Query T0631 AaR89, , 303 residues
Match_columns 303
No_of_seqs 121 out of 1256
Neff 7.1
Searched_HMMs 11830
Date Thu Jul 22 15:06:19 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0631.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0631.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03816 LytR_cpsA_psr: Cell e 100.0 0 0 323.1 17.2 145 56-204 1-148 (148)
2 PF04518 DUF582: Protein of un 31.3 11 0.00095 14.5 6.0 125 159-293 188-318 (379)
3 PF11053 DNA_Packaging: Termin 23.0 16 0.0014 13.6 4.5 76 162-251 42-117 (153)
4 PF01726 LexA_DNA_bind: LexA D 16.5 23 0.0019 12.8 3.4 46 188-244 5-51 (65)
5 PF02995 DUF229: Protein of un 10.7 33 0.0028 11.8 2.6 35 103-137 148-182 (498)
6 PF01722 BolA: BolA-like prote 8.6 40 0.0034 11.3 2.3 21 184-204 40-60 (75)
7 PF05378 Hydant_A_N: Hydantoin 8.5 41 0.0035 11.3 1.4 25 52-79 6-30 (176)
8 PF10869 DUF2666: Protein of u 8.3 42 0.0035 11.2 2.7 37 101-137 29-65 (131)
9 PF07079 DUF1347: Protein of u 7.7 44 0.0038 11.1 6.4 74 167-243 396-469 (549)
10 PF04614 Pex19: Pex19 protein 7.5 36 0.003 11.6 0.0 66 172-238 155-220 (248)
No 1
>PF03816 LytR_cpsA_psr: Cell envelope-related transcriptional attenuator domain; InterPro: IPR004474 This entry describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is protein psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. These proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor.
Probab=100.00 E-value=0 Score=323.09 Aligned_cols=145 Identities=47% Similarity=0.703 Sum_probs=138.9
Q ss_pred CCCEEEEEEECCCCCEEEEEEECCCCEEECCCC---CCCCHHHHHHHCCHHHHHHHHHHHHCCCCCEEEEECHHHHHHHH
Q ss_conf 663899999818998799999755321324888---86401113321238999999998718874527898158999999
Q T0631 56 RADTLMLVHVPADRKKTYAISLMRDLWIDIPGV---GESKINAALAYGGVPLMVQTVESLLQQRIDHVAMIDFQGFKGLT 132 (303)
Q Consensus 56 rsDsi~l~~v~~~~~~i~lvSIPRDt~V~ip~~---~~~Kln~ay~~gG~~~~~~tV~~llgi~Id~yv~v~~~~f~~lV 132 (303)
|||+|||+|+|+++++++++||||||+|++|++ +..|||++|++||+++++++|++++|++||||+.|||++|.+||
T Consensus 1 rtD~i~l~~i~~~~~~~~~~siPRDt~v~i~~~~~~~~~kin~ay~~GG~~~~~~~V~~l~gi~Id~yv~v~~~~f~~lv 80 (148)
T PF03816_consen 1 RTDTIMLVSINPKTKKVTLVSIPRDTYVDIPGGPETGYDKINAAYAYGGPEATVETVEDLLGIPIDYYVVVDFDGFVKLV 80 (148)
T ss_pred CCCEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCEEEEECHHHHHHHH
T ss_conf 98589999986999979999967874235789754205889998872483689999999879898779998288899999
Q ss_pred HHCCCEEEECCCCCCCCCCCCCCEEECCCCEEECHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 721881552275423267876752522784472779999999863589985689999999999999998723
Q T0631 133 DALGGVEVDVRIPFAPSSGPKAGQVYDAGKQTLNGDEALAFVRERKAFSDGDYQRVRNQQAYLKAIIGKVIA 204 (303)
Q Consensus 133 D~lGGV~V~v~~~~~~~~~~~~~~~~~~G~q~L~G~qAl~y~R~R~~~~~~D~~R~~RQq~vl~al~~k~~s 204 (303)
|++|||+||+|.++.+.+ .+++|++|+|||||+||++|+|+|+..+ +|++|++|||+||+|+++|++|
T Consensus 81 D~lGGV~V~v~~~~~~~~---~~~~~~~G~~~L~G~~Al~y~R~R~~~~-gD~~R~~RQq~~l~al~~k~~s 148 (148)
T PF03816_consen 81 DALGGVDVDVPQDMDYPD---SGIDLPAGEQHLDGEQALAYVRYRHDDD-GDFGRMQRQQQVLKALLEKLKS 148 (148)
T ss_pred HHCCCEEEECCCCCCCCC---CCEEECCCCEEECHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHC
T ss_conf 871896983687631367---7666679759987789988898737998-6677999999999999999639
No 2
>PF04518 DUF582: Protein of unknown function, DUF582; InterPro: IPR007606 This family contains several uncharacterised chlamydial proteins.
