Query 028939
Match_columns 201
No_of_seqs 171 out of 1002
Neff 6.5
Searched_HMMs 29240
Date Mon Mar 25 07:34:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028939.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/028939hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4a2n_B Isoprenylcysteine carbo 99.6 4.8E-15 1.6E-19 121.7 10.6 65 135-199 75-142 (194)
2 3b5d_A Multidrug transporter E 31.0 1.4E+02 0.0047 20.9 6.5 53 17-69 39-93 (110)
3 2dn5_A General transcription f 21.5 17 0.00059 25.6 -0.3 20 170-189 42-63 (89)
4 2jqt_A H-NS/STPA-binding prote 21.5 71 0.0024 21.5 2.8 32 150-182 38-71 (71)
5 2i68_A Protein EMRE; transmemb 14.7 2.4E+02 0.0082 20.7 4.7 54 17-70 39-94 (137)
6 2klq_A CBD, P105MCM, DNA repli 13.7 43 0.0015 24.3 0.2 10 178-187 102-111 (114)
7 1szw_A TRNA pseudouridine synt 12.7 29 0.00099 30.5 -1.2 8 183-190 178-185 (379)
8 2wmm_A Chromosome partition pr 11.5 52 0.0018 25.5 0.1 17 87-103 25-41 (162)
9 3lgb_A DNA primase large subun 11.2 58 0.002 26.1 0.3 11 180-190 178-189 (194)
10 1q60_A General transcription f 11.2 47 0.0016 23.8 -0.2 20 170-189 42-63 (99)
No 1
>4a2n_B Isoprenylcysteine carboxyl methyltransferase; membrane protein, RAS and RHO gtpases signallin; HET: SAH PLM CDL; 3.40A {Methanosarcina acetivorans}
Probab=99.59 E-value=4.8e-15 Score=121.66 Aligned_cols=65 Identities=12% Similarity=0.114 Sum_probs=57.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHh-cC--CCCCCCccccccccccccccchHHHHHHHhhhhcc
Q 028939 135 QAVDVIGWIMWSVGVSIEAIADQQKLSF-KN--SPENRGKWCNVGFWKYSRHPNYFGEVGPSLLLNVT 199 (201)
Q Consensus 135 ~~~~~ig~~l~~~G~~~E~~AD~Ql~~F-r~--~~~~~gk~~~~GLw~ysRHPNYfGE~l~~l~~~l~ 199 (201)
.+...+|++++++|+.++..||.|+.++ +. +++++++++++|+|+|||||||+||++.++++++.
T Consensus 75 ~~~~~~G~~l~l~G~~l~~~a~~~Lg~~f~~~~~~~~~~~Lvt~G~y~~vRHP~Y~G~~l~~~g~~l~ 142 (194)
T 4a2n_B 75 DSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGII 142 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHGGGCCSSCCEETTCCCCCSSTTTTBSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcccCCCCCCCCeeeecCcchhccCccHHHHHHHHHHHHHH
Confidence 4678899999999999999999998654 43 34567889999999999999999999999998874
No 2
>3b5d_A Multidrug transporter EMRE; helical membrane protein, multidrug resistance transporter, SMR, antiport, inner membrane, transmembrane; HET: P4P; 3.80A {Escherichia coli K12} PDB: 3b61_A 3b62_A*
Probab=30.95 E-value=1.4e+02 Score=20.93 Aligned_cols=53 Identities=9% Similarity=0.125 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHhccCcEeeccc-chHHHHHHHHHH-HHhCCchhHHHHHHHH
Q 028939 17 TVGYQLLFFVITALFKFDKVTDFAG-STNFIIIALLTL-ILKGSWHFRQVVLTFL 69 (201)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~D~~w-~~~~~~~~~~~~-~~~~~~~~r~~l~~~l 69 (201)
