Query 038992
Match_columns 286
No_of_seqs 132 out of 753
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 05:17:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038992.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038992hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0829 UreH Urease accessory 100.0 3E-50 6.5E-55 363.1 25.6 233 14-278 2-261 (269)
2 PF01774 UreD: UreD urease acc 100.0 4.8E-44 1E-48 315.4 23.1 182 61-269 1-209 (209)
3 PF04314 DUF461: Protein of un 58.2 22 0.00048 27.8 4.8 36 57-92 75-110 (110)
4 COG2996 Predicted RNA-bindinin 48.7 60 0.0013 30.0 6.5 85 72-157 116-204 (287)
5 COG2847 Copper(I)-binding prot 36.1 95 0.0021 26.1 5.4 36 57-92 102-137 (151)
6 TIGR00013 taut 4-oxalocrotonat 23.1 2.2E+02 0.0047 19.2 4.7 32 253-284 3-36 (63)
7 PF11604 CusF_Ec: Copper bindi 22.1 1.4E+02 0.0029 21.4 3.5 25 69-93 41-65 (70)
8 PF10610 Tafi-CsgC: Thin aggre 18.8 1E+02 0.0022 24.3 2.3 24 71-94 75-98 (106)
9 PF11012 DUF2850: Protein of u 18.1 4.2E+02 0.0092 19.7 6.0 47 59-106 15-61 (79)
10 PF04328 DUF466: Protein of un 16.7 1.1E+02 0.0023 21.9 1.9 24 263-286 3-26 (65)
No 1
>COG0829 UreH Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3e-50 Score=363.14 Aligned_cols=233 Identities=25% Similarity=0.378 Sum_probs=199.6
Q ss_pred cccccceeEEEEEEEeCCeeEEeeeeeeccEEEeccccCCCCCCCcEEEEEeccCcceecCcEEEEEEEEcCCcEEEEeC
Q 038992 14 ESKIEAATGKLVVKKVGGKSTVTRCFSKYPLKFIIPNKVGSSETDAVWVYTLTYGGGIVSGDSISCEITVADACTAVLTT 93 (286)
Q Consensus 14 ~~~~~~~~g~L~~~~~~g~T~l~~~~~~~Plkl~~p~~~~~~~~~~~~v~ll~~~GGl~~GD~l~i~i~v~~ga~l~ltT 93 (286)
+.+.....++|.|++++|+|++.+++|++||||++|++.+ ++.|++||+|+|||+++||+++++|++++||+++|||
T Consensus 2 ~~~~~~~~L~L~~~~~~g~t~l~~~~~~~plkV~~p~y~~---~~~~~~~li~~~GGv~gGD~l~~di~lg~~a~~~iTT 78 (269)
T COG0829 2 GTKGWNGKLRLRFARRDGRTRLATLFQTGPLKVQRPFYPD---EGLCEAMLIHPSGGVVGGDRLEIDIELGDNAKALITT 78 (269)
T ss_pred CcccccceEEEEEEecCCcEEehhhhccCCeEEEccCcCC---CCCeEEEEEeCCCCccccceEEEEEEECCCceEEEEc
Confidence 4455566777889999999999999999999999997644 5789999999999999999999999999999999999
Q ss_pred cccceeecCCCCCcceeE----------EE----------------EEEEEEcCCceEEEeeeeccCCCCCCCccccceE
Q 038992 94 QASTKVYKSLGSKSSEQI----------LE----------------KQIFRVVLDSSLVIVDWITSGRHESGEKWDFELY 147 (286)
Q Consensus 94 Qsatkvy~~~~~~~s~q~----------le----------------~~~i~L~~~A~ll~~d~i~~GR~a~GE~f~~~~~ 147 (286)
|||||||||.++.+ +|. || .++|+|+++|+|++|||+++||+++||+|+|++|
T Consensus 79 QsatKvYrs~~g~A-~Q~~~i~vg~nA~LewlPq~tI~F~~a~f~q~~~~~L~~sA~l~~~E~~~~GR~~~GE~f~~~~~ 157 (269)
T COG0829 79 QSATKVYRSPGGQA-TQTTNITVGENARLEWLPQETIPFEGARFKQHTRFELASSATLLYWEILALGRVAMGERFAYGRF 157 (269)
T ss_pred cccceeEeCCCCce-EEEEEEEECCCCEEEecCCcceecCCceeEEEEEEEeCCCceehhhhhhhcCcccccchhhhhhh
Confidence 99999999999875 544 22 9999999999999999999999999999999999
Q ss_pred EEEEEEEEcCCEEEEEEeeeeeCCCc-CchhhccCCCcEEEEEEEECCCchhHHHHHHHHHHHHhhhcccCCCCCCCCCC
Q 038992 148 RSTNHIFLEGDQPLFLDSVLLEQGNI-TNIAERMQDYQVIAMVILLGPKLKQIQIQVQENVRRMMSEQLYLPSTGLRPHG 226 (286)
Q Consensus 148 ~s~~~I~~~gg~ll~~D~~~L~~~~~-~~~~~~~~g~~~~gtl~~v~p~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~ 226 (286)
+++|+||.+| +||+.|++.|.|++. ......|+||.|+|++|++++... +.+++++++.+...
