Query T0628 APC38818, Klebsiella pneumoniae, 295 residues
Match_columns 295
No_of_seqs 116 out of 235
Neff 5.7
Searched_HMMs 11830
Date Thu Jul 22 15:03:01 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0628.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0628.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05035 DGOK: 2-keto-3-deoxy- 100.0 0 0 682.2 29.6 278 12-291 1-287 (287)
2 PF00370 FGGY_N: FGGY family o 92.9 0.066 5.6E-06 28.8 4.8 34 7-40 1-35 (245)
3 PF00349 Hexokinase_1: Hexokin 70.3 1.2 1E-04 20.7 2.6 25 7-31 64-90 (206)
4 PF06723 MreB_Mbl: MreB/Mbl pr 63.1 0.89 7.6E-05 21.5 0.8 44 248-291 275-320 (326)
5 PF01869 BcrAD_BadFG: BadF/Bad 61.2 3.5 0.0003 17.6 3.6 122 9-161 1-132 (268)
6 PF09608 Alph_Pro_TM: Putative 44.4 5.7 0.00049 16.3 2.5 19 141-159 169-188 (236)
7 PF00012 HSP70: Hsp70 protein; 44.1 3.4 0.00028 17.8 1.2 44 248-291 330-375 (602)
8 PF07318 DUF1464: Protein of u 37.2 9 0.00076 15.0 18.1 255 10-295 1-318 (343)
9 PF05378 Hydant_A_N: Hydantoin 35.5 9.5 0.0008 14.9 4.7 44 9-57 2-50 (176)
10 PF03652 UPF0081: Uncharacteri 33.6 9.8 0.00083 14.8 2.3 88 7-106 2-94 (135)
11 PF12534 DUF3733: Leucine-rich 32.0 8.1 0.00069 15.3 1.6 19 128-146 43-61 (65)
12 PF03490 Varsurf_PPLC: Variant 30.3 6.1 0.00051 16.1 0.7 12 136-147 25-36 (51)
13 PF03309 Bvg_acc_factor: Borde 24.6 15 0.0012 13.7 5.3 130 8-157 1-144 (206)
14 PF00374 NiFeSe_Hases: Nickel- 24.2 15 0.0013 13.6 2.8 17 143-159 436-452 (507)
15 PF11795 DUF3322: Uncharacteri 20.2 10 0.00088 14.6 0.4 21 260-280 161-181 (190)
No 1
>PF05035 DGOK: 2-keto-3-deoxy-galactonokinase; InterPro: IPR007729 2-keto-3-deoxy-galactonokinase 2.7.1.58 from EC catalyses the second step in D-galactonate degradation.
Probab=100.00 E-value=0 Score=682.23 Aligned_cols=278 Identities=42% Similarity=0.723 Sum_probs=263.7
Q ss_pred ECCCHHHEEEEEC-CCCEEEECCCCCCHHHCCCCCHHHHHHHHHHHHCCC-CCCEEEECCCCCCCCCCCCCCCCCCCCHH
Q ss_conf 6276314676640-784412001210022158756489999999862178-98189975515512462378545788978
Q T0628 12 DWGSTNLRAWLYQ-GEECLESRQSEAGVTRLNGRSPAAVLAEITQHWRDG-ATPVVMAGMVGSNVGWKIAPYLPLPAAFS 89 (295)
Q Consensus 12 DwGTtnlR~~l~~-~~~vl~~~~~~~Gv~~~~~~~f~~~l~~~~~~~~~~-~~PVi~~GMigS~~Gw~Eapy~~~Pa~l~ 89 (295)
||||||+|+|+|| +++|+++++++.||+++++++|+++|.+++++|+.+ .+|||+||||||+|||+|+||++||++++
T Consensus 1 DWGTS~lR~~l~~~~g~vl~~~~~~~Gv~~~~~~~f~~~L~~~~~~w~~~~~~pVi~~GMvGS~~GW~EapY~~~Pa~~~ 80 (287)
T PF05035_consen 1 DWGTSNLRAWLMDADGEVLDERRSDEGVLQLAPGGFEAVLEDLLGDWLAAGDLPVIACGMVGSRQGWVEAPYLACPAGLA 80 (287)
T ss_pred CCCHHHHHHHEECCCCCEEEEECCCCCHHHCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCCHH
T ss_conf 98610255513339997897740886744479756799999999987407998599977623433661166667998956
Q ss_pred HHHHHHHCC---CCCEEEECCEECCCCCCCCCCCCHHHHHHHHHHCCC--CCEEEECCCCCEEEEEECCEEEEEECCCHH
