Query 012779
Match_columns 456
No_of_seqs 231 out of 1961
Neff 5.7
Searched_HMMs 29240
Date Mon Mar 25 16:04:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012779.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/012779hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2vv5_A MSCS, small-conductance 100.0 1.4E-27 4.7E-32 237.0 18.6 158 284-447 26-198 (286)
2 3udc_A Small-conductance mecha 99.9 3.2E-24 1.1E-28 212.7 23.5 119 324-448 62-195 (285)
3 2vv5_A MSCS, small-conductance 68.9 31 0.001 33.3 10.7 95 200-313 27-122 (286)
4 3udc_A Small-conductance mecha 61.1 1.2E+02 0.004 29.0 15.7 104 198-313 18-121 (285)
5 2do3_A Transcription elongatio 56.9 16 0.00053 28.5 4.8 41 388-435 15-60 (69)
6 1nz9_A Transcription antitermi 48.8 16 0.00054 26.7 3.6 22 389-410 3-29 (58)
7 3cnr_A Type IV fimbriae assemb 46.1 16 0.00056 31.0 3.7 19 381-399 32-50 (117)
8 2e6z_A Transcription elongatio 36.9 13 0.00043 27.8 1.3 23 388-410 5-32 (59)
9 3sgr_A Tandem repeat of amyloi 30.1 25 0.00086 21.5 1.6 16 393-408 6-24 (25)
10 3p8b_B Transcription antitermi 21.7 68 0.0023 27.8 3.6 23 388-410 89-116 (152)
No 1
>2vv5_A MSCS, small-conductance mechanosensitive channel; ION transport, transmembrane, inner membrane, membrane struc membrane protein, membrane; 3.45A {Escherichia coli} SCOP: b.38.1.3 d.58.43.1 f.34.1.1 PDB: 2oau_A
Probab=99.95 E-value=1.4e-27 Score=237.05 Aligned_cols=158 Identities=19% Similarity=0.225 Sum_probs=146.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHH
Q 012779 284 QYLAQAWRGAVILSFVWFLHRWKTNVFTRAMASQSIAGLDREKMLALDRISSVGLFVIGLMALAEACGVAVQSILTVGGI 363 (456)
Q Consensus 284 ~~l~~il~~~iIl~i~~~l~r~l~~~i~~~l~~~~~~~~~~~~i~~i~~i~kili~ii~iiiiL~~lGi~~~sLLa~lGv 363 (456)
.++++++.++++++++|++.+++..++.+++.+.. .+++....+.++++++++++++++++..+|++++++++++|+
T Consensus 26 ~~~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~i~~~~i~~i~~~~~l~~~gi~~~~l~a~~g~ 102 (286)
T 2vv5_A 26 SYAVNIVAALAIIIVGLIIARMISNAVNRLMISRK---IDATVADFLSALVRYGIIAFTLIAALGRVGVQTASVIAVLGA 102 (286)
T ss_dssp GGGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---SCHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCSTTHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CChHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 45678889999999999999999999888876543 367788899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCcEEEECCceeeEE---------------EEEEeceeeeeeEEEEccCCC
Q 012779 364 GGVATAFASRDVLGNVLSGLSMQFSKPFSLGDTIKVKRAYTPLK---------------MIFISFFQIGNKVCRSRDFML 428 (456)
Q Consensus 364 ~GlalgLAaqD~L~Nl~AGI~I~~~rPFrVGD~I~I~g~~G~Ve---------------~I~IPNs~I~~~~I~N~t~~~ 428 (456)
+|+++|||+||+++|++||++|+++|||++||||+++|.+|+|+ .+.+||+++.+..++|+|+.+
T Consensus 103 ~g~aig~a~q~~l~n~~sGi~i~~~~pf~vGD~I~i~g~~G~V~~I~l~~T~i~t~dg~~v~IPNs~l~~~~i~N~s~~~ 182 (286)
T 2vv5_A 103 AGLVVGLALQGSLSNLAAGVLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSREP 182 (286)
T ss_dssp HHHHHHHHHTHHHHHHHHHHHHHTTCSSCTTCEEESSSCEEEEEEECSSEEEEECTTSCEEEEEHHHHHTSCEEESSSSS