..+.....+..+...-.-+..=..| +.+++..+.... .+++..++++++=.++
T Consensus 39 ~~~~~~~~~~~al~~~p~s~ay~i~~g~~~v~~~l~~~~~~~E~~s~~~~~Gi~l 93 (110)
T 3b5d_A 39 CYCASFWLLAQTLAYIPTGIAYAIWSGVGIVLISLLSWGFFGQRLDLPAIIGMML 93 (110)
T ss_pred HHHHHHHHHHHHHHhCChhhHHHHHhhHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence 3444444444444444456665666 677777776654 3466666666544333
No 3
>2dn5_A General transcription factor II-I repeat domain- containing protein 1; structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=21.53 E-value=17 Score=25.63 Aligned_cols=20 Identities=20% Similarity=0.135 Sum_probs=13.1
Q ss_pred Cccccccccc--cccccchHHH
Q 028939 170 GKWCNVGFWK--YSRHPNYFGE 189 (201)
Q Consensus 170 gk~~~~GLw~--ysRHPNYfGE 189 (201)
+.+.-+||=. --|||||+|-
T Consensus 42 ~~v~V~GlP~gi~FR~P~~y~I 63 (89)
T 2dn5_A 42 DAVEVTGLPDDIPFRNPNTYDI 63 (89)
T ss_dssp TSEEEESCCTTCCCCCSSSCCH
T ss_pred CeEEEEeCCCCccccCCccccH
Confidence 4455555544 4689999874
No 4
>2jqt_A H-NS/STPA-binding protein 2; CNU, YDGT, replication origin associated, ORIC, protein binding; NMR {Escherichia coli}
Probab=21.48 E-value=71 Score=21.46 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHhcC-CCCC-CCcccccccccccc
Q 028939 150 SIEAIADQQKLSFKN-SPEN-RGKWCNVGFWKYSR 182 (201)
Q Consensus 150 ~~E~~AD~Ql~~Fr~-~~~~-~gk~~~~GLw~ysR 182 (201)
.+...||.-+.+-.. ++-- -||++ .++|+|+|
T Consensus 38 ~f~~AaDHRrAEl~~~gkLyD~~kVP-~~VW~yV~ 71 (71)
T 2jqt_A 38 NMYRAADHRRAELVSGGRLFDLGQVP-KSVWHYVQ 71 (71)
T ss_dssp HHHHHHHHHHHHHHTTCCCC---------------
T ss_pred HHHHHHHHHHHHHhcCCcccccccCC-HHHhhhcC
Confidence 356788988888775 2211 12332 57999876
No 5
>2i68_A Protein EMRE; transmembrane protein, small-multidrug resistance, transporter, homodimer, dual topology, transport protein; NMR {Escherichia coli}
Probab=14.70 E-value=2.4e+02 Score=20.73 Aligned_cols=54 Identities=9% Similarity=0.118 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHhccCcEeeccc-chHHHHHHHHHH-HHhCCchhHHHHHHHHH
Q 028939 17 TVGYQLLFFVITALFKFDKVTDFAG-STNFIIIALLTL-ILKGSWHFRQVVLTFLA 70 (201)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~D~~w-~~~~~~~~~~~~-~~~~~~~~r~~l~~~l~ 70 (201)
+.++...+|..+...-..+..=..| +++++..+++.. ++++..++++++=.+++
T Consensus 39 ~~~ls~~l~~~alk~i~~s~ay~iw~~l~pv~~~l~g~l~lgE~ls~~~~~Gi~LI 94 (137)
T 2i68_A 39 CYCASFWLLAQTLAYIPTGIAYAIWSGVGIVLISLLSWGFFGQRLDLPAIIGMMLI 94 (137)
T ss_dssp HHHHHHHHHHHHHC-----CHHHHHHHHHHHHHHHHHHHHHC------CHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 3334344444443333344444555 677777777764 45666666665444333
No 6