T Consensus 158 ~s~~~I~~~~-~lv~~d~~~l~p~~~~l~~~~~~~g~~~~g~~~~~~~~~~---~~~l~~~~~~l~~~------------ 221 (269)
T COG0829 158 RSRWEIYQDG-RLLLLDRLLLDPDEPNLNARGAMAGYHHAGALYLLNEPVD---EALLEKLREALEGY------------ 221 (269)
T ss_pred heeeEEEECC-EEEEEEeEEecCCcccccccccccCceEEEEEEEeccchh---HHHHHHHHHhhhcc------------
Confidence 9999999998 999999999999985 567788999999999999998775 23444444332211
Q ss_pred CccCccccCCCceEEEEeeeccCCcEEEEEEccCCHHHHHHHHHHHHHHhhH
Q 038992 227 KTQSDHFLAKPSFVVSCSAFGPKGIGIVVRIAAMTTESVYRFLQHQLAGMET 278 (286)
Q Consensus 227 ~~~~~~~~~~~~~~~~~s~l~~~~~glvvR~la~~~e~lr~~l~~~~~~lr~ 278 (286)
+ +..++.|.. ..+++++|++|++++.+|+++..+|+.+|.
T Consensus 222 ----~------~~~~~~s~~--~~~~l~~R~la~~~~~lr~~l~~l~~~lr~ 261 (269)
T COG0829 222 ----D------GGASGVSQT--ATSGLLARVLAASTEELRALLEKLWSLLRG 261 (269)
T ss_pred ----C------CcceeeEEc--CCCcEEEEEecCCcHHHHHHHHHHHHHhhc
Confidence 0 112334432 358999999999999999999999999987
No 2
>PF01774 UreD: UreD urease accessory protein; InterPro: IPR002669 UreD is a urease accessory protein. Urease IPR005848 from INTERPRO hydrolyses urea into ammonia and carbamic acid []. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex [] and is required for urease nickel metallocentre assembly []. See also UreF IPR002639 from INTERPRO, UreG IPR004400 from INTERPRO.; GO: 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 3SF5_D.
Probab=100.00 E-value=4.8e-44 Score=315.42 Aligned_cols=182 Identities=32% Similarity=0.519 Sum_probs=126.7
Q ss_pred EEEEeccCcceecCcEEEEEEEEcCCcEEEEeCcccceeecCCCCCcceeE----------EE----------------E
Q 038992 61 WVYTLTYGGGIVSGDSISCEITVADACTAVLTTQASTKVYKSLGSKSSEQI----------LE----------------K 114 (286)
Q Consensus 61 ~v~ll~~~GGl~~GD~l~i~i~v~~ga~l~ltTQsatkvy~~~~~~~s~q~----------le----------------~ 114 (286)
|+||+|+||||++||+++++|+|++||+++|||||||||||++++..++|. || +
T Consensus 1 h~yl~~~~gGl~~GD~l~~~i~v~~ga~~~ltTqaatkvy~~~~~~~a~q~~~~~v~~ga~Le~lP~p~I~f~~A~~~q~ 80 (209)
T PF01774_consen 1 HVYLMNPSGGLLGGDRLRIDITVGPGARLLLTTQAATKVYRMRGGRPARQRIRITVEEGAYLEYLPDPTIPFAGARFRQR 80 (209)
T ss_dssp -EEEEE--S-B-TT-EEEEEEEE-TT-EEEEE----EEE---TTS--EEEEEEEEE-TT-EEEE----EEE-TT-EEEEE
T ss_pred CEEEEeCCCcCcCCCEEEEEEEECCCCEEEEechhhhhhcCCCCCCcEEEEEEEEECCCCEEEEcCCCCEeeCCCEEEEE
Confidence 689999999999999999999999999999999999999999888644554 22 9
