Query T0601 APC5750, , 449 residues
Match_columns 449
No_of_seqs 117 out of 1371
Neff 8.1
Searched_HMMs 11830
Date Mon Jul 5 09:09:47 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0601.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0601.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01523 PmbA_TldD: Putative m 100.0 0 0 397.2 22.2 291 33-326 1-293 (293)
2 PF08756 YfkB: YfkB-like domai 28.0 11 0.00093 13.5 1.9 18 81-98 11-28 (153)
3 PF04936 DUF658: Protein of un 18.7 12 0.00099 13.3 0.3 22 316-337 33-54 (186)
4 PF07229 VirE2: VirE2; InterP 16.6 19 0.0016 12.0 1.4 70 8-77 87-156 (552)
5 PF07619 DUF1581: Protein of u 14.9 18 0.0015 12.1 0.5 17 280-296 50-66 (84)
6 PF10692 DUF2498: Protein of u 11.6 24 0.002 11.3 0.4 24 394-420 49-72 (82)
7 PF08169 RBB1NT: RBB1NT (NUC16 10.7 27 0.0023 10.9 1.6 38 63-100 42-89 (96)
8 PF08508 DUF1746: Fungal domai 9.8 19 0.0016 11.9 -0.6 45 245-289 54-101 (116)
9 PF10107 Endonuc_Holl: Endonuc 9.0 15 0.0013 12.6 -1.4 25 263-287 62-86 (156)
10 PF00724 Oxidored_FMN: NADH:fl 8.2 34 0.0029 10.3 3.8 31 243-273 163-194 (341)
No 1
>PF01523 PmbA_TldD: Putative modulator of DNA gyrase; InterPro: IPR002510 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. 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-, 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. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to MEROPS peptidase family U62 (clan U-). The type example is microcin-processing peptidase 1 from Escherichia coli, which is the product of the gene PmbA. It has been suggests that the pmbA gene product acts to inhibit the interaction between the letD protein and the A subunit of DNA gyrase. The letA (ccdA) and letD (ccdB) genes of the F plasmid, located just outside the sequence essential for F-plasmid replication, contribute to stable maintenance of the plasmid in E. coli cells. The letD gene product acts to inhibit partitioning of chromosomal DNA and cell division by inhibiting DNA gyrase activity, whereas the letA gene product acts to reverse the inhibitory activity of the letD gene product . It has also been proposed that PmbA facilitates the secretion of microcin B17 (MccB17) the by completing its maturation . Microcin B17 (MccB17) is a peptide antibiotic produced by E. coli strains harbouring plasmid pMccB17. ; PDB: 1vl4_A 1vpb_A.
Probab=100.00 E-value=0 Score=397.20 Aligned_cols=291 Identities=29% Similarity=0.443 Sum_probs=262.7
Q ss_pred CEEEEEEEEECCEEEEEECCEEEEEEECCCCCEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 78999999612138999777754432010034499999978499998626898999999999999984357776667887
Q T0601 33 SACEVAVSLEQGLSTSVRQGEVETVEFNRDQGFGITLYAGQRKGSASTSATGEAAIRETVAAALAIARHTSEDECAGLAD 112 (449)
Q Consensus 33 ~~~ev~~~~~~~~~~~~~~~~i~~~~~~~~~gigvRv~~~gk~G~~st~~l~~~~i~~~i~~A~~~a~~~~~~~~~~l~~ 112 (449)
|+|||+++++++.++++++|+++++..+.+.|++|||++|||+||+++++++++++++++++|+++|+++++ ++..+|.