Probab=31.31 E-value=11 Score=14.51 Aligned_cols=125 Identities=14% Similarity=0.229 Sum_probs=67.4
Q ss_pred CCCCEEECHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCEEECCCCCHHHH
Q ss_conf 278447277999999986358--998568999999999999999872330013778999999875503786579898999
Q T0631 159 DAGKQTLNGDEALAFVRERKA--FSDGDYQRVRNQQAYLKAIIGKVIARETLTNPVTISNMVSAVSPFVSVDKDFDAAAI 236 (303)
Q Consensus 159 ~~G~q~L~G~qAl~y~R~R~~--~~~~D~~R~~RQq~vl~al~~k~~s~~~~~~~~kl~~l~~~~~~~~~tdtnl~~~~l 236 (303)
+.|.+.+-|..-.+..|.-+. .-..|+.|.+|-+.++.++++++..-..+++- +-.++.+.+..|.. .-+.-...|
T Consensus 188 ~~g~~~F~g~~~~a~~~l~~Ek~~~~~di~~~~~A~~~l~~~~~~V~~d~~lT~~-Qk~~i~d~l~~Y~~-~l~~i~~qL 265 (379)
T PF04518_consen 188 KMGTDNFPGSYFEALDKLEKEKEQIRRDIKSCERAKAVLEQQLARVKADAKLTSE-QKSEILDTLNNYAS-NLNIISNQL 265 (379)
T ss_pred HCCHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH-HHHHHHHHHHHHHH-HHHHHHHHH
T ss_conf 0542105651999999999999999999999999999999999998725004899-99999999997999-999999899
Q ss_pred HHHHHHHHCCCCCCEEEEEEECCCCCCCCCCEEEEEE--C--HHHHHHHHHHHHCCCCCCC
Q ss_conf 9999998447877557999523347666586379983--8--7999999999863887400
Q T0631 237 GSLALSMKDVRAQDTVMFTLPTLGTGTSPDGQSIVLA--D--TTAIADVTAALAKDQVDAY 293 (303)
Q Consensus 237 ~~l~~~~~~~~~~~i~~~tlP~~~~~~~~~g~~~~~~--d--~~~~~~l~~~l~~~~~~~~ 293 (303)
..|-..+..+. +-.+| .+..+++.+-+.- | ...++.+-..+-+|.+...
T Consensus 266 ~~L~~~L~~L~-----~~~~~---~~~~~~~~f~i~gg~~~Wi~~L~~lE~~vv~G~~~~~ 318 (379)
T PF04518_consen 266 SNLQSYLAPLS-----IQGVP---DNNEVDGAFKIMGGSDDWIRTLQSLESFVVSGFPNGT 318 (379)
T ss_pred HHHHHHHHCCE-----EECCC---CCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf 99998631357-----51468---9887677458860640289999999999870776788
No 3
>PF11053 DNA_Packaging: Terminase DNA packaging enzyme
Probab=23.01 E-value=16 Score=13.62 Aligned_cols=76 Identities=16% Similarity=0.182 Sum_probs=50.5
Q ss_pred CEEECHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCEEECCCCCHHHHHHHHH
Q ss_conf 44727799999998635899856899999999999999987233001377899999987550378657989899999999
Q T0631 162 KQTLNGDEALAFVRERKAFSDGDYQRVRNQQAYLKAIIGKVIARETLTNPVTISNMVSAVSPFVSVDKDFDAAAIGSLAL 241 (303)
Q Consensus 162 ~q~L~G~qAl~y~R~R~~~~~~D~~R~~RQq~vl~al~~k~~s~~~~~~~~kl~~l~~~~~~~~~tdtnl~~~~l~~l~~ 241 (303)
.+.-|=++-..++|. .+.-|++-+....+.++.-..-+.-++...++..+.+.|. + +..+|+.+-.
