Query T0610 YP_324426.1 , Anabaena variab ilis ATCC 29413, 186 residues
Match_columns 186
No_of_seqs 109 out of 1632
Neff 8.4
Searched_HMMs 11830
Date Mon Jul 5 09:01:18 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0610.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0610.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05685 DUF820: Protein of un 99.8 1.2E-21 1E-25 143.3 6.2 108 41-150 1-111 (111)
2 PF06054 CoiA: Competence prot 89.7 0.44 3.8E-05 22.7 9.4 84 36-143 66-149 (375)
3 PF06319 DUF1052: Protein of u 84.5 0.34 2.9E-05 23.4 3.3 89 34-143 10-98 (157)
4 PF06616 BsuBI_PstI_RE: BsuBI/ 74.2 1.9 0.00016 18.9 6.3 87 23-127 147-248 (306)
5 PF07864 DUF1651: Protein of u 52.7 3.8 0.00032 17.2 2.6 20 135-154 1-20 (75)
6 PF06666 DUF1173: Protein of u 39.6 8.2 0.00069 15.3 4.3 35 107-142 350-385 (386)
7 PF10500 SR-25: Nuclear RNA-sp 15.8 7.1 0.0006 15.6 -1.3 10 7-16 158-167 (225)
8 PF03550 LolB: Outer membrane 15.2 24 0.002 12.5 2.5 14 172-185 78-91 (157)
9 PF04424 DUF544: Protein of un 15.2 20 0.0017 13.0 0.9 24 122-145 76-101 (121)
10 PF06526 DUF1107: Protein of u 13.5 27 0.0023 12.3 1.5 35 20-54 28-62 (64)
No 1
>PF05685 DUF820: Protein of unknown function (DUF820); InterPro: IPR008538 This entry consists of a number of hypothetical proteins from the Anabaena and Synechocystis cyanobacterial species. The function of this protein is completely unknown. In a small number of proteins this protein also contains Clp_N domains (IPR004176 from INTERPRO) that are involved in protein interactions.; PDB: 1wdj_A.
Probab=99.83 E-value=1.2e-21 Score=143.27 Aligned_cols=108 Identities=23% Similarity=0.372 Sum_probs=86.8
Q ss_pred HHHHHHHHHHHHHHHHCCCCCEE-EEEEEEEEC--CCCCCCCCEEEEECCCCCCCCCCCCCCCEECCEEEEEEEECCCCC
Q ss_conf 03688999999998521389579-855568505--877523542798434110004645443100111699998438870
Q T0610 41 HSAIQSECVSVINSVVKPQRIAR-AFLELRCTF--GDHSTVPDISVFIWSRIPREENGEIANIFLIAPDWTIEILSPDQS 117 (186)
Q Consensus 41 H~~i~~~L~~~l~~~~~~~~~~~-~~~~~~~~~--~~~~~~PDv~v~~~~~~~~~~~~~~~~~~~~~P~LvVEV~Sps~~ 117 (186)
|++++.+|...|..++...+.+. +.....+.. ....+.||+++++.... ............+|+|||||+|||++
T Consensus 1 H~~i~~~L~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~PDv~v~~~~~~--~~~~~~~~~~~~~P~lvvEV~S~s~~ 78 (111)
T PF05685_consen 1 HQRIASNLTRLLRPWLRRQGLGWVVASEVGVRLPPPRDVRIPDVAVVCGERP--RWSYDEWQEFPGPPDLVVEVLSPSTR 78 (111)
T ss_dssp ---HHHHHHHHHHHHHHH-----EEETT---B------B---SEEE----TT--S-HHHH----SS--SEEEEE--TTS-
T ss_pred CHHHHHHHHHHHHHHHHHCCCCEEEECCCEEEEECCCCEECCCEEEEECCCC--CCCCCCCCCCCCCCEEEEEEEECCCC
T ss_conf 9679999999999999855999999738789993899548898999966666--53101134478796599999977864
Q ss_pred HHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEE
Q ss_conf 367777789888458965999960578999999
Q T0610 118 QTKVTKNILHCLKHGTQMGWLIDPDEQTVFVYR 150 (186)
Q Consensus 118 ~~D~~~K~~~Y~~~Gv~~ywiVdp~~~~v~v~~ 150 (186)
..|+..|+..|+++||++||+|||..++|++||
T Consensus 79 ~~D~~~K~~~Y~~~GV~eywivdp~~~~v~vyr 111 (111)
T PF05685_consen 79 RRDREDKLALYARAGVPEYWIVDPEERRVEVYR 111 (111)
T ss_dssp HHHHHHH---TTT----E-EEEETTTTEEEE--
T ss_pred HHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEC
T ss_conf 213426799999849999999999949999979
No 2
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=89.71 E-value=0.44 Score=22.71 Aligned_cols=84 Identities=15% Similarity=0.130 Sum_probs=51.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCEEEEECCCCCCCCCCCCCCCEECCEEEEEEEECCC
Q ss_conf 98931036889999999985213895798555685058775235427984341100046454431001116999984388
Q T0610 36 MPQGKHSAIQSECVSVINSVVKPQRIARAFLELRCTFGDHSTVPDISVFIWSRIPREENGEIANIFLIAPDWTIEILSPD 115 (186)
Q Consensus 36 ~~~~~H~~i~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~PDv~v~~~~~~~~~~~~~~~~~~~~~P~LvVEV~Sps 115 (186)
+.+..|-..-..|...|.. .+.. + .+....+.....||+.+-... -.+||||=-..
