Query T0602 3NKZ, Yersinia enterocolitica, 123 residues
Match_columns 123
No_of_seqs 89 out of 91
Neff 5.6
Searched_HMMs 11830
Date Mon Jul 5 08:59:14 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0602.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0602.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05400 FliT: Flagellar prote 100.0 6.8E-35 5.8E-39 230.8 9.6 109 4-112 1-109 (109)
2 PF05130 FlgN: FlgN protein; 89.0 0.53 4.5E-05 23.9 6.4 104 8-111 11-137 (143)
3 PF12535 Nudix_N: Hydrolase of 59.4 4.7 0.0004 18.1 4.0 32 8-39 25-56 (58)
4 PF07439 DUF1515: Protein of u 26.8 16 0.0014 14.8 5.1 38 63-100 16-53 (112)
5 PF04844 DUF623: Protein of un 24.5 18 0.0015 14.6 4.0 35 12-46 3-37 (59)
6 PF10488 PP1c_bdg: Phosphatase 19.5 23 0.0019 13.9 4.2 43 26-69 263-305 (307)
7 PF05633 DUF793: Protein of un 18.0 24 0.0021 13.7 7.3 73 8-81 311-385 (389)
8 PF08332 CaMKII_AD: Calcium/ca 17.5 25 0.0021 13.7 3.7 25 15-39 3-27 (128)
9 PF06884 DUF1264: Protein of u 17.0 24 0.002 13.8 1.6 21 103-123 104-131 (171)
10 PF05731 TROVE: TROVE domain; 15.7 28 0.0023 13.4 3.0 59 30-93 283-341 (385)
No 1
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This family contains several bacterial flagellar FliT proteins. The flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium .; GO: 0019861 flagellum; PDB: 3h3m_B.
Probab=100.00 E-value=6.8e-35 Score=230.82 Aligned_cols=109 Identities=50% Similarity=0.718 Sum_probs=108.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 66417899999999999999999886238189999999999999998730588999988899999999999864899999
Q T0602 4 MERHQHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITISSCSSLMLQDLLREKLRAILDNEIEIKR 83 (123)
Q Consensus 4 M~~~~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~ndaeIr~ 83 (123)
|+++.++|+.|++|+++|++||++|++||||+|+++|.+|+.+|+.++..+++++++++++++++++|++||+||++||+
T Consensus 1 M~~~~~ll~~y~~i~~lS~~ML~aA~~gdWd~l~~lE~~y~~~ve~l~~~~~~~~l~~~~~~~~~~lL~~IL~nDaeIr~ 80 (109)
T PF05400_consen 1 MNNSQELLARYEAILALSEQMLEAARAGDWDELVELEREYLQLVEQLREAEPPPPLSPAEQERKRELLRRILANDAEIRD 80 (109)
T ss_dssp ------CHHHHHHHHHHHHHHHHHHHTT-HHHHHH---HHHHHHHHHHHH-------TTT---HHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 98567899999999999999999987787777999999999999999746899999999999999999999976999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999998535567898766424
Q T0602 84 LLQLRLDRLSDLVGQSTKQQAVNNTYGQF 112 (123)
Q Consensus 84 Llq~rldeL~~li~q~~~q~~l~~aYgqf 112 (123)
|++|||++|+.+|+++++++++|+|||+|
T Consensus 81 L~~~rl~~L~~li~~~~~q~~l~~aYg~f 109 (109)
T PF05400_consen 81 LLQPRLDELSQLIGQSRRQRSLNNAYGQF 109 (109)
T ss_dssp HHHHHHHHHHHH-----------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 98999999999999878889999866779
No 2
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 This family includes the FlgN protein, an export chaperone involved in flagellar synthesis .; GO: 0009296 flagellum biogenesis, 0019861 flagellum; PDB: 2fup_A.
Probab=89.04 E-value=0.53 Score=23.87 Aligned_cols=104 Identities=21% Similarity=0.230 Sum_probs=69.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCC---------C-----------CCH---HHH
Q ss_conf 78999999999999999998862381899999999999999987305889---------9-----------998---889
Q T0602 8 QHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITISS---------C-----------SSL---MLQ 64 (123)
Q Consensus 8 ~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~---------~-----------l~~---~~q 64 (123)
......|+.+..+..+-..+-..+|++.|.++-..--.+++.+......- . ..+ ...
T Consensus 11 ~~~~~~~~~L~~ll~~e~~~l~~~d~~~L~~l~~~k~~l~~~l~~~~~~r~~~~~~~~~~~~~~~l~~l~~~~~~l~~~~ 90 (143)
T PF05130_consen 11 EEEIELLQELLELLEQEREALIARDIDELEELTEKKQELLEQLERLEKKRRQLLEALGQQPSEASLSELLEEDEELQALW 90 (143)
T ss_dssp HHH---HHHHHHHHHHHHHHHHTT--HHHHHH---HHHHHHHHHH---HHHHHHHH----SS----HHHHT---HHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHH
T ss_conf 99999999999999999999980999999999999999999999999999999998346446216999986449999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999998648999999999999999999853556789876642
Q T0602 65 DLLREKLRAILDNEIEIKRLLQLRLDRLSDLVGQSTKQQAVNNTYGQ 111 (123)
Q Consensus 65 ~~~~~lL~~IL~ndaeIr~Llq~rldeL~~li~q~~~q~~l~~aYgq 111 (123)
..+..++.+|-.-...-..+++..++..+..+........-+.+||.
