Query T0556 HR4435B, , 73 residues
Match_columns 73
No_of_seqs 8 out of 10
Neff 1.6
Searched_HMMs 11830
Date Tue May 25 15:43:34 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0556.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0556.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09048 Cro: Cro; InterPro: 60.2 2.4 0.0002 21.1 2.6 29 15-43 5-33 (59)
2 PF04552 Sigma54_DBD: Sigma-54 49.7 1.4 0.00012 22.4 0.0 31 19-49 46-76 (160)
3 PF07205 DUF1413: Protein of u 46.4 4.6 0.00039 19.6 2.2 41 29-69 19-59 (97)
4 PF01381 HTH_3: Helix-turn-hel 42.2 9.3 0.00078 18.0 3.2 31 20-50 7-37 (55)
5 PF05703 DUF828: Plant protein 27.4 9.7 0.00082 17.9 1.4 44 22-70 71-114 (242)
6 PF04218 CENP-B_N: CENP-B N-te 27.1 9.6 0.00081 17.9 1.3 34 13-46 13-46 (53)
7 PF08708 PriCT_1: Primase C te 25.1 21 0.0018 16.1 2.7 33 12-47 34-66 (71)
8 PF07022 Phage_CI_repr: Bacter 23.0 25 0.0021 15.7 2.8 47 14-60 4-52 (66)
9 PF01499 Herpes_UL25: Herpesvi 21.2 25 0.0021 15.7 2.5 31 33-69 139-169 (540)
10 PF08673 RsbU_N: Phosphoserine 19.3 22 0.0018 16.0 1.9 12 54-65 21-32 (77)
No 1
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change . Most Cro proteins, such as P22 Cro and phage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement . This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1cop_D 2a63_A 2ovg_A 1d1m_A 6cro_A 5cro_B 1orc_A 2ecs_B 1d1l_A 3orc_A ....
Probab=60.19 E-value=2.4 Score=21.13 Aligned_cols=29 Identities=31% Similarity=0.403 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf 99999986205545543330388899886
Q T0556 15 ALKDLLKDMNQSSLAKECPLSQSMISSIV 43 (73)
Q Consensus 15 Alk~LLkemnQStLakecpLsQSmiSsIV 43 (73)
.|.+.+.++.|+++|+..-..||-||--+
T Consensus 5 ~L~dY~~~~GQak~A~~lGV~qsAISKai 33 (59)
T PF09048_consen 5 TLADYVEEHGQAKAAKALGVTQSAISKAI 33 (59)
T ss_dssp EHHHHHHH--HHHHHHH----HHHHHHHH
T ss_pred EHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 09999999767999998297689999999
No 2
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins .; PDB: 2o9l_A 2ahq_A 2o8k_A.
Probab=49.73 E-value=1.4 Score=22.40 Aligned_cols=31 Identities=29% Similarity=0.400 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHCCCHHC
Q ss_conf 9986205545543330388899886131000
Q T0556 19 LLKDMNQSSLAKECPLSQSMISSIVNSTYYA 49 (73)
Q Consensus 19 LLkemnQStLakecpLsQSmiSsIVNstyya 49 (73)
-|+-|....+|.+.-++.|+||-+|+++|..
T Consensus 46 ~l~Pltl~~vA~~lglheSTVSRav~~Ky~~ 76 (160)
T PF04552_consen 46 ALKPLTLKDVAEELGLHESTVSRAVSNKYIQ 76 (160)
T ss_dssp -------------------------------
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCCCEEE
T ss_conf 5768549999998398830577987485363
No 3
>PF07205 DUF1413: Protein of unknown function (DUF1413); InterPro: IPR010813 This family consists of several hypothetical bacterial proteins, which seem to be specific to Staphylococcus species. Members of this family are typically around 100 residues in length. The function of this family is unknown.
Probab=46.36 E-value=4.6 Score=19.62 Aligned_cols=41 Identities=29% Similarity=0.358 Sum_probs=25.2
Q ss_pred HHHCCHHHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 54333038889988613100022488889999999998753
Q T0556 29 AKECPLSQSMISSIVNSTYYANVSAAKCQEFGRWYKHFKKT 69 (73)
Q Consensus 29 akecpLsQSmiSsIVNstyyanvsa~kCqEFGrWyk~ykk~ 69 (73)
+.-.|.-+..----.|..+-.-.|++--||-||||-.|-|.