T Consensus 1 D~~ei~~~~~~~~~~~~~~~~~~~~~~~~~~g~~vRv~~~g~~g~~~~~~l~~~~l~~~i~~a~~~a~~~~~-~~~~~~~ 79 (293)
T PF01523_consen 1 DEAEIRLEESESLSIRFENGEIEQVSSSEDSGIGVRVIKDGKWGFASTNDLDEESLEDAIERAIEMAKLSPE-DYNELPD 79 (293)
T ss_dssp -EEEEEEEEEEEEEEEEE---EEEEEEEEEEEEEEEEE-------EEESS--HHHHHHHHHHHHCCGGGS---TT-----
T ss_pred CEEEEEEEEEEEEEEEEECCEEEEEEEEEECCEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCC-CCCCCCC
T ss_conf 969999999887999998999887125256139999998998999998989979999999999998751267-7546687
Q ss_pred CCCCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCEEEEEEECCCCEEEEEEEEEEEEEEE
Q ss_conf 0005666-766555687888989999999999999996099636776776430206999981782689884018999999
Q T0601 113 AALMARE-LPELDLYHPWSLSPEQAVERALACEAAAFAADKRVTKADGTTLNTHQGCRVYGNSHGFIGGYASTRHSLSCV 191 (449)
Q Consensus 113 ~~~~~~~-~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nS~G~~~~~~~~~~~~~~~ 191 (449)
+...+.. ..+....++...+++++++++.++.+.+++.++.+..+ +.++....+++|+||+|..+++..++++++++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~i~nS~G~~~~~~~~~~~~~~~ 157 (293)
T PF01523_consen 80 PSPEPYVEIYDPEIEDPDEVSLEEKIELLKEAEEAARAADPRIIAV--GSYSESVSEKIIANSNGVDVSQERSRFSLSVS 157 (293)
T ss_dssp GGGS-----S-TTGGGS----HHHHHHHHHHHHHCCH-STTCEEEE--EEEEEEEEEEEEEE----EEEEEE--EEEEEE
T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEE--EEEEEEEEEEEEEECCCCEEEEEEEEEEEEEE
T ss_conf 4435664555755477466999999999999999986049966998--88889999999997899879999618999999
Q ss_pred EEEECCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHHHHHHHHHHC-CCHHHHHC
Q ss_conf 99957983553102343455200268889999999999997087788994378997716899999998611-25688860
Q T0601 192 MIAEGEGQMQRDYWYDVNRRGEALASAESIGRRAAERAASRLGARPVQTAEVPVLFAPEIAVGLFGHFLGA-ISGGSLYR 270 (449)
Q Consensus 192 ~~a~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~a~~~l~~~~~~~g~y~VVl~P~a~~~ll~~~~~~-~~~~~~~~ 270 (449)
+++++++....+|++.......+..+++.+++++++++..+++++++++|+|+|||+|.+++.|||++++| ++++++++
T Consensus 158 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~a~~~l~~~~~~~g~y~Vil~p~~~~~ll~e~~~~~~~~~~v~~ 237 (293)
T PF01523_consen 158 AIAEDGGEVESGFGYGGAERFLDDIDPEELAEEAAERAVALLGAKPIPSGKYPVILSPEAAGELLHEAFGHAFEADNVYK 237 (293)
T ss_dssp EEE-SSS-B-EEEEEEEESSCGGGS-TTT---HHHHHHHCT---B------EEEEE-CCCHHHHHHHHHHHCCBHHCCCT
T ss_pred EEEECCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCHHHHC
T ss_conf 99977998999864334211222258999999999999996489889996578998707899999877430046714445
Q ss_pred CCCCCCCCCCCEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEECCEEEEE
Q ss_conf 88711037896643851579865877555533565877733566056217878120
Q T0601 271 KSSFLEGALGQRLFPEWLSIDERPHLVGALGSASFDSDGLATYAKPFVENGELVSY 326 (449)
Q Consensus 271 g~S~l~~k~G~~vas~~lti~ddp~~~~~~gs~~fDdEG~~~~~~~LIe~Gvlk~~ 326 (449)
|+|+|++|+|+||+||.|||+|||+++.++|+++|||||+|+++++||||||||+|
T Consensus 238 g~S~l~~klGe~V~s~~lti~Ddp~~~~~~gs~~fDdEGv~~~~~~LIe~GvL~~f 293 (293)
T PF01523_consen 238 GRSPLKGKLGEKVASENLTIIDDPTLPGGPGSYPFDDEGVPTQRTPLIENGVLKNF 293 (293)
T ss_dssp T--TTTT-TTS--S-TT--EEEETT-TT-----SB-----B---EEEE----B---
T ss_pred CCCCCCCCCCCEECCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEECCEEECC
T ss_conf 98701015897140895499988989898658449989980757589968999679
No 2
>PF08756 YfkB: YfkB-like domain; InterPro: IPR014866 This protein is adjacent to YfkA in Bacillus subtilis. In other bacterial species, it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Probab=28.00 E-value=11 Score=13.47 Aligned_cols=18 Identities=22% Similarity=0.292 Sum_probs=11.4
Q ss_pred CCCCHHHHHHHHHHHHHH
Q ss_conf 268989999999999999
Q T0601 81 SATGEAAIRETVAAALAI 98 (449)
Q Consensus 81 ~~l~~~~i~~~i~~A~~~ 98 (449)
+.++.++++++|.+.+..