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHhcCCccCCCEEEECCEEEEEEEEEeEEEEEEeCCCCEEEechHHHhhCceEECCCCC
Confidence 99999999999999999999999999999999999999999998 469999999999999999998
Q ss_pred ceEEEEEeeeEEeeCCCCh
Q 012779 429 KQRLSVFLTTIHRSCHTCP 447 (456)
Q Consensus 429 ~rRi~~~~t~igv~Ydt~p 447 (456)
.||+.+. ++++|++|+
T Consensus 183 ~~r~~~~---v~v~y~~d~ 198 (286)
T 2vv5_A 183 VRRNEFI---IGVAYDSDI 198 (286)
T ss_dssp EEEEEEE---EEECTTSCH
T ss_pred cEEEEEE---EEEcCCCCH
Confidence 8899888 999999986
No 2
>3udc_A Small-conductance mechanosensitive channel, C-TER peptide from small-conductance...; membrane protein; 3.35A {Thermoanaerobacter tengcongensis} PDB: 3t9n_A*
Probab=99.93 E-value=3.2e-24 Score=212.67 Aligned_cols=119 Identities=17% Similarity=0.230 Sum_probs=108.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCcEEEECCce
Q 012779 324 REKMLALDRISSVGLFVIGLMALAEACGVAVQSILTVGGIGGVATAFASRDVLGNVLSGLSMQFSKPFSLGDTIKVKRAY 403 (456)
Q Consensus 324 ~~~i~~i~~i~kili~ii~iiiiL~~lGi~~~sLLa~lGv~GlalgLAaqD~L~Nl~AGI~I~~~rPFrVGD~I~I~g~~ 403 (456)
++....+.++++++++++++++++..+|++.+++++++|++|+++|||+||+++|++||++|+++|||++||||+++|.+
T Consensus 62 ~tl~~~~~~~~~~~i~~~~~~~~l~~~g~~~~~l~a~~g~~g~aig~a~q~~l~n~~~Gi~i~~~~pf~vGD~I~i~~~~ 141 (285)
T 3udc_A 62 DTLTSLTKNAVRYIIYFLAGASILKLFNIDMTSLLAVAGIGSLAIGFGAQNLVKDMISGFFIIFEDQFSVGDYVTINGIS 141 (285)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTTSCCTTCEEEETTEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCccCCCEEEECCEE
Confidence 35567889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEE---------------EEEEeceeeeeeEEEEccCCCceEEEEEeeeEEeeCCCChH
Q 012779 404 TPLK---------------MIFISFFQIGNKVCRSRDFMLKQRLSVFLTTIHRSCHTCPI 448 (456)
Q Consensus 404 G~Ve---------------~I~IPNs~I~~~~I~N~t~~~~rRi~~~~t~igv~Ydt~p~ 448 (456)
|+|+ .+.+||+++ ..++|++++. +|..+. ++++|++|++
T Consensus 142 G~V~~I~l~~T~i~t~d~~~v~iPN~~l--~~i~N~s~~~-~~~~~~---v~v~~~~d~~ 195 (285)
T 3udc_A 142 GTVEEIGLRVTKIRGFSDGLHIIPNGEI--KMVTNLTKDS-MMAVVN---IAFPIDEDVD 195 (285)
T ss_dssp EEEEEECSSEEEEEETTTEEEEEEGGGC--SCEEECSSSC-EEEEEE---EEEETTSCHH
T ss_pred EEEEEeeeeEEEEecCCCCEEEeccccc--ccccccCCCC-ceEEEE---EeeecCCCHH
Confidence 9997 469999999 4599999765 455677 9999999874
No 3
>2vv5_A MSCS, small-conductance mechanosensitive channel; ION transport, transmembrane, inner membrane, membrane struc membrane protein, membrane; 3.45A {Escherichia coli} SCOP: b.38.1.3 d.58.43.1 f.34.1.1 PDB: 2oau_A
Probab=68.92 E-value=31 Score=33.28 Aligned_cols=95 Identities=17% Similarity=0.093 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCccccccCCcccccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-
Q 012779 200 VIVPVSCYLTGTVLAWVVMPRVLRRFHKYAIQGPVSLLSGGLSIEQVPYEKSFWGALEDPVRYLITFMAFVQIGMMVAP- 278 (456)
Q Consensus 200 ~i~~ll~~ll~~ll~wlv~~~Ilrrl~~~i~~~~~~~l~~~~~kt~~~~d~~l~~~L~~Pl~l~i~li~~~~l~~~~~p- 278 (456)
+...++.+++..+++|++.+.+.+.+.+...+ ...+..+...+.+.++++++++++..+...+..