Q ss_conf 863542047---986688354100788887652226999999872388--978984488721688628868886302018
Q T0628 90 DIGQQLTAV---GDNIWIIPGLCVSRDDNHNVMRGEETQLLGARALAP--SSVYVMPGTHCKWVLADRRQIHDFRTVLTG 164 (295)
Q Consensus 90 ~l~~~~~~~---~~~v~iiPGl~~~~~~~~DVMRGEEtqi~G~l~~~~--~~~icLPGTHsKWv~v~~g~I~~f~T~mTG 164 (295)
+++.+++++ +.+||||||||+ +.+.|||||||||||+|++++++ +++|||||||||||+|++|+|++|+|||||
T Consensus 81 ~l~~~~~~v~~~~~~v~ivPGl~~-~~~~pDVMRGEETQi~G~l~~~~~~~~~icLPGTHsKWv~v~~g~I~~F~T~mTG 159 (287)
T PF05035_consen 81 ELAAALVRVDDPGRPVHIVPGLKQ-QQGSPDVMRGEETQIAGALALNPDWDGVICLPGTHSKWVRVSAGEIVSFQTFMTG 159 (287)
T ss_pred HHHHCCEECCCCCCEEEEECCCCC-CCCCCCCCCCHHHHHHHHHHCCCCCCEEEEECCCCCEEEEECCCEEEEEECCCHH
T ss_conf 876112744589953899677167-8999764458999998887217899858991389866999829909998511079
Q ss_pred HHHHHHHCCCEECCCCCCCCCCHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999986085002347876579899999999974061-058899999999984268987889999999999999999973
Q T0628 165 ELHHLLLQLSLVGAGLPPQETSAAAFAAGLQRGINNP-AVLPQLFEVRASHVLGALPREQVSEFLSGLLIGAEVATLSDT 243 (295)
Q Consensus 165 ELf~~L~~~siL~~~~~~~~~d~~aF~~gv~~~~~~~-~l~~~LF~~Ra~~L~~~~~~~~~~~~LsGlLIG~Elaa~~~~ 243 (295)
|||++|++||||+++++++++|.++|.+||++++++| ++++.||++|+++|+++++++++++||||||||+||++++++
T Consensus 160 ELfalL~~hsiL~~~~~~~~~d~~aF~~gv~~a~~~~~~l~~~LF~~Ra~~L~~~l~~~~~~~~LSGlLIG~Elaa~~~~ 239 (287)
T PF05035_consen 160 ELFALLSNHSILGHSLPAAAWDDDAFAAGVEDALSRPEGLAHRLFSVRALQLLGGLPPAEAAAYLSGLLIGAELAAARPY 239 (287)
T ss_pred HHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99999964863444677776688999999999885831388999899999985689977999999989999999985215
Q ss_pred -CCCCCEEEEECCHHHHHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHH
Q ss_conf -179963899848589999999999809843433879999999999999
Q T0628 244 -FAGQQAISLVAGSSLTSRYQQAFAAIGREVSAVAGDTAFQTGIRSIAY 291 (295)
Q Consensus 244 -~~~~~~v~LiG~~~L~~~Y~~AL~~~G~~~~~~d~d~a~~~Gl~~ia~ 291 (295)
|.++ +|+|||+++|+++|++||+.+|++++.+|+|+|+++||+++||
T Consensus 240 ~~~~~-~v~liG~~~L~~~Y~~AL~~~G~~~~~~d~~~a~~~GL~~~ar 287 (287)
T PF05035_consen 240 FWLGQ-PVVLIGSGALAALYAQALAAQGVPVRRVDADEATLAGLWAAAR 287 (287)
T ss_pred CCCCC-EEEEEECHHHHHHHHHHHHHCCCCEEEECHHHHHHHHHHHHHC
T ss_conf 37898-5999958799999999999779973763499999999999859
No 2
>PF00370 FGGY_N: FGGY family of carbohydrate kinases, N-terminal domain; InterPro: IPR000577 It has been shown that four different type of carbohydrate kinases seem to be evolutionary related. These enzymes include L-fucolokinase () (gene fucK); gluconokinase () (gene gntK); glycerol kinase () (gene glpK); xylulokinase () (gene xylB); and L-xylulose kinase () (gene lyxK). These enzymes are proteins of from 480 to 520 amino acid residues.; GO: 0005975 carbohydrate metabolic process; PDB: 2dpn_B 3ezw_H 1bwf_Y 1bu6_Z 1gll_Y 1glc_G 1bo5_O 1glf_X 1glj_Y 1bot_Z ....