>2klq_A CBD, P105MCM, DNA replication licensing factor MCM6; PRE-RC, CDT1, CBD structure, ATP-BIND cycle, DNA-binding, nucleotide-binding, nucleus; HET: DNA; NMR {Homo sapiens}
Probab=13.69 E-value=43 Score=24.26 Aligned_cols=10 Identities=30% Similarity=0.411 Sum_probs=7.7
Q ss_pred cccccccchH
Q 028939 178 WKYSRHPNYF 187 (201)
Q Consensus 178 w~ysRHPNYf 187 (201)
.-|+=||||-
T Consensus 102 ~~lvVHPNy~ 111 (114)
T 2klq_A 102 PYLVVNPNYL 111 (114)
T ss_dssp CBCEECSCCC
T ss_pred eEEEECCCCC
Confidence 3578899994
No 7
>1szw_A TRNA pseudouridine synthase D; novel fold, RNA modification, TRUD, structural proteomics in europe, spine, structural genomics; 2.00A {Escherichia coli} SCOP: d.265.1.4 PDB: 1si7_A 1sb7_A
Probab=12.73 E-value=29 Score=30.54 Aligned_cols=8 Identities=63% Similarity=1.219 Sum_probs=6.7
Q ss_pred ccchHHHH
Q 028939 183 HPNYFGEV 190 (201)
Q Consensus 183 HPNYfGE~ 190 (201)
-|||||++
T Consensus 178 fpNYFG~Q 185 (379)
T 1szw_A 178 VPNYFGAQ 185 (379)
T ss_dssp EECCCCGG
T ss_pred ccccChhh
Confidence 59999975
No 8
>2wmm_A Chromosome partition protein MUKB; cell division, DNA condensation, nucleotide-binding, cell cycle, coiled coil, ATP-binding, DNA-binding, SMC; 2.30A {Escherichia coli}
Probab=11.50 E-value=52 Score=25.54 Aligned_cols=17 Identities=24% Similarity=0.505 Sum_probs=13.0
Q ss_pred CcCcchhHHHHHHhhhh
Q 028939 87 NWGEDRRFDEMRSNLGK 103 (201)
Q Consensus 87 ~~~eD~Ry~~~r~~~~~ 103 (201)
..+||.|-..+.++.+.
T Consensus 25 ~G~~d~rL~~LAer~GG 41 (162)
T 2wmm_A 25 GGSEDQRLNALAERFGG 41 (162)
T ss_dssp CCCCCTHHHHHHHHHTC
T ss_pred CCCCCHHHHHHHHHhCC
Confidence 34689999999888653
No 9
>3lgb_A DNA primase large subunit; Fe-S cluster, DNA-binding, DNA-directed RNA POL iron, iron-sulfur, metal-binding, nucleotidyltransferase; HET: DNA MSE EPE; 1.54A {Saccharomyces cerevisiae}
Probab=11.18 E-value=58 Score=26.05 Aligned_cols=11 Identities=45% Similarity=0.794 Sum_probs=8.2
Q ss_pred cccccc-hHHHH
Q 028939 180 YSRHPN-YFGEV 190 (201)
Q Consensus 180 ysRHPN-YfGE~ 190 (201)
-..||| ||-|-
T Consensus 178 ~i~HPN~Yf~~S 189 (194)
T 3lgb_A 178 HIAHPNLYFERS 189 (194)
T ss_dssp CCCCHHHHHHHH
T ss_pred CccCcHHHHHHH
Confidence 458999 88664
No 10
>1q60_A General transcription factor II-I; TFII-I, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.288.1.1
Probab=11.16 E-value=47 Score=23.78 Aligned_cols=20 Identities=25% Similarity=0.341 Sum_probs=12.9
Q ss_pred Cccccccccc--cccccchHHH
Q 028939 170 GKWCNVGFWK--YSRHPNYFGE 189 (201)
Q Consensus 170 gk~~~~GLw~--ysRHPNYfGE 189 (201)
+.+..+||=. --||||+||-
T Consensus 42 ~~v~V~GLP~gi~FR~P~~ygi 63 (99)
T 1q60_A 42 EDFYVEGLPEGVPFRRPSTFGI 63 (99)
T ss_dssp TTEEEESCCTTCCSCCTTTSCH
T ss_pred ceEEeecCCCCccccCCCcccH
Confidence 4455566533 4689998874
Done!