Q ss_pred EEEEEcCCceEEEeeeeccCCCCCCCccccceEEEEEEEEEcCCEEEEEEeeeeeCCCc-CchhhccCCCcEEEEEEEEC
Q 038992 115 QIFRVVLDSSLVIVDWITSGRHESGEKWDFELYRSTNHIFLEGDQPLFLDSVLLEQGNI-TNIAERMQDYQVIAMVILLG 193 (286)
Q Consensus 115 ~~i~L~~~A~ll~~d~i~~GR~a~GE~f~~~~~~s~~~I~~~gg~ll~~D~~~L~~~~~-~~~~~~~~g~~~~gtl~~v~ 193 (286)
++|+|+++|+|+++||+++||+++||+|+|++|+++++|+++| +|++.|+++|+|++. ...++.|++|+++||+|+++
T Consensus 81 ~~v~l~~~A~l~~~e~i~~GR~a~GE~f~~~~~~~~~~I~~~g-~ll~~d~~~l~p~~~~~~~~~~~~g~~~~~tl~~~~ 159 (209)
T PF01774_consen 81 TRVDLAPGASLIYWEIITPGRPARGERFAFGRYRSRLEIYRDG-RLLLRDRLRLEPGENNLSSPGGLGGYTHFGTLYLVG 159 (209)
T ss_dssp EEEEE-TT-EEEEEEEEE-S-GGGT--S-SSEEEEEEEEEETT-EEEEEEEEEE-TTTS-TTSTTTTTT--EEEEEEEES
T ss_pred EEEEECCCCEEEEEEecccCCCcCCCCccceEEEEEEEEEECC-EEEEEEeeEECCCCcCccCchhhCCCCEEEEEEEEe
Confidence 9999999999999999999999999999999999999999988 999999999999874 56678999999999999999
Q ss_pred CCchhHHHHHHHHHHHHhhhcccCCCCCCCCCCCccCccccCCCceEEEEeeeccCCcEEEEEEccCCHHHHHHHH
Q 038992 194 PKLKQIQIQVQENVRRMMSEQLYLPSTGLRPHGKTQSDHFLAKPSFVVSCSAFGPKGIGIVVRIAAMTTESVYRFL 269 (286)
Q Consensus 194 p~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~~~~~glvvR~la~~~e~lr~~l 269 (286)
|......+.+.+.+++.+. .+++.+|+|.+ ++|++||+||++++.++++|
T Consensus 160 p~~~~~~~~~~~~l~~~~~-----------------------~~~~~~g~S~l---~~g~~vR~la~~~~~l~~~~ 209 (209)
T PF01774_consen 160 PDSEEDAEALLERLRALLD-----------------------DPGVYAGASRL---GGGLVVRILANDAEDLRRAL 209 (209)
T ss_dssp -S--------HHHHHHHHT------------------------TTEEEEEEE----TS-EEEEEEESSHHHHHH--
T ss_pred CccchhHHHHHHHHHHhhh-----------------------cCCcEEEEEEc---CCeEEEEEeeCCHHHHhcCC
Confidence 9743333556666665431 12588999986 78999999999999999986
No 3
>PF04314 DUF461: Protein of unknown function (DUF461); InterPro: IPR007410 This entry represents a domain found in of proteins of unknown function, including DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus (Caulobacter vibrioides), which share a potential metal binding motif H(M)X10MX21HXM. DR1885 was found to bind copper(I) through a histidine and three Mets in a cupredoxin-like fold []. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria (Cox17 being an accessory protein required for correct assembly of eukaryotic cyochrome c oxidase). ; PDB: 2K6W_A 2K6Z_A 2K6Y_A 2K70_A 1X9L_A 2JQA_A.