Probab=92.91 E-value=0.066 Score=28.78 Aligned_cols=34 Identities=24% Similarity=0.375 Sum_probs=26.9
Q ss_pred CEEEEECCCHHHEEEEECC-CCEEEECCCCCCHHH
Q ss_conf 4478862763146766407-844120012100221
Q T0628 7 RYIAIDWGSTNLRAWLYQG-EECLESRQSEAGVTR 40 (295)
Q Consensus 7 ~~IaiDwGTtnlR~~l~~~-~~vl~~~~~~~Gv~~ 40 (295)
++|+||-|||+.|+-++|. ++++++.+.+..+..
T Consensus 1 y~lgiDiGTss~Ka~l~d~~g~v~~~~~~~~~~~~ 35 (245)
T PF00370_consen 1 YVLGIDIGTSSVKAVLFDEDGRVLASASRPYPLIR 35 (245)
T ss_dssp EEEEEEE-SSEEEEEEEETTSCEEEEEEEE--EBE
T ss_pred CEEEEEECCCCEEEEEEECCCCEEEEEEEECCCCC
T ss_conf 99999980544299999689998999998624447
No 3
>PF00349 Hexokinase_1: Hexokinase; InterPro: IPR001312 Hexokinase is an important enzyme that catalyses the ATP-dependent conversion of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). The enzyme can catalyse this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways . The addition of a phosphate group to the sugar acts to trap it in a cell, since the negatively charged phosphate cannot easily traverse the plasma membrane. The enzyme is widely distributed in eukaryotes. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase is specific for aldo-hexoses. All three isozymes contain two domains . Structural studies of yeast hexokinase reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar . Vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P, though in types I an III only the C-terminal half supports catalysis, while both halves support catalysis in type II. The N-terminal half is the regulatory region. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains, and is sometimes incorrectly referred to as glucokinase. The different vertebrate isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues . Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. Type IV enzyme is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus.; GO: 0004396 hexokinase activity, 0005524 ATP binding, 0006096 glycolysis; PDB: 3b8a_X 1ig8_A 2nzt_A 1hkc_A 1dgk_N 1hkb_B 1cza_N 1qha_A 1bg3_B 3fr0_A ....
Probab=70.30 E-value=1.2 Score=20.72 Aligned_cols=25 Identities=44% Similarity=0.745 Sum_probs=18.7
Q ss_pred CEEEEECCCHHHEEEEEC--CCCEEEE
Q ss_conf 447886276314676640--7844120
Q T0628 7 RYIAIDWGSTNLRAWLYQ--GEECLES 31 (295)
Q Consensus 7 ~~IaiDwGTtnlR~~l~~--~~~vl~~ 31 (295)
.|+|+|-|-||||+-+++ +++..+.
T Consensus 64 ~~LAlDlGGTnlRV~~V~L~g~~~~~~ 90 (206)
T PF00349_consen 64 RFLALDLGGTNLRVALVELGGDGIVEI 90 (206)
T ss_dssp -EEEEEE---EEEEEEEEEEEETEEEE
T ss_pred EEEEEEECCCEEEEEEEEECCCCCEEE
T ss_conf 499999768368999999779994478
No 4
>PF06723 MreB_Mbl: MreB/Mbl protein; InterPro: IPR004753 Bacterial cell shape varies greatly between species, and characteristic morphologies are used for identification purposes. In addition to individual cell shape, the way in which groups of cells are arranged is also typical of some bacterial species, especially Gram-positive coccoids. For many years, it was believed that micro-organisms with other than spheroidal cell shapes maintained morphology by means of their external cell walls. Recently, however, studies of the Gram-positive rod Bacillus subtilis have revealed two related genes that are essential for the integrity of cell morphogenesis . Termed mreB and mbl, the gene products localise close to the cell surface, forming filamentous helical structures. Many homologues have been found in diverse bacterial groups, suggesting a common ancestor . The crystal structure of MreB from Thermotoga maritima has been resolved using X-ray crystallography . It consists of 19 beta-strands and 15 alpha- helices, and shows remarkable structural similarity to eukaryotic actin. MreB crystals also contain proto-filaments, with individual proteins assembling into polymers like F-actin, in the same orientation. It is hypothesised therefore, that MreB was the forerunner of actin in early eukaryotes .; GO: 0000902 cell morphogenesis; PDB: 1jcf_A 1jce_A 1jcg_A 3h1q_B.