T Consensus 19 ~f~lp~g~~ftf~DLn~~aNV~cst~vQq~vGRwfaYfVK~ 59 (97)
T PF07205_consen 19 AFNLPEGQEFTFHDLNSRANVQCSTNVQQNVGRWFAYFVKH 59 (97)
T ss_pred EEECCCCCEEEEECCCHHHCEECCHHHHHHHHHHHHHHHHH
T ss_conf 64158884587500134345443688988775688898740
No 4
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2ef8_B 3f6w_A 3eus_A 1x57_A 1utx_A 2gzu_A 1rio_A 1lli_A 1lmb_3 3bdn_B ....
Probab=42.20 E-value=9.3 Score=18.02 Aligned_cols=31 Identities=29% Similarity=0.342 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHCCCHHCC
Q ss_conf 9862055455433303888998861310002
Q T0556 20 LKDMNQSSLAKECPLSQSMISSIVNSTYYAN 50 (73)
Q Consensus 20 LkemnQStLakecpLsQSmiSsIVNstyyan 50 (73)
-+.|+|..+|+.+-++++.||.+.|+.....
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~e~g~~~~~ 37 (55)
T PF01381_consen 7 ERGLSQEELARRLGISRSTISRIENGKRNPS 37 (55)
T ss_dssp HTT--HHHHHHHHTS-HHHHHHHHTTSSGSB
T ss_pred HCCCCHHHHHHHCCCCHHHHHHHHCCCCCCC
T ss_conf 8699999998864987878889976998999
No 5
>PF05703 DUF828: Plant protein of unknown function (DUF828); InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=27.41 E-value=9.7 Score=17.92 Aligned_cols=44 Identities=32% Similarity=0.438 Sum_probs=25.2
Q ss_pred HHHHHHHHHHCCHHHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 6205545543330388899886131000224888899999999987531
Q T0556 22 DMNQSSLAKECPLSQSMISSIVNSTYYANVSAAKCQEFGRWYKHFKKTK 70 (73)
Q Consensus 22 emnQStLakecpLsQSmiSsIVNstyyanvsa~kCqEFGrWyk~ykk~k 70 (73)
-|.|+.....-|++-+-+-.++.. |..+ .-.-.|||+++.|..|
T Consensus 71 ~~~~s~~~~spPi~p~~~~~~~~~-~r~~----~~~tvg~w~~~~~~kk 114 (242)
T PF05703_consen 71 IMSQSSIADSPPISPRDVDDMKKI-RRSN----GGKTVGRWLKDRKEKK 114 (242)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHH-HHHC----CCCCHHHHHHHHHHHH
T ss_conf 335332346999880789999999-9853----6751889998888887
No 6
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure .; GO: 0003677 DNA binding, 0000775 chromosome, pericentric region; PDB: 2elh_A 1hlv_A 1bw6_A.
Probab=27.06 E-value=9.6 Score=17.93 Aligned_cols=34 Identities=26% Similarity=0.343 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCC
Q ss_conf 9999999986205545543330388899886131
Q T0556 13 RNALKDLLKDMNQSSLAKECPLSQSMISSIVNST 46 (73)
Q Consensus 13 rnAlk~LLkemnQStLakecpLsQSmiSsIVNst 46 (73)
..++..+-...+++.+|++--.+.|.|+.|+.+.
T Consensus 13 ~~ii~~~e~g~s~~~iAr~fgi~~sTi~~i~k~k 46 (53)
T PF04218_consen 13 IEIIKRYEEGKSQREIAREFGISRSTISRILKNK 46 (53)
T ss_dssp HHHHHHHHC-T-HHHHHHHHT--CCHHHHHCCTH
T ss_pred HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 9999999849989999989199888999999839
No 7
>PF08708 PriCT_1: Primase C terminal 1 (PriCT-1); InterPro: IPR014820 This alpha helical domain is found at the C-terminal of primases.