Probab=58.23 E-value=22 Score=27.84 Aligned_cols=36 Identities=11% Similarity=0.222 Sum_probs=29.5
Q ss_pred CCcEEEEEeccCcceecCcEEEEEEEEcCCcEEEEe
Q 038992 57 TDAVWVYTLTYGGGIVSGDSISCEITVADACTAVLT 92 (286)
Q Consensus 57 ~~~~~v~ll~~~GGl~~GD~l~i~i~v~~ga~l~lt 92 (286)
++..|++|+..---+..||.+.+.++.+.|-.+.++
T Consensus 75 pgg~HlmL~g~~~~l~~G~~v~ltL~f~~gg~v~v~ 110 (110)
T PF04314_consen 75 PGGYHLMLMGLKRPLKPGDTVPLTLTFEDGGKVTVE 110 (110)
T ss_dssp CCCCEEEEECESS-B-TTEEEEEEEEETTTEEEEE-
T ss_pred CCCEEEEEeCCcccCCCCCEEEEEEEECCCCEEEeC
Confidence 355899999999999999999999999999887764
No 4
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=48.70 E-value=60 Score=30.02 Aligned_cols=85 Identities=16% Similarity=0.159 Sum_probs=63.6
Q ss_pred ecCcEEEEEEEEcCCcEEEEeCcccceeecCCCCCcc----eeEEEEEEEEEcCCceEEEeeeeccCCCCCCCccccceE
Q 038992 72 VSGDSISCEITVADACTAVLTTQASTKVYKSLGSKSS----EQILEKQIFRVVLDSSLVIVDWITSGRHESGEKWDFELY 147 (286)
Q Consensus 72 ~~GD~l~i~i~v~~ga~l~ltTQsatkvy~~~~~~~s----~q~le~~~i~L~~~A~ll~~d~i~~GR~a~GE~f~~~~~ 147 (286)
=.||++-+.+.+.+-.|+.=| .+..+++.-...++. .|.++-+..++.+.+++++.|---.|=+...|+|+.-++
T Consensus 116 q~Gd~l~v~l~~Dkk~Ri~g~-~a~~~~l~~l~~~~~~~l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~~~prl 194 (287)
T COG2996 116 QKGDKLLVYLYVDKKGRIWGT-LAIEKILENLATPAYNNLKNQEVDATVYRLLESGTFVITENGYLGFIHKSERFAEPRL 194 (287)
T ss_pred CCCCEEEEEEEEccCCcEEEE-ecchhHHHhcCCccchhhhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhcccccC
Confidence 469999999999887776554 445555532222222 345667778889999999999999999999999999888
Q ss_pred EEEEEEEEcC
Q 038992 148 RSTNHIFLEG 157 (286)
Q Consensus 148 ~s~~~I~~~g 157 (286)
-.++..++-+
T Consensus 195 G~~l~~rVi~ 204 (287)
T COG2996 195 GERLTARVIG 204 (287)
T ss_pred CceEEEEEEE
Confidence 8888777643
No 5
>COG2847 Copper(I)-binding protein [Inorganic ion transport and metabolism]
Probab=36.14 E-value=95 Score=26.11 Aligned_cols=36 Identities=11% Similarity=0.192 Sum_probs=33.5
Q ss_pred CCcEEEEEeccCcceecCcEEEEEEEEcCCcEEEEe
Q 038992 57 TDAVWVYTLTYGGGIVSGDSISCEITVADACTAVLT 92 (286)
Q Consensus 57 ~~~~~v~ll~~~GGl~~GD~l~i~i~v~~ga~l~lt 92 (286)
+|.-|++|+..-=.|..||.+.+++..+.+..+.+.
T Consensus 102 pGgyHvMlm~lK~pl~eGd~v~vtL~f~~~~~~~v~ 137 (151)
T COG2847 102 PGGYHVMLMGLKKPLKEGDKVPVTLKFEKAGKVTVE 137 (151)
T ss_pred CCCEEEEEeccCCCccCCCEEEEEEEEecCCeEEEE
Confidence 567899999999999999999999999999888887
No 6
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=23.11 E-value=2.2e+02 Score=19.20 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=26.0
Q ss_pred EEEEEc--cCCHHHHHHHHHHHHHHhhHhhCCCC
Q 038992 253 IVVRIA--AMTTESVYRFLQHQLAGMETLLGVSP 284 (286)
Q Consensus 253 lvvR~l--a~~~e~lr~~l~~~~~~lr~~lG~~p 284 (286)
+-|.+. |.+.+.-+++.+.+-+.+...+|.+|
T Consensus 3 i~i~i~~~grt~eqK~~l~~~it~~l~~~lg~~~ 36 (63)
T TIGR00013 3 VNIYILKEGRTDEQKRQLIEGVTEAMAETLGANL 36 (63)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHHHhCCCc
Confidence 456666 46788888899999999999999886
No 7
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=22.11 E-value=1.4e+02 Score=21.43 Aligned_cols=25 Identities=24% Similarity=0.435 Sum_probs=19.5
Q ss_pred cceecCcEEEEEEEEcCCcEEEEeC
Q 038992 69 GGIVSGDSISCEITVADACTAVLTT 93 (286)
Q Consensus 69 GGl~~GD~l~i~i~v~~ga~l~ltT 93 (286)
.|+-.||++.+.+...++....||.
