPEE---FDQTIFPVQKGRTIGPAEDLALKLVKEQQR 53 (180)
Q Consensus 9 YD~l~l~----~~~~~~~~---~d~t~F~~~d~~~l~~~~~~A~~L~~~lk~ 53 (180)
|||+.+. ++++-|++ .|+|.|=+.| .|++|...|++
T Consensus 24 YDAmmirlhyLss~~Q~~e~A~v~~tlwLTtd---------vArqlI~iLea 66 (84)
T PRK12301 24 YDALMLRLHYQSPNDQEPEGAEVGQTLWLTTD---------VARQFISILEA 66 (84)
T ss_pred HhhHHHhhhhcCCCCCCcccccccceEEecHH---------HHHHHHHHHHH
Confidence 7888764 23333332 5778775543 45666665543
No 32
>COG5554 NifU Nitrogen fixation protein [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.77 E-value=16 Score=25.30 Aligned_cols=21 Identities=24% Similarity=0.503 Sum_probs=15.5
Q ss_pred CChHHHHHhcCCCCCcccHHH
Q 030263 98 KSNQDYCSWIQDPEKWGGAIE 118 (180)
Q Consensus 98 ~~~~eYc~~I~~~~~WGG~IE 118 (180)
++.+|=.-.+.+++-|||.|=
T Consensus 19 KDLEEpii~V~nedlwGG~il 39 (69)
T COG5554 19 KDLEEPIIVVKNEDLWGGKIL 39 (69)
T ss_pred cccccceEEEeccccccceEE
Confidence 556666667788899999763
No 33
>PRK10963 hypothetical protein; Provisional
Probab=20.73 E-value=87 Score=26.14 Aligned_cols=37 Identities=14% Similarity=0.205 Sum_probs=29.4
Q ss_pred hHHHHHHHHhccccccccccCCChHHHHHhcCCCCCcccHHHH
Q 030263 77 QKAIAATVASDTVKHSEAFIGKSNQDYCSWIQDPEKWGGAIEL 119 (180)
Q Consensus 77 r~~vA~~I~~~p~~y~~~~L~~~~~eYc~~I~~~~~WGG~IEL 119 (180)
.+.+|+|.+.||+-|.. ..+-...|+=|..+||+|=|
T Consensus 5 ~~~V~~yL~~~PdFf~~------h~~Ll~~L~lph~~~gaVSL 41 (223)
T PRK10963 5 DRAVVDYLLQNPDFFIR------NARLVEQMRVPHPVRGTVSL 41 (223)
T ss_pred HHHHHHHHHHCchHHhh------CHHHHHhccCCCCCCCeecH
Confidence 45799999999998765 45667789989889997643
No 34
>cd02426 Pol_gamma_b_Cterm C-terminal domain of mitochondrial DNA polymerase gamma B subunit, which is required for processivity. Polymerase gamma replicates and repairs mitochondrial DNA. The c-terminal domain of its B subunit is strikingly similar to the anticodon-binding domain of glycyl tRNA synthetase.
Probab=20.67 E-value=1.9e+02 Score=22.02 Aligned_cols=31 Identities=16% Similarity=0.088 Sum_probs=24.1
Q ss_pred CCeeeeeCCCCCccchHHHHHHHHHHHHHhcCC
Q 030263 24 FDQTIFPVQKGRTIGPAEDLALKLVKEQQRKKT 56 (180)
Q Consensus 24 ~d~t~F~~~d~~~l~~~~~~A~~L~~~lk~~~~ 56 (180)
++..|+|++... +.+.+.|.+|.++|++++.
T Consensus 28 ~qV~Iipi~~~~--~~~~~~a~~l~~~L~~~gi 58 (128)
T cd02426 28 YKVAIDCGKGDT--AELRDLCQGLKNELREAGL 58 (128)
T ss_pred eEEEEEeccCCh--HHHHHHHHHHHHHHHHcCC
Confidence 678899985432 5677899999999988763
No 35
>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=20.01 E-value=95 Score=15.87 Aligned_cols=17 Identities=6% Similarity=0.174 Sum_probs=12.0
Q ss_pred eecccccccchhHHHHH
Q 030263 66 CYGVCQIGVIGQKAIAA 82 (180)
Q Consensus 66 ~C~~C~~~l~lr~~vA~ 82 (180)
+|..|+..+.-+.....
T Consensus 2 ~C~~C~~~f~~~~~l~~ 18 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKR 18 (23)
T ss_dssp EETTTTEEESSHHHHHH
T ss_pred CCCCCCCccCCHHHHHH
Confidence 58899988776654444
Done!