T Consensus 42 ~r~~Dle~DY~~vR~----------nlh~q~qml~~a~ki~LE~AknSdsPR~~EVf~~LM~qmt-~---tnkelldlhK 107 (153)
T PF11053_consen 42 ERTPDLEDDYETVRR----------NLHFQQQMLMDAAKIALENAKNSDSPRHYEVFAQLMKQMT-D---TNKELLDLHK 107 (153)
T ss_pred CCCCHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH-H---HHHHHHHHHH
T ss_conf 356207776999999----------9999999999999999986113599469999999999987-6---4899999999
Q ss_pred HHHCCCCCCE
Q ss_conf 9844787755
Q T0631 242 SMKDVRAQDT 251 (303)
Q Consensus 242 ~~~~~~~~~i 251 (303)
.|+.+....+
T Consensus 108 ~MK~it~e~~ 117 (153)
T PF11053_consen 108 KMKDITAEQA 117 (153)
T ss_pred HHHHHHHHHC
T ss_conf 9998667540
No 4
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif . This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0008992 repressor LexA activity, 0006508 proteolysis; PDB: 1lea_A 1jhh_A 1jhf_A 1leb_A.
Probab=16.46 E-value=23 Score=12.77 Aligned_cols=46 Identities=15% Similarity=0.220 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCEEECCCC-CHHHHHHHHHHHH
Q ss_conf 99999999999998723300137789999998755037865798-9899999999984
Q T0631 188 VRNQQAYLKAIIGKVIARETLTNPVTISNMVSAVSPFVSVDKDF-DAAAIGSLALSMK 244 (303)
Q Consensus 188 ~~RQq~vl~al~~k~~s~~~~~~~~kl~~l~~~~~~~~~tdtnl-~~~~l~~l~~~~~ 244 (303)
..||++++..|.+-....+. ++.+.++...+. + |...+-..+..+.
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~---~Pt~rEI~~~~g--------l~S~~tV~~~L~~Le 51 (65)
T PF01726_consen 5 TPRQQEVLDFIKDYIREHGY---PPTVREIAEALG--------LKSPSTVHKHLKALE 51 (65)
T ss_dssp -HHHHHHHHHHHHHHHH---------HHHHHHH------------SHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHCC--------CCCCHHHHHHHHHHH
T ss_conf 99999999999999998388---988999998819--------998099999999999
No 5
>PF02995 DUF229: Protein of unknown function (DUF229); InterPro: IPR004245 Members of this family are uncharacterised with a long conserved region that may contain several domains.
Probab=10.74 E-value=33 Score=11.79 Aligned_cols=35 Identities=17% Similarity=0.152 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHCCC
Q ss_conf 99999999871887452789815899999972188
Q T0631 103 PLMVQTVESLLQQRIDHVAMIDFQGFKGLTDALGG 137 (303)
Q Consensus 103 ~~~~~tV~~llgi~Id~yv~v~~~~f~~lVD~lGG 137 (303)
..+.+.+.++=.+...+|=.|.-+.+..++=.+-|
T Consensus 148 PkT~~fl~~~~~~ef~GynkVgdnT~pNl~alltG 182 (498)
T PF02995_consen 148 PKTAEFLRQLGWFEFQGYNKVGDNTFPNLMALLTG 182 (498)
T ss_pred HHHHHHHHHCCCEEECCCCCCCCCCHHHHHHHHHC
T ss_conf 28999996389689668400243326789999717
No 6
>PF01722 BolA: BolA-like protein; InterPro: IPR002634 This family consist of the morpho-protein BolA from Escherichia coli and its various homologs. In E. coli, over-expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division . The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase . BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5 , .; PDB: 1ny8_A 1xs3_A 2kdn_A 1v9j_A 1v60_A 2dhm_A.
Probab=8.63 E-value=40 Score=11.31 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHC
Q ss_conf 689999999999999998723
Q T0631 184 DYQRVRNQQAYLKAIIGKVIA 204 (303)
Q Consensus 184 D~~R~~RQq~vl~al~~k~~s 204 (303)
+..|++|||.|..+|-..+.+
T Consensus 40 g~s~v~rhr~Vy~~L~~~~~~ 60 (75)
T PF01722_consen 40 GKSLVKRHRLVYKALKDEIKS 60 (75)
T ss_dssp T--HHHHHHHHHHHTHHHHHG
T ss_pred CCCHHHHHHHHHHHHHHHHHC
T ss_conf 997889999999999998708
No 7
>PF05378 Hydant_A_N: Hydantoinase/oxoprolinase N-terminal region; InterPro: IPR008040 This domain is found at the N terminus of the hydantoinase/oxoprolinase IPR002821 from INTERPRO family.