T Consensus 11 ~vlsL~e~r~aIh~lLd~ 28 (153)
T PF08756_consen 11 EVLSLDEMREAIHHLLDI 28 (153)
T ss_pred CCCCHHHHHHHHHHHHHC
T ss_conf 236899999999999835
No 3
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=18.67 E-value=12 Score=13.32 Aligned_cols=22 Identities=23% Similarity=0.250 Sum_probs=7.5
Q ss_pred EEEECCEEEEEECCHHHHHHHC
Q ss_conf 5621787812022507999708
Q T0601 316 PFVENGELVSYVLGTYSGRKLG 337 (449)
Q Consensus 316 ~LIe~Gvlk~~l~d~~~A~~~g 337 (449)
.||+||++----.+-+-++.+|
T Consensus 33 ~WvKNG~~p~~a~~~yKhAVlN 54 (186)
T PF04936_consen 33 LWVKNGKDPKKANNAYKHAVLN 54 (186)
T ss_pred HHHHCCCCCCCCCCCHHHHHHC
T ss_conf 9998388872334302356745
No 4
>PF07229 VirE2: VirE2; InterPro: IPR009868 This family consists of several VirE2 proteins which seem to be specific to Agrobacterium tumefaciens and Rhizobium etli. VirE2 is known to interact, via its C terminus, with VirD4. A. tumefaciens transfers oncogenic DNA and effector proteins to plant cells during the course of infection. Substrate translocation across the bacterial cell envelope is mediated by a type IV secretion (TFS) system composed of the VirB proteins, as well as VirD4, a member of a large family of inner membrane proteins implicated in the coupling of DNA transfer intermediates to the secretion machine. VirE2 is therefore thought to be a protein substrate of a type IV secretion system which is recruited to a member of the coupling protein superfamily .; GO: 0003677 DNA binding; PDB: 3btp_A.
Probab=16.56 E-value=19 Score=11.99 Aligned_cols=70 Identities=9% Similarity=0.067 Sum_probs=47.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCEEEEEECCEEEEEEECCCCCEEEEEEECCEEEE
Q ss_conf 6820279999999999999995699789999996121389997777544320100344999999784999
Q T0601 8 VGPSVLPDLREQVEQIIAEARRQGASACEVAVSLEQGLSTSVRQGEVETVEFNRDQGFGITLYAGQRKGS 77 (449)
Q Consensus 8 ~~~~~~~~~~~~~e~ll~~a~~~g~~~~ev~~~~~~~~~~~~~~~~i~~~~~~~~~gigvRv~~~gk~G~ 77 (449)
.+.+..+++..++..+.=-....-.|++-++.+.......-..+|.+.++-+..+....-|++.||.--|
T Consensus 87 ~q~e~~~els~lf~~m~lpg~drr~deyilv~qtg~d~f~gt~kg~l~~lptkaefna~crlyrdg~gny 156 (552)
T PF07229_consen 87 NQSEVENELSSLFANMALPGHDRRPDEYILVRQTGQDRFAGTVKGNLDHLPTKAEFNASCRLYRDGAGNY 156 (552)
T ss_dssp ------------------------TTSEEEEEE-----EE-EEGGG-SS---HHHHHHSEEEEE-----E
T ss_pred CHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCCCCEECCCCCCCCCCHHHHHHHHHHHCCCCCCC
T ss_conf 2688888999999608888867888736999851676432011355355872777643344301577775
No 5
>PF07619 DUF1581: Protein of unknown function (DUF1581); InterPro: IPR011475 Several Rhodopirellula baltica proteins share this probable domain. Most of these proteins are predicted to be secreted or membrane-associated.