Probab=63.08 E-value=0.89 Score=21.49 Aligned_cols=44 Identities=23% Similarity=0.241 Sum_probs=30.4
Q ss_pred CEEEEECCHHHHHHHHHHH-HHCCCCEEECC-HHHHHHHHHHHHHH
Q ss_conf 6389984858999999999-98098434338-79999999999999
Q T0628 248 QAISLVAGSSLTSRYQQAF-AAIGREVSAVA-GDTAFQTGIRSIAY 291 (295)
Q Consensus 248 ~~v~LiG~~~L~~~Y~~AL-~~~G~~~~~~d-~d~a~~~Gl~~ia~ 291 (295)
+-|+|-|.+++-.--.+-| +..|++++..+ ...++..|...+..
T Consensus 275 ~GI~LtGGgall~Gld~~i~~~~~i~V~~~~~P~~~v~~G~~~~l~ 320 (326)
T PF06723_consen 275 RGIVLTGGGALLPGLDEYIQEETGIPVRVAEDPLTAVARGAGKILE 320 (326)
T ss_dssp ---EEE---------HHHHHHH-----EE-SSTTTTTT-----GGG
T ss_pred CCEEEECCHHCCCCHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHH
T ss_conf 6909977232047889999885698689889878999984999985
No 5
>PF01869 BcrAD_BadFG: BadF/BadG/BcrA/BcrD ATPase family; InterPro: IPR002731 This domain is found in the BadF (O07462 from SWISSPROT) and BadG (O07463 from SWISSPROT) proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase (P11568 from SWISSPROT). The hypothetical protein AQ_278 from Aquifex aeolicus O66634 from SWISSPROT contains two copies of this region suggesting that the family may structurally dimerise.; PDB: 1zc6_B 2e2n_A 2e2o_A 2e2p_A 2e2q_A 2ch6_A 2ch5_C 1zbs_A 1zxo_D 1hux_A ....
Probab=61.18 E-value=3.5 Score=17.63 Aligned_cols=122 Identities=16% Similarity=0.201 Sum_probs=62.1
Q ss_pred EEEECCCHHHEEEEECC-CCEEEECCCC-CCHHHCCCCCHH----HHHHHHHHHHCCC--CCCEEEECCCCCCCCCCCCC
Q ss_conf 78862763146766407-8441200121-002215875648----9999999862178--98189975515512462378
Q T0628 9 IAIDWGSTNLRAWLYQG-EECLESRQSE-AGVTRLNGRSPA----AVLAEITQHWRDG--ATPVVMAGMVGSNVGWKIAP 80 (295)
Q Consensus 9 IaiDwGTtnlR~~l~~~-~~vl~~~~~~-~Gv~~~~~~~f~----~~l~~~~~~~~~~--~~PVi~~GMigS~~Gw~Eap 80 (295)
|.||-|.|++|+.++|. ++++.+..+. ........+... ..+..++.+.... .+..++-|+.|.-.