Probab=8.50 E-value=41 Score=11.28 Aligned_cols=25 Identities=12% Similarity=0.080 Sum_probs=14.8
Q ss_pred CCCCCCCEEEEEEECCCCCEEEEEEECC
Q ss_conf 6776663899999818998799999755
Q T0631 52 ATDQRADTLMLVHVPADRKKTYAISLMR 79 (303)
Q Consensus 52 ~~~~rsDsi~l~~v~~~~~~i~lvSIPR 79 (303)
.+|..||..++- .+++.+...-.|.
T Consensus 6 vGGTfTD~V~~d---~~~~~i~~~K~~T 30 (176)
T PF05378_consen 6 VGGTFTDAVLLD---PDTGVIATAKVPT 30 (176)
T ss_pred CCCCCEEEEEEE---CCCCEEEEEECCC
T ss_conf 377867799992---8987899998688
No 8
>PF10869 DUF2666: Protein of unknown function (DUF2666)
Probab=8.25 E-value=42 Score=11.22 Aligned_cols=37 Identities=11% Similarity=0.347 Sum_probs=29.9
Q ss_pred CHHHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHCCC
Q ss_conf 3899999999871887452789815899999972188
Q T0631 101 GVPLMVQTVESLLQQRIDHVAMIDFQGFKGLTDALGG 137 (303)
Q Consensus 101 G~~~~~~tV~~llgi~Id~yv~v~~~~f~~lVD~lGG 137 (303)
.+..+...|++.....|..|+.+|++++..+.+.+-.
T Consensus 29 ~IArlLAsI~eTv~~KIp~yl~iDv~~i~e~~~~~~~ 65 (131)
T PF10869_consen 29 DIARLLASINETVNSKIPEYLGIDVKGIEEIAEEIKK 65 (131)
T ss_pred HHHHHHHHHHHHHHHHCHHHCCCCHHHHHHHHHHHHH
T ss_conf 9999999988888760421104169999999988876
No 9
>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=7.70 E-value=44 Score=11.07 Aligned_cols=74 Identities=14% Similarity=0.231 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCEEECCCCCHHHHHHHHHHH
Q ss_conf 79999999863589985689999999999999998723300137789999998755037865798989999999998
Q T0631 167 GDEALAFVRERKAFSDGDYQRVRNQQAYLKAIIGKVIARETLTNPVTISNMVSAVSPFVSVDKDFDAAAIGSLALSM 243 (303)
Q Consensus 167 G~qAl~y~R~R~~~~~~D~~R~~RQq~vl~al~~k~~s~~~~~~~~kl~~l~~~~~~~~~tdtnl~~~~l~~l~~~~ 243 (303)
-+.|+..+|.--...+-|..-..+-=.|++...+++++.-.++..-++.+++..++= |.+-++..+++.+...+
T Consensus 396 dekalnLL~lil~Ft~ydiecen~v~lfiKq~Y~Q~Ls~h~~~rLlklEdFi~e~gl---t~i~i~e~EiANfLADA 469 (549)
T PF07079_consen 396 DEKALNLLKLILQFTDYDIECENIVFLFIKQFYKQALSMHAITRLLKLEDFITEVGL---TPITISEAEIANFLADA 469 (549)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCCCHHHHHHHHHHH
T ss_conf 389999999999871410988899999999999999733017899999988764299---85112589998777648
No 10
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid ß-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognized as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2w85_B.
Probab=7.55 E-value=36 Score=11.61 Aligned_cols=66 Identities=11% Similarity=0.058 Sum_probs=0.0
Q ss_pred HHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCEEECCCCCHHHHHH
Q ss_conf 9998635899856899999999999999987233001377899999987550378657989899999
Q T0631 172 AFVRERKAFSDGDYQRVRNQQAYLKAIIGKVIARETLTNPVTISNMVSAVSPFVSVDKDFDAAAIGS 238 (303)
Q Consensus 172 ~y~R~R~~~~~~D~~R~~RQq~vl~al~~k~~s~~~~~~~~kl~~l~~~~~~~~~tdtnl~~~~l~~ 238 (303)
|+.--+.....-|+.|=++|..++..|+.++-++..-..-.+-...+..+...|+ +..-++.+|+.
T Consensus 155 wL~~nk~~l~~ed~~rY~~Q~~~v~~I~~~fE~~~y~d~~~~~~~~i~~lmqemQ-~~G~PP~eLv~ 220 (248)
T PF04614_consen 155 WLEENKSKLSAEDYERYEKQYELVKEIVEIFEKPGYDDSDPKDREKIWDLMQEMQ-ELGQPPEELVG 220 (248)
T ss_dssp -------------------------------------------------------------------
T ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHH-HHCCCCHHHHH
T ss_conf 8984778799999999999999999999998179998635888999999999999-82899599884
Done!