Probab=14.94 E-value=18 Score=12.13 Aligned_cols=17 Identities=29% Similarity=0.602 Sum_probs=9.2
Q ss_pred CCEECCCEEEEEECCCC
Q ss_conf 96643851579865877
Q T0601 280 GQRLFPEWLSIDERPHL 296 (449)
Q Consensus 280 G~~vas~~lti~ddp~~ 296 (449)
|..+.++.++++.||.+
T Consensus 50 G~P~iP~~I~lv~~~~L 66 (84)
T PF07619_consen 50 GSPEIPDQINLVESPEL 66 (84)
T ss_pred CCCCCCCCCCCCCCCCC
T ss_conf 89868763244468551
No 6
>PF10692 DUF2498: Protein of unknown function (DUF2498)
Probab=11.58 E-value=24 Score=11.29 Aligned_cols=24 Identities=17% Similarity=0.162 Sum_probs=9.8
Q ss_pred EEEECCEEECCCCCEEEECCHHHHHHH
Q ss_conf 999788870103141897167998631
Q T0601 394 YWVENGEIQFPVQEVTIAANLRDLFRR 420 (449)
Q Consensus 394 ~~IenG~i~~~v~~~~i~gn~~~~L~~ 420 (449)
|+=++|=++ ...+-.-|+|..|.+
T Consensus 49 FLde~GlPT---~kttAvFNMfK~LAh 72 (82)
T PF10692_consen 49 FLDEQGLPT---AKTTAVFNMFKHLAH 72 (82)
T ss_pred EECCCCCCC---CCHHHHHHHHHHHHH
T ss_conf 636899988---730899999999998
No 7
>PF08169 RBB1NT: RBB1NT (NUC162) domain; InterPro: IPR012603 This domain is found N-terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family .; PDB: 2yrv_A.
Probab=10.71 E-value=27 Score=10.91 Aligned_cols=38 Identities=11% Similarity=0.149 Sum_probs=21.2
Q ss_pred CCEEEEEEECCEEEEEEECC--------C--CHHHHHHHHHHHHHHHH
Q ss_conf 34499999978499998626--------8--98999999999999984
Q T0601 63 QGFGITLYAGQRKGSASTSA--------T--GEAAIRETVAAALAIAR 100 (449)
Q Consensus 63 ~gigvRv~~~gk~G~~st~~--------l--~~~~i~~~i~~A~~~a~ 100 (449)
--+-||.++|||.....--+ + .+...+.++++|+.-.+
T Consensus 42 D~~lVRSFkDgKf~sV~rkd~~e~~~~~~~k~e~s~k~a~d~A~~fl~ 89 (96)
T PF08169_consen 42 DQCLVRSFKDGKFYSVARKDLREFDRDSLPKSESSLKPALDAAIEFLD 89 (96)
T ss_dssp T-EEEEESSS--EEEE-TTTEE---STTS-HHHHHH----HHHHHHHH
T ss_pred CEEEEEEECCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 508999712681799771202101424456655320189999999985
No 8
>PF08508 DUF1746: Fungal domain of unknown function (DUF1746); InterPro: IPR013715 This is a fungal domain of unknown function.