T Consensus 91 ~~l~~~~~~~~~~n~~N~~ll~~~~~~~~~~l~~l~~~~~~~~tY~~ 137 (143)
T PF05130_consen 91 DELRELLEELQELNERNGKLLEAALEFIQELLNILRQAADASKTYGA 137 (143)
T ss_dssp -----HHHHHHHHHHH-------TTT----HHHHH------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf 99999999999999999999999999999999998625777688297
No 3
>PF12535 Nudix_N: Hydrolase of X-linked nucleoside diphosphate N terminal
Probab=59.38 E-value=4.7 Score=18.09 Aligned_cols=32 Identities=16% Similarity=0.210 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf 78999999999999999998862381899999
Q T0602 8 QHLLSEYQQILTLSEQMLVLATEGNWDALVDL 39 (123)
Q Consensus 8 ~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~l 39 (123)
..=...|++|..+|.+|++..-.-+++.+-++
T Consensus 25 ~yD~eRye~Lr~ia~emla~~s~~~~e~v~~l 56 (58)
T PF12535_consen 25 VYDRERYEELREIAAEMLAQYSDLPVEKVKDL 56 (58)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 61399999999999999997519999999987
No 4
>PF07439 DUF1515: Protein of unknown function (DUF1515); InterPro: IPR010889 This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium species. The function of this family is unknown.
Probab=26.75 E-value=16 Score=14.82 Aligned_cols=38 Identities=21% Similarity=0.207 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999999986489999999999999999998535
Q T0602 63 LQDLLREKLRAILDNEIEIKRLLQLRLDRLSDLVGQST 100 (123)
Q Consensus 63 ~q~~~~~lL~~IL~ndaeIr~Llq~rldeL~~li~q~~ 100 (123)
+-+..|+-|++-.+--+..|.-.-.|+|+|.+.++..-
T Consensus 16 ei~~~Redik~SEdRsd~sR~~M~~R~DELverV~tLE 53 (112)
T PF07439_consen 16 EIKELREDIKRSEDRSDASRASMHRRIDELVERVHTLE 53 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999998788764000888753899999999999
No 5
>PF04844 DUF623: Protein of unknown function, DUF623; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=24.51 E-value=18 Score=14.56 Aligned_cols=35 Identities=23% Similarity=0.372 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
Q ss_conf 99999999999999988623818999999999999
Q T0602 12 SEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKA 46 (123)
Q Consensus 12 ~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~ 46 (123)
+.|..--.--.+|...-.-.+|+.|-+|-..|+.+
T Consensus 3 DPy~DFR~SM~EMI~~~~i~~~~~LeeLL~cYL~L 37 (59)
T PF04844_consen 3 DPYEDFRRSMVEMIEENGIRDWDDLEELLACYLSL 37 (59)
T ss_pred CHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC
T ss_conf 67899999999999985778999999999999870
No 6
>PF10488 PP1c_bdg: Phosphatase-1 catalytic subunit binding region
Probab=19.49 E-value=23 Score=13.94 Aligned_cols=43 Identities=14% Similarity=0.336 Sum_probs=32.7
Q ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
Q ss_conf 98862381899999999999999987305889999888999999
Q T0602 26 VLATEGNWDALVDLEMTYLKAVESTANITISSCSSLMLQDLLRE 69 (123)
Q Consensus 26 ~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~ 69 (123)
.+||.|.|+.+..=-.++..-|..+... ....+++.-+++...
T Consensus 263 RaARKG~Weq~ArDR~RFqrRI~~~E~~-L~~~Lsp~HR~kv~~ 305 (307)
T PF10488_consen 263 RAARKGPWEQMARDRDRFQRRIAETEPV-LGPCLSPEHREKVYA 305 (307)
T ss_pred HHHHCCHHHHHHHHHHHHHHHHHHHHHH-HHHHCCHHHHHHHHH
T ss_conf 7763371999887699999999999998-875159999999986
No 7
>PF05633 DUF793: Protein of unknown function (DUF793); InterPro: IPR008511 This family consists of several plant proteins of unknown function.