T Consensus 66 ~ES~~Hl~~K~~l~~~l~~----~~~~-v--~lE~~l~~~~qraDV~v~~~~-----------------~~~aiEiQ~S~ 121 (375)
T PF06054_consen 66 GESEEHLQGKELLYQWLKR----QGFP-V--ELEHYLPEIQQRADVLVNKGG-----------------QMLAIEIQCSP 121 (375)
T ss_pred CCCHHHHHHHHHHHHHHHH----CCCC-E--EEEEECCCCCEECCEEEECCC-----------------CEEEEEEEECC
T ss_conf 9719999999999999997----8970-8--985455765762989997776-----------------25999998458
Q ss_pred CCHHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf 7036777778988845896599996057
Q T0610 116 QSQTKVTKNILHCLKHGTQMGWLIDPDE 143 (186)
Q Consensus 116 ~~~~D~~~K~~~Y~~~Gv~~ywiVdp~~ 143 (186)
-...++...-..|.++|++.+||+....
T Consensus 122 is~~el~~Rt~~Y~~~Gi~viWilg~~~ 149 (375)
T PF06054_consen 122 ISIEELRERTAGYKRAGIQVIWILGRRQ 149 (375)
T ss_pred CCHHHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf 9989999999999976984899952432
No 3
>PF06319 DUF1052: Protein of unknown function (DUF1052); InterPro: IPR009394 This family consists of several bacterial proteins of unknown function.; PDB: 3dnx_A.
Probab=84.51 E-value=0.34 Score=23.41 Aligned_cols=89 Identities=19% Similarity=0.329 Sum_probs=56.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCCCCCCCEEEEECCCCCCCCCCCCCCCEECCEEEEEEEEC
Q ss_conf 16989310368899999999852138957985556850587752354279843411000464544310011169999843
Q T0610 34 KPMPQGKHSAIQSECVSVINSVVKPQRIARAFLELRCTFGDHSTVPDISVFIWSRIPREENGEIANIFLIAPDWTIEILS 113 (186)
Q Consensus 34 ~~~~~~~H~~i~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~PDv~v~~~~~~~~~~~~~~~~~~~~~P~LvVEV~S 113 (186)
.|+++.+.+..+..+.+-...++...+.. +..++... +++.-|++-+.+ +++ -.+|||=|
T Consensus 10 ~p~~d~rqse~a~~v~RGv~Rll~~~g~a-~l~E~~l~---~GRRaDv~al~~-------kGe---------i~iVEiKS 69 (157)
T PF06319_consen 10 NPLPDGRQSETALAVARGVCRLLASLGFA-CLPEFPLP---NGRRADVMALGP-------KGE---------IWIVEIKS 69 (157)
T ss_dssp --------------TT---HHHHHH------EEEE-S--------EEEE------------------------EEEEE-S
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHCCCE-EEEEECCC---CCCEEEEEEECC-------CCC---------EEEEEEEC
T ss_conf 11110000037899999999999978964-87865489---996788998889-------982---------99999854
Q ss_pred CCCCHHHHHHHHHHHHHCCCCEEEEEECCC
Q ss_conf 887036777778988845896599996057
Q T0610 114 PDQSQTKVTKNILHCLKHGTQMGWLIDPDE 143 (186)
Q Consensus 114 ps~~~~D~~~K~~~Y~~~Gv~~ywiVdp~~ 143 (186)
|-.......|-..|+..-=+-||-|++.-
T Consensus 70 -s~~DF~~D~KW~~Y~~~CDRfffAv~~~~ 98 (157)
T PF06319_consen 70 -SRADFRADRKWPDYLDWCDRFFFAVDPDF 98 (157)
T ss_dssp -SHHHHHHTTT----GGG-SEEEEEE-TTS
T ss_pred -CHHHHHCCCCCHHHHHHHHEEEEECCCCC
T ss_conf -68886124762789986410014068678
No 4
>PF06616 BsuBI_PstI_RE: BsuBI/PstI restriction endonuclease C-terminus; InterPro: IPR009528 Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases , . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone . There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents the C terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (3.1.21.4 from EC). The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system .; GO: 0000287 magnesium ion binding, 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 2ixs_A.