T Consensus 27 ~~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~i~~~~i~~i~~~~~l~~~gi~ 92 (286)
T 2vv5_A 27 YAVNIVAALAIIIVGLIIARMISNAVNRLMIS--------------RKIDATVADFLSALVRYGIIAFTLIAALGRVGVQ 92 (286)
T ss_dssp GGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HCSCHHHHHHHHHHHHHHHHHHHHHHHHHTTTCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--------------cCCChHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 33445555556666777775554444444332 123455666677777777777666443333322
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012779 279 TTIASQYLAQAWRGAVILSFVWFLHRWKTNVFTRA 313 (456)
Q Consensus 279 ~~~~~~~l~~il~~~iIl~i~~~l~r~l~~~i~~~ 313 (456)
...+. ....+.-+.+++.+...+.+++..+
T Consensus 93 ~~~l~-----a~~g~~g~aig~a~q~~l~n~~sGi 122 (286)
T 2vv5_A 93 TASVI-----AVLGAAGLVVGLALQGSLSNLAAGV 122 (286)
T ss_dssp STTHH-----HHHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred HHHHH-----HHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 11111 1222344455555566666665443
No 4
>3udc_A Small-conductance mechanosensitive channel, C-TER peptide from small-conductance...; membrane protein; 3.35A {Thermoanaerobacter tengcongensis} PDB: 3t9n_A*
Probab=61.08 E-value=1.2e+02 Score=29.05 Aligned_cols=104 Identities=15% Similarity=0.097 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCccccccCCcccccccchHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 012779 198 RDVIVPVSCYLTGTVLAWVVMPRVLRRFHKYAIQGPVSLLSGGLSIEQVPYEKSFWGALEDPVRYLITFMAFVQIGMMVA 277 (456)
Q Consensus 198 ~~~i~~ll~~ll~~ll~wlv~~~Ilrrl~~~i~~~~~~~l~~~~~kt~~~~d~~l~~~L~~Pl~l~i~li~~~~l~~~~~ 277 (456)
...+..++.+++..++++.+.+.+.+++.+...+.. ...+....+.+...+.+.++++++++++..+...+.
T Consensus 18 ~~~~~~il~~lii~~i~~~i~~~l~~~~~~~~~~~~--------~~~~~~~~~tl~~~~~~~~~~~i~~~~~~~~l~~~g 89 (285)
T 3udc_A 18 VKFLLDVLKILIIAFIGIKFADFLIYRFYKLYSKSK--------IQLPQRKIDTLTSLTKNAVRYIIYFLAGASILKLFN 89 (285)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSC--------SSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--------ccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 344445555555555555556566666666655421 012223334556667777777777766643333332
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012779 278 PTTIASQYLAQAWRGAVILSFVWFLHRWKTNVFTRA 313 (456)
Q Consensus 278 p~~~~~~~l~~il~~~iIl~i~~~l~r~l~~~i~~~ 313 (456)
... ..++ ....+.-+.+++.+...+.+++...
T Consensus 90 ~~~--~~l~--a~~g~~g~aig~a~q~~l~n~~~Gi 121 (285)
T 3udc_A 90 IDM--TSLL--AVAGIGSLAIGFGAQNLVKDMISGF 121 (285)
T ss_dssp CCH--HHHH--HHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred CCH--HHHH--HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 221 1111 1222334455555556666655433
No 5
>2do3_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.5.5
Probab=56.91 E-value=16 Score=28.53 Aligned_cols=41 Identities=20% Similarity=0.205 Sum_probs=28.3
Q ss_pred cCCCCCCcEEEE-----CCceeeEEEEEEeceeeeeeEEEEccCCCceEEEEE
Q 012779 388 SKPFSLGDTIKV-----KRAYTPLKMIFISFFQIGNKVCRSRDFMLKQRLSVF 435 (456)
Q Consensus 388 ~rPFrVGD~I~I-----~g~~G~Ve~I~IPNs~I~~~~I~N~t~~~~rRi~~~ 435 (456)
.|-|++||.|++ .|..|.|..+. ...+..++-.+...+.+.