Probab=18.03 E-value=24 Score=13.73 Aligned_cols=73 Identities=22% Similarity=0.186 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCC--CCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 789999999999999999988623818999999999999999873058--89999888999999999998648999
Q T0602 8 QHLLSEYQQILTLSEQMLVLATEGNWDALVDLEMTYLKAVESTANITI--SSCSSLMLQDLLREKLRAILDNEIEI 81 (123)
Q Consensus 8 ~~ll~~Yq~il~lS~~ML~lA~~gdWD~Lv~lE~~y~~~Ve~l~~~~~--~~~l~~~~q~~~~~lL~~IL~ndaeI 81 (123)
..+|..++++-+..+.+-+++....-+.--+.+.+-...|+.|...-. ..++. +...+.+++.++|+.-=.++
T Consensus 311 ~gLLkEL~~vea~vr~L~elid~~~fp~~~Ek~eEvr~~V~EL~~~~e~L~~GLd-pLe~QVrEvFh~IV~sR~el 385 (389)
T PF05633_consen 311 CGLLKELDQVEACVRRLHELIDGFQFPLEEEKEEEVREAVEELAEVCERLSEGLD-PLERQVREVFHRIVRSRTEL 385 (389)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
T ss_conf 7799999999999999999997056886265899999999999999999972006-89999999999999989988
No 8
>PF08332 CaMKII_AD: Calcium/calmodulin dependent protein kinase II Association; InterPro: IPR013543 Protein kinases are a group of enzymes that possess a catalytic subunit which transfers the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. The enzymes fall into two broad classes, characterised with respect to substrate specificity: serine/threonine specific and tyrosine specific . Protein kinase function has been evolutionarily conserved from Escherichia coli to Homo sapiens. Protein kinases play a role in a mulititude of cellular processes, including division, proliferation, apoptosis, and differentiation . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved , leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases . This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus . The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers . ; PDB: 2ux0_D 2w2c_L 1hkx_M 2f86_B 3h51_A 3f7s_A.
Probab=17.48 E-value=25 Score=13.66 Aligned_cols=25 Identities=28% Similarity=0.320 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf 9999999999998862381899999
Q T0602 15 QQILTLSEQMLVLATEGNWDALVDL 39 (123)
Q Consensus 15 q~il~lS~~ML~lA~~gdWD~Lv~l 39 (123)
++|..+.++...+-..||+|.+.++
T Consensus 3 ~eI~~l~~~~~~A~~~~D~~~~~~l 27 (128)
T PF08332_consen 3 QEIRALFDAWNEALATGDIDAVMAL 27 (128)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 8999999999999980899999975
No 9
>PF06884 DUF1264: Protein of unknown function (DUF1264); InterPro: IPR010686 This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins.
Probab=17.02 E-value=24 Score=13.80 Aligned_cols=21 Identities=33% Similarity=0.536 Sum_probs=16.3
Q ss_pred HHHHHHHHHC-------CCCCCCCCCCC
Q ss_conf 7898766424-------79844789899
Q T0602 103 QAVNNTYGQF-------PDHALLLGETQ 123 (123)
Q Consensus 103 ~~l~~aYgqf-------~~~~l~~~~~~ 123 (123)
+.+.++||+| .|+.|=.|.||
T Consensus 104 ~~~~~tYGKtwH~WqvDrgd~LPLG~P~ 131 (171)
T PF06884_consen 104 EDLAKTYGKTWHTWQVDRGDKLPLGPPQ 131 (171)
T ss_pred HHHHHHHCCEEEECCCCCCCCCCCCCHH
T ss_conf 9999750871680406999978898303
No 10
>PF05731 TROVE: TROVE domain; InterPro: IPR008858 The TROVE (Telomerase, Ro and Vault) domain is a module of ~300-500 residues that is found in TEP1 and Ro60 the protein components of three ribonucleoprotein particles. The TROVE domain is also found in bacterial ribonucleoproteins suggesting an ancient origin of these ribonucleoproteins. The TROVE domain can be found associated with other domains, such as the VWFA domain, the TEP1 N-terminal domain, the NACHT-NTPase domain, and WD-40 repeats. The TROVE domain may be involved in binding the RNA components of the three RNPs, which are telomerase RNA, Y RNA and vault RNA . The TROVE domain contains a few absolutely conserved residues. As none of these conserved residues are the polar type of amino acids found in active sites, it seems unlikely that this region has an enzymatic function .; GO: 0003723 RNA binding, 0030529 ribonucleoprotein complex; PDB: 1yvp_B 2i91_B 1yvr_A 2nvo_A.
Probab=15.69 E-value=28 Score=13.38 Aligned_cols=59 Identities=20% Similarity=0.318 Sum_probs=34.5
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 2381899999999999999987305889999888999999999998648999999999999999
Q T0602 30 EGNWDALVDLEMTYLKAVESTANITISSCSSLMLQDLLREKLRAILDNEIEIKRLLQLRLDRLS 93 (123)
Q Consensus 30 ~gdWD~Lv~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~ndaeIr~Llq~rldeL~ 93 (123)
..-|+.|+...+.|..++.+|..+...- .....-. .+-..|.|+.+|+.==+-=+.-|+
T Consensus 283 ~~~We~Li~~~mp~~AllRNL~nl~~~g-v~~~~~~----~V~~rL~d~~~v~~sr~~P~~~l~ 341 (385)
T PF05731_consen 283 KEVWEALIPSKMPYMALLRNLRNLLRAG-VSDEAHE----RVAARLSDPEAVRKSRQHPFRFLS 341 (385)
T ss_dssp HHHHHHHHTT---HHHHHHC---TTTTT-TT-TT-H----HHHHHHT-HHHHHHTT--HHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHCC-CCHHHHH----HHHHHHCCHHHHHHHCCCHHHHHH
T ss_conf 9999999986288999999898898869-9856799----999984899999983339699999
Done!