Probab=25.11 E-value=21 Score=16.14 Aligned_cols=33 Identities=27% Similarity=0.280 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCH
Q ss_conf 999999999862055455433303888998861310
Q T0556 12 VRNALKDLLKDMNQSSLAKECPLSQSMISSIVNSTY 47 (73)
Q Consensus 12 VrnAlk~LLkemnQStLakecpLsQSmiSsIVNsty 47 (73)
-..++.+++..+|+.. .-||..+-+-+|+.|-+
T Consensus 34 ~~~~v~~~~~~~N~~~---~~PL~~~Ev~~~~~Si~ 66 (71)
T PF08708_consen 34 WLRAVYDLLHQANSNF---NPPLPDSEVKATARSIA 66 (71)
T ss_pred HHHHHHHHHHHHHHHC---CCCCCHHHHHHHHHHHH
T ss_conf 9999999999999847---99979999999999998
No 8
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic .; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0016481 negative regulation of transcription; PDB: 2fjr_A 3bd1_B.
Probab=23.00 E-value=25 Score=15.69 Aligned_cols=47 Identities=21% Similarity=0.138 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHH-HH-HCCCHHCCCCHHHHHHHH
Q ss_conf 999999986205545543330388899-88-613100022488889999
Q T0556 14 NALKDLLKDMNQSSLAKECPLSQSMIS-SI-VNSTYYANVSAAKCQEFG 60 (73)
Q Consensus 14 nAlk~LLkemnQStLakecpLsQSmiS-sI-VNstyyanvsa~kCqEFG 60 (73)
.-+++.+.--+|..||+..-.++|.+| .- -.++.-...-..-|.+||
T Consensus 4 ~Rl~~~~g~~~~~elA~~LgIs~stvs~~~~~r~~~P~~~~i~~a~~~g 52 (66)
T PF07022_consen 4 ERLKEAYGIKTDKELAEKLGISQSTVSHTWKKRNSIPFEWLIKIALETG 52 (66)
T ss_dssp HHHHHH----SCHHHHCCTT--HHHHH-HHHH-----HHHHHHHHHHT-
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHC
T ss_conf 9999996899699999991998888556764168898999999999989
No 9
>PF01499 Herpes_UL25: Herpesvirus UL25 family; InterPro: IPR002493 The Herpesvirus UL25 gene product is a virion component involved in virus penetration and capsid assembly. The product of the UL25 gene is required for packaging but not cleavage of replicated viral DNA . This family includes a number of Herpesvirus proteins: Epstein-Barr virus (strain B95-8) BVRF1 P03233 from SWISSPROT, Human cytomegalovirus (strain AD169) UL77 P16726 from SWISSPROT, Infectious laryngotracheitis virus (strain Thorne V882) ORF2 P23987 from SWISSPROT, and Varicella-zoster virus (strain Dumas) gene 34 P09287 from SWISSPROT.; PDB: 2f5u_A.
Probab=21.19 E-value=25 Score=15.72 Aligned_cols=31 Identities=16% Similarity=0.439 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 3038889988613100022488889999999998753
Q T0556 33 PLSQSMISSIVNSTYYANVSAAKCQEFGRWYKHFKKT 69 (73)
Q Consensus 33 pLsQSmiSsIVNstyyanvsa~kCqEFGrWyk~ykk~ 69 (73)
-|..-+|+++-++.--.+-| ||-||...+.+
T Consensus 139 nf~~e~l~~lY~~~~~w~~s------FG~WY~~Lq~~ 169 (540)
T PF01499_consen 139 NFRVEFLATLYANRQQWLPS------FGPWYRTLQDN 169 (540)
T ss_dssp -HHHHHHHHHH------------------HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCCCCCC------CCHHHHHHHHH
T ss_conf 75699999998620467887------67799999999
No 10
>PF08673 RsbU_N: Phosphoserine phosphatase RsbU, N-terminal domain; InterPro: IPR014787 RsbU is a phosphoserine phosphatase which acts as a positive regulator of the general stress-response factor of Gram-positive organisms, sigma-B. The phosphatase activity of RsbU is stimulated by association with the RsbT kinase. Deletions in the N-terminal domain are deleterious to the activity of RsbU . ; PDB: 2j6z_A 2j6y_D 1w53_A 2j70_A.
Probab=19.31 E-value=22 Score=16.03 Aligned_cols=12 Identities=33% Similarity=0.260 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHH
Q ss_conf 888999999999
Q T0556 54 AKCQEFGRWYKH 65 (73)
Q Consensus 54 ~kCqEFGrWyk~ 65 (73)
.+||+|||+-.+
T Consensus 21 y~~~~fsre~ie 32 (77)
T PF08673_consen 21 YKAQKFSREAIE 32 (77)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
T ss_conf 999998899998
Done!