T Consensus 15 rK~F~~GDHVkVi~G~~~getGlVV~v~-------~d~v~v~SD~t~~Ei~V~ 60 (69)
T 2do3_A 15 RKYFKMGDHVKVIAGRFEGDTGLIVRVE-------ENFVILFSDLTMHELKVL 60 (69)
T ss_dssp CSSCCTTCEEEESSSTTTTCEEEEEEEC-------SSCEEEEESSSCSEEEEC
T ss_pred eeeccCCCeEEEeccEEcCceEEEEEEe-------CCEEEEEeCCCCCEEEEE
Confidence 478999999999 36788887653 445666665555555444
No 6
>1nz9_A Transcription antitermination protein NUSG; transcription elongation, riken structural genomics/proteomics initiative, RSGI; NMR {Thermus thermophilus} SCOP: b.34.5.4
Probab=48.75 E-value=16 Score=26.73 Aligned_cols=22 Identities=23% Similarity=0.255 Sum_probs=18.3
Q ss_pred CCCCCCcEEEEC-----CceeeEEEEE
Q 012779 389 KPFSLGDTIKVK-----RAYTPLKMIF 410 (456)
Q Consensus 389 rPFrVGD~I~I~-----g~~G~Ve~I~ 410 (456)
-+|++||.|++- |.+|.|++++
T Consensus 3 ~~~~~Gd~V~V~~Gpf~g~~g~v~~v~ 29 (58)
T 1nz9_A 3 VAFREGDQVRVVSGPFADFTGTVTEIN 29 (58)
T ss_dssp CSCCTTCEEEECSGGGTTCEEEEEEEE
T ss_pred cccCCCCEEEEeecCCCCcEEEEEEEc
Confidence 478999999993 6899998775
No 7
>3cnr_A Type IV fimbriae assembly protein; PILZ, xanthomonas citri, type IV pilus assembly, unknown function; HET: MSE; 1.90A {Xanthomonas axonopodis PV} PDB: 3dsg_A
Probab=46.12 E-value=16 Score=30.97 Aligned_cols=19 Identities=26% Similarity=0.517 Sum_probs=17.5
Q ss_pred HHHHHhhcCCCCCCcEEEE
Q 012779 381 SGLSMQFSKPFSLGDTIKV 399 (456)
Q Consensus 381 AGI~I~~~rPFrVGD~I~I 399 (456)
+|++|-.++|+++||.|.+
T Consensus 32 GGlFI~T~~~~~~G~~V~l 50 (117)
T 3cnr_A 32 GGIFVPTPKRYMLGDEVFL 50 (117)
T ss_dssp CEEEEECCSCCCTTCEEEE
T ss_pred CeEEEeeCCccCCCCEEEE
Confidence 5889999999999999987
No 8
>2e6z_A Transcription elongation factor SPT5; KOW motif, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=36.89 E-value=13 Score=27.76 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=18.6
Q ss_pred cCCCCCCcEEEEC-----CceeeEEEEE
Q 012779 388 SKPFSLGDTIKVK-----RAYTPLKMIF 410 (456)
Q Consensus 388 ~rPFrVGD~I~I~-----g~~G~Ve~I~ 410 (456)
.-.|++||.|++- |..|.|++++
T Consensus 5 ~~~f~~GD~V~V~~Gpf~g~~G~V~evd 32 (59)
T 2e6z_A 5 SSGFQPGDNVEVCEGELINLQGKILSVD 32 (59)
T ss_dssp CSSCCTTSEEEECSSTTTTCEEEECCCB
T ss_pred cccCCCCCEEEEeecCCCCCEEEEEEEe
Confidence 3469999999993 5899998765
No 9
>3sgr_A Tandem repeat of amyloid-related segment of alpha crystallin residues 90-100 mutant...; amyloid oligomer, beta cylindrin, protein fibril; 2.17A {Homo sapiens}
Probab=30.08 E-value=25 Score=21.48 Aligned_cols=16 Identities=31% Similarity=0.372 Sum_probs=11.6
Q ss_pred CCcEEEECC---ceeeEEE
Q 012779 393 LGDTIKVKR---AYTPLKM 408 (456)
Q Consensus 393 VGD~I~I~g---~~G~Ve~ 408 (456)
.||.|+++| +-|+|.+
T Consensus 6 lgdvievggklkvlgdvie 24 (25)
T 3sgr_A 6 LGDVIEVGGKLKVLGDVIE 24 (26)
T ss_dssp EEEEEEETTEEEEEEEEEE
T ss_pred eeeeeeeCcEEEEeeeEEe
Confidence 589999987 5566654
No 10
>3p8b_B Transcription antitermination protein NUSG; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus} PDB: 3qqc_D
Probab=21.68 E-value=68 Score=27.78 Aligned_cols=23 Identities=17% Similarity=0.117 Sum_probs=18.7
Q ss_pred cCCCCCCcEEEEC-----CceeeEEEEE
Q 012779 388 SKPFSLGDTIKVK-----RAYTPLKMIF 410 (456)
Q Consensus 388 ~rPFrVGD~I~I~-----g~~G~Ve~I~ 410 (456)
...|++||+|++- |..|.|++++
T Consensus 89 ~~~~~~Gd~VrI~~Gpf~g~~g~V~~vd 116 (152)
T 3p8b_B 89 VSGLEPGDLVEVIAGPFKGQKAKVVKID 116 (152)
T ss_dssp TTTCCTTCEEEECSSTTTTCEEEEEEEE
T ss_pred cccCCCCCEEEEeeecCCCCEEEEEEEe
Confidence 3579999999993 5889998775
Done!