Probab=9.76 E-value=19 Score=11.87 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=30.2
Q ss_pred EEECCHHHHHHHHHHHHCCCHHHHHCC---CCCCCCCCCCEECCCEEE
Q ss_conf 997716899999998611256888608---871103789664385157
Q T0601 245 VLFAPEIAVGLFGHFLGAISGGSLYRK---SSFLEGALGQRLFPEWLS 289 (449)
Q Consensus 245 VVl~P~a~~~ll~~~~~~~~~~~~~~g---~S~l~~k~G~~vas~~lt 289 (449)
+++-+..+..++|.+.+.+.+...-+| .+.+-|-+|||-.+..+.
T Consensus 54 ~i~~~Nl~cll~H~~~~~p~age~~~GYLhGGl~IdFIGqk~p~sr~~ 101 (116)
T PF08508_consen 54 AILFSNLFCLLLHLIFGPPSAGEASRGYLHGGLIIDFIGQKAPSSRFE 101 (116)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCEECCEEEEECCCCCCCCHHH
T ss_conf 999999999999998489888888887011334788614789862479
No 9
>PF10107 Endonuc_Holl: Endonuclease related to archaeal Holliday junction resolvase
Probab=8.97 E-value=15 Score=12.56 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=16.6
Q ss_pred CCHHHHHCCCCCCCCCCCCEECCCE
Q ss_conf 2568886088711037896643851
Q T0601 263 ISGGSLYRKSSFLEGALGQRLFPEW 287 (449)
Q Consensus 263 ~~~~~~~~g~S~l~~k~G~~vas~~ 287 (449)
.--+++.+-++.+.++++|+.+|=+
T Consensus 62 irkdav~rSr~vl~G~v~EqlaP~~ 86 (156)
T PF10107_consen 62 IRKDAVNRSRAVLKGRVTEQLAPFF 86 (156)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 9999999889998206776643336
No 10
>PF00724 Oxidored_FMN: NADH:flavin oxidoreductase / NADH oxidase family; InterPro: IPR001155 The TIM-barrel fold is a closed barrel structure composed of an eight-fold repeat of beta-alpha units, where the eight parallel beta strands on the inside are covered by the eight alpha helices on the outside . It is a widely distributed fold which has been found in many enzyme families that catalyse completely unrelated reactions . The active site is always found at the C-terminal end of this domain. Proteins in this entry are a variety of NADH:flavin oxidoreductase/NADH oxidase enzymes, found mostly in bacteria or fungi, that contain a TIM-barrel fold. They commonly use FMN/FAD as cofactor and include: dimethylamine dehydrogenase trimethylamine dehydrogenase 12-oxophytodienoate reductase NADPH dehydrogenase NADH oxidase ; GO: 0010181 FMN binding, 0016491 oxidoreductase activity; PDB: 2tmd_A 1djq_A 1o95_B 1o94_A 1djn_A 1ps9_A 2gou_A 2gq8_A 2gq9_A 2gqa_A ....
Probab=8.22 E-value=34 Score=10.29 Aligned_cols=31 Identities=13% Similarity=-0.086 Sum_probs=14.9
Q ss_pred EEEEECCHHHHHHHHHHH-HCCCHHHHHCCCC
Q ss_conf 789977168999999986-1125688860887
Q T0601 243 VPVLFAPEIAVGLFGHFL-GAISGGSLYRKSS 273 (449)
Q Consensus 243 y~VVl~P~a~~~ll~~~~-~~~~~~~~~~g~S 273 (449)
++.|-=..+-+-|++.|+ +.+|-++=.-|.|
T Consensus 163 fDgVEIH~ahGYLl~QFlSp~tN~RtDeYGGs 194 (341)
T PF00724_consen 163 FDGVEIHAAHGYLLSQFLSPLTNKRTDEYGGS 194 (341)
T ss_dssp --EEEEEESTTSHHHHHHSTTT---SS-----
T ss_pred CCEEEECCCCCCCHHHHCCCCCCCCCCCCCCC
T ss_conf 88799815787418864487547987778997
Done!