Probab=74.21 E-value=1.9 Score=18.95 Aligned_cols=87 Identities=14% Similarity=0.169 Sum_probs=53.4
Q ss_pred CEEEECCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCEE-EE-EE-------------EEEECCCCCCCCCEEEEECC
Q ss_conf 48988788998169893103688999999998521389579-85-55-------------68505877523542798434
Q T0610 23 ASEYIEGKIIQKPMPQGKHSAIQSECVSVINSVVKPQRIAR-AF-LE-------------LRCTFGDHSTVPDISVFIWS 87 (186)
Q Consensus 23 r~ElidG~iv~~~~~~~~H~~i~~~L~~~l~~~~~~~~~~~-~~-~~-------------~~~~~~~~~~~PDv~v~~~~ 87 (186)
-+.+-+|+.+.++|+. |+.+...+...|.....++.... ++ ++ +.+....+..-||+..+...
T Consensus 147 pV~~p~G~~~~LsPG~--~s~L~KaiIEeFaPRF~~g~~VlyigDtg~K~~~~d~~ll~~LGl~i~~~~klPDvVl~~~~ 224 (306)
T PF06616_consen 147 PVTFPNGEEITLSPGP--HSELIKAIIEEFAPRFAPGPEVLYIGDTGNKVVYFDDELLKELGLDIDSHGKLPDVVLYDLG 224 (306)
T ss_dssp EEES----EEEE-------HHHHHHHHHTHHHHH----EEEEE--------EE-HHHHHH------------SEEEEETT
T ss_pred EEECCCCCEEEECCCC--CHHHHHHHHHHHHHHHCCCCEEEEECCCCCCEEECCHHHHHHCCCCCCCCCCCCCEEEEECC
T ss_conf 5986899778757887--14889999998756517996499972788811323599999769974656788867999568
Q ss_pred CCCCCCCCCCCCCEECCEEEEEEEECCCCCHHHHHHHHHH
Q ss_conf 1100046454431001116999984388703677777898
Q T0610 88 RIPREENGEIANIFLIAPDWTIEILSPDQSQTKVTKNILH 127 (186)
Q Consensus 88 ~~~~~~~~~~~~~~~~~P~LvVEV~Sps~~~~D~~~K~~~ 127 (186)
.+ +. +.||+++ |..-.|...|..+
T Consensus 225 ---------~~--wl----~liEaVt-S~GPv~~~R~~eL 248 (306)
T PF06616_consen 225 ---------KN--WL----VLIEAVT-SHGPVDPKRKNEL 248 (306)
T ss_dssp ---------TT--EE----EEEEE---------HHHHHHH
T ss_pred ---------CC--EE----EEEEEEC-CCCCCCHHHHHHH
T ss_conf ---------98--08----9999975-7899898999999
No 5
>PF07864 DUF1651: Protein of unknown function (DUF1651); InterPro: IPR012447 The proteins in this entry have not been characterised.
Probab=52.74 E-value=3.8 Score=17.24 Aligned_cols=20 Identities=35% Similarity=0.898 Sum_probs=17.1
Q ss_pred EEEEEECCCCEEEEEEECCC
Q ss_conf 59999605789999994797
Q T0610 135 MGWLIDPDEQTVFVYRPQQE 154 (186)
Q Consensus 135 ~ywiVdp~~~~v~v~~~~~~ 154 (186)
|.|||||....+..|..+..
T Consensus 1 egWLin~~~~~~~~F~~d~~ 20 (75)
T PF07864_consen 1 EGWLINPQRSWVIRFHPDKK 20 (75)
T ss_pred CCEEECCCCCEEEEEEECCC
T ss_conf 90238899996999998999
No 6
>PF06666 DUF1173: Protein of unknown function (DUF1173); InterPro: IPR009553 This family contains a group of hypothetical bacterial proteins that contain three conserved cysteine residues towards the N-terminal. The function of these proteins is unknown.
Probab=39.57 E-value=8.2 Score=15.28 Aligned_cols=35 Identities=9% Similarity=0.208 Sum_probs=24.5
Q ss_pred EEEEEEC-CCCCHHHHHHHHHHHHHCCCCEEEEEECC
Q ss_conf 9999843-88703677777898884589659999605
Q T0610 107 WTIEILS-PDQSQTKVTKNILHCLKHGTQMGWLIDPD 142 (186)
Q Consensus 107 LvVEV~S-ps~~~~D~~~K~~~Y~~~Gv~~ywiVdp~ 142 (186)
-+++|++ ..+..+....|...|++.|++. |+.|+.