T Consensus 41 ~~l~~Gd~V~F~~~~~~~~~~~I~~ 65 (70)
T PF11604_consen 41 AGLKPGDKVRFTFERTDDGSYVITA 65 (70)
T ss_dssp SS-STT-EEEEEEEEETTCEEEEEE
T ss_pred hcCCCCCEEEEEEEECCCCcEEEEE
Confidence 6889999999999999887666663
No 8
>PF10610 Tafi-CsgC: Thin aggregative fimbriae synthesis protein; InterPro: IPR014491 Thin aggressive fibres known as curli fibres or fimbriae (curli; Tafi) are cell-surface protein polymers found in Salmonella typhimurium and Escherichia coli that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonisation and invasion of cells, and conjugation []. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), which differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localised to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organised into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly [].; PDB: 2XSK_A 2Y2T_A 2Y2Y_A.
Probab=18.83 E-value=1e+02 Score=24.27 Aligned_cols=24 Identities=33% Similarity=0.462 Sum_probs=17.1
Q ss_pred eecCcEEEEEEEEcCCcEEEEeCc
Q 038992 71 IVSGDSISCEITVADACTAVLTTQ 94 (286)
Q Consensus 71 l~~GD~l~i~i~v~~ga~l~ltTQ 94 (286)
+-+||.+.|.|+|-+|=.++|+-|
T Consensus 75 i~p~D~v~I~VtvSDG~sl~LsqQ 98 (106)
T PF10610_consen 75 ISPGDKVKIIVTVSDGKSLHLSQQ 98 (106)
T ss_dssp --TT-EEEEEEEEE-SSS-EEEEE
T ss_pred eCCCCeEEEEEEEcCCCeEEeEec
Confidence 567999999999999999999854
No 9
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=18.06 E-value=4.2e+02 Score=19.72 Aligned_cols=47 Identities=21% Similarity=0.210 Sum_probs=43.0
Q ss_pred cEEEEEeccCcceecCcEEEEEEEEcCCcEEEEeCcccceeecCCCCC
Q 038992 59 AVWVYTLTYGGGIVSGDSISCEITVADACTAVLTTQASTKVYKSLGSK 106 (286)
Q Consensus 59 ~~~v~ll~~~GGl~~GD~l~i~i~v~~ga~l~ltTQsatkvy~~~~~~ 106 (286)
.+..+.+|..|=...|-.+..+++.. |..+.+++-+.+.+|...+..
T Consensus 15 a~e~~~l~~~GV~~ngrlV~T~F~fD-G~~l~~~~G~~~~~y~~~~~~ 61 (79)
T PF11012_consen 15 AAEEFTLNESGVFRNGRLVATSFEFD-GKTLEYRTGSGTYRYQISGEN 61 (79)
T ss_pred cccEEEECCCcEEECCCEEeeEEEEC-CCEEEEEECCeEEEEEEcCCC
Confidence 46678899999999999999999998 999999999999999998764
No 10
>PF04328 DUF466: Protein of unknown function (DUF466); InterPro: IPR007423 This is a small bacterial protein of unknown function.
Probab=16.75 E-value=1.1e+02 Score=21.90 Aligned_cols=24 Identities=17% Similarity=0.149 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHhhHhhCCCCCC
Q 038992 263 ESVYRFLQHQLAGMETLLGVSPYS 286 (286)
Q Consensus 263 e~lr~~l~~~~~~lr~~lG~~py~ 286 (286)
..++++++.++..++.++|.+-|.
T Consensus 3 ~~l~~~~~~~~~~~r~l~G~~~Ye 26 (65)
T PF04328_consen 3 QRLRRAWRRVRWYARLLVGEPDYE 26 (65)
T ss_pred HHHHHHHHHHHHHHHHhcCcHHHH
Confidence 457889999999999999998873
Done!