T Consensus 350 ~a~~vv~~~~~~~yr~~~k~~~~~~~~~~~-W~W~~~ 385 (386)
T PF06666_consen 350 TALMVVPGMADPDYRKALKEAIYARSGMPA-WIWDAS 385 (386)
T ss_pred CEEEEECCCCCHHHHHHHHHHHHHCCCCCC-EEEECC
T ss_conf 228995599997999999999984358873-496138
No 7
>PF10500 SR-25: Nuclear RNA-splicing-associated protein
Probab=15.83 E-value=7.1 Score=15.64 Aligned_cols=10 Identities=30% Similarity=0.438 Sum_probs=4.6
Q ss_pred CCCCHHHHHH
Q ss_conf 7558899985
Q T0610 7 KPITLDEFLK 16 (186)
Q Consensus 7 ~~~T~ee~~~ 16 (186)
.|+|-|||.+
T Consensus 158 aP~TkEEyea 167 (225)
T PF10500_consen 158 APETKEEYEA 167 (225)
T ss_pred CCCCHHHHHH
T ss_conf 8998899999
No 8
>PF03550 LolB: Outer membrane lipoprotein LolB; InterPro: IPR004565 This protein, LolB, is known so far only in the gamma subdivision of the Proteobacteria. It is a processed, lipid-modified outer membrane protein. In Escherichia coli, lipoproteins are anchored to the periplasmic side of either the inner or outer membrane through N-terminal lipids, depending on the lipoprotein-sorting signal present at position 2 . Five Lol proteins are involved in the sorting and outer membrane localization of lipoproteins. LolCDE, an ATP binding cassette (ABC) transporter, in the inner membrane releases outer membrane-directed lipoproteins from the inner membrane in an ATP-dependent manner, leading to the formation of a water-soluble complex between the lipoprotein and LolA. The LolA-lipoprotein complex crosses the periplasm and then interacts with outer membrane receptor LolB, which is essential for the anchoring of lipoproteins to the outer membrane.; GO: 0015031 protein transport, 0009279 cell outer membrane; PDB: 1iwn_A 1iwm_B.
Probab=15.24 E-value=24 Score=12.55 Aligned_cols=14 Identities=21% Similarity=0.491 Sum_probs=8.3
Q ss_pred CCCEEEHHHHHHHH
Q ss_conf 68777388985440
Q T0610 172 SELHLSIKDLFSWL 185 (186)
Q Consensus 172 p~l~l~v~~lf~~~ 185 (186)
.|++|+|+.|..||
T Consensus 78 ~G~~lPv~~L~~Wi 91 (157)
T PF03550_consen 78 LGWSLPVSQLRYWI 91 (157)
T ss_dssp ------HHHHHHHT
T ss_pred HCCCCHHHHHHHHH
T ss_conf 79713288889986
No 9
>PF04424 DUF544: Protein of unknown function (DUF544) ; InterPro: IPR007518 This is a eukaryotic protein of unknown function.
Probab=15.19 E-value=20 Score=12.97 Aligned_cols=24 Identities=29% Similarity=0.541 Sum_probs=16.2
Q ss_pred HHHHHHHHHCCC--CEEEEEECCCCE
Q ss_conf 777898884589--659999605789
Q T0610 122 TKNILHCLKHGT--QMGWLIDPDEQT 145 (186)
Q Consensus 122 ~~K~~~Y~~~Gv--~~ywiVdp~~~~ 145 (186)
..-...|.-+|| -+.|++||....
T Consensus 76 t~e~~lFdlf~I~LvHGWlvdp~~~~ 101 (121)
T PF04424_consen 76 TPELSLFDLFNIPLVHGWLVDPDDPE 101 (121)
T ss_pred CCCCHHHHHCCCCEEEEEECCCCCHH
T ss_conf 86531376549860687542898457
No 10
>PF06526 DUF1107: Protein of unknown function (DUF1107); InterPro: IPR009491 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2jro_A.
Probab=13.46 E-value=27 Score=12.25 Aligned_cols=35 Identities=23% Similarity=0.207 Sum_probs=26.8
Q ss_pred CCCCEEEECCEEEECCCCCCCHHHHHHHHHHHHHH
Q ss_conf 89848988788998169893103688999999998
Q T0610 20 TEPASEYIEGKIIQKPMPQGKHSAIQSECVSVINS 54 (186)
Q Consensus 20 ~~~r~ElidG~iv~~~~~~~~H~~i~~~L~~~l~~ 54 (186)
+-.++|+.+|.+..-.....+|-.+++.++..+..
T Consensus 28 g~G~feFd~Gkil~p~~~~~~~~~~~~EvN~~I~~ 62 (64)
T PF06526_consen 28 GLGRFEFDNGKILLPKKADKQHLSVMSEVNQEIMR 62 (64)
T ss_dssp ----B-B----B---SS--HHHHHHHHHHHHHHHH
T ss_pred ECCCEEECCCEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf 22347874988967843028999999999999986
Done!