T Consensus 1 lGIDgGgTkt~avl~d~~g~il~~~~~g~~n~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~i~~~~~g~aG~g~------ 74 (268)
T PF01869_consen 1 LGIDGGGTKTKAVLVDENGKILGRGRSGPSNIQSVGFEAAIKNIEEAIEEALEQAGLSPDDISAVCLGAAGYGR------ 74 (268)
T ss_dssp E-EE----EEEEEEEE---EEEEEEEE----TTTSH-HHHHHHHHHHHHHHHHHCT--TTCCCEEEEEEE-EET------
T ss_pred CEEECCHHHEEEEEEECCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHEEEEEEEEEECC------
T ss_conf 97983823254479969895999999689897777742022689999999999809972110035434666645------
Q ss_pred CCCCCCCHH-HHHHHHHCCCCCEEEECCEECCCCCCCCCCCCHHHHHHHHHHCCCCCEEEECCCCCEEEEEE-CCEEEEE
Q ss_conf 545788978-86354204798668835410078888765222699999987238897898448872168862-8868886
Q T0628 81 YLPLPAAFS-DIGQQLTAVGDNIWIIPGLCVSRDDNHNVMRGEETQLLGARALAPSSVYVMPGTHCKWVLAD-RRQIHDF 158 (295)
Q Consensus 81 y~~~Pa~l~-~l~~~~~~~~~~v~iiPGl~~~~~~~~DVMRGEEtqi~G~l~~~~~~~icLPGTHsKWv~v~-~g~I~~f 158 (295)
.... .+....... ++.+. .| +. .-+.+ ..+ +++++-||-||-..++ +|++..|
T Consensus 75 -----~~~~~~~~~~~~~~--~v~~~----------~d---a~-~a~~~---~~~-giv~I~GTGs~~~~~~~~g~~~r~ 129 (268)
T PF01869_consen 75 -----AGADQEFAAEIVRS--EVTVH----------ND---AA-IALYG---ATG-GIVVIAGTGSIAYGRDEDGRVARF 129 (268)
T ss_dssp -----TTHHTCHHHHHHHH--EEEEC----------CC---HH-CCHHH---HC--EEEEEE---EEEEEE----EEEEE
T ss_pred -----CCHHHHHHHHHHCC--EEEEE----------HH---HH-HHHCC---CCC-EEEEECCCCCEEEEEECCCCEEEE
T ss_conf -----41255667753003--59985----------74---99-97247---898-899985898579999779968986
Q ss_pred ECC
Q ss_conf 302
Q T0628 159 RTV 161 (295)
Q Consensus 159 ~T~ 161 (295)
..+
T Consensus 130 gg~ 132 (268)
T PF01869_consen 130 GGW 132 (268)
T ss_dssp EEE
T ss_pred CCC
T ss_conf 789
No 6
>PF09608 Alph_Pro_TM: Putative transmembrane protein (Alph_Pro_TM)
Probab=44.45 E-value=5.7 Score=16.28 Aligned_cols=19 Identities=11% Similarity=0.083 Sum_probs=12.1
Q ss_pred CCCCCEEEEE-ECCEEEEEE
Q ss_conf 4887216886-288688863
Q T0628 141 PGTHCKWVLA-DRRQIHDFR 159 (295)
Q Consensus 141 PGTHsKWv~v-~~g~I~~f~ 159 (295)
.|+|.-=+.+ ++|++++-.
T Consensus 169 ~G~Y~v~~~L~r~G~vv~~~ 188 (236)
T PF09608_consen 169 VGTYTVRIFLFRDGRVVASQ 188 (236)
T ss_pred CCEEEEEEEEEECCEEEEEE
T ss_conf 71389999998399699988
No 7
>PF00012 HSP70: Hsp70 protein; InterPro: IPR013126 A family of heat shock proteins, the hsp70 proteins have an average molecular weight of 70 kDa , , . In most species, there are many proteins that belong to the hsp70 family. Some of these are only expressed under stress conditions (strictly inducible), while some are present in cells under normal growth conditions and are not heat-inducible (constitutive or cognate) , . Hsp70 proteins can be found in different cellular compartments (nuclear, cytosolic, mitochondrial, endoplasmic reticulum, etc...). Little is known of the function of hsp70 proteins. Some evidence suggests that the constitutive members have a role in the disassembly of clathrin cages , and may also participate in the post-translational transmembrane targetting of proteins to cellular organelles. No specific activities or associations have been found for the inducible members , although it has been suggested that they may accept incoming precursor proteins, keep them unfolded, then pass them on to the hsp60/hsp10 (cpn60/cpn10) complex for folding and assembly.; PDB: 3fzk_A 3fzf_A 3fzl_A 3fzm_A 3fzh_A 1kax_A 1yuw_A 1qqo_A 1nga_A 2qw9_A ....
Probab=44.07 E-value=3.4 Score=17.78 Aligned_cols=44 Identities=25% Similarity=0.332 Sum_probs=31.3
Q ss_pred CEEEEECCHHHHHHHHHHHH-HCCCC-EEECCHHHHHHHHHHHHHH
Q ss_conf 63899848589999999999-80984-3433879999999999999
Q T0628 248 QAISLVAGSSLTSRYQQAFA-AIGRE-VSAVAGDTAFQTGIRSIAY 291 (295)
Q Consensus 248 ~~v~LiG~~~L~~~Y~~AL~-~~G~~-~~~~d~d~a~~~Gl~~ia~ 291 (295)
+.|.|+|........+..++ .+|.. ...++.|+++-.|-.-.+.
T Consensus 330 ~~V~lvGG~sriP~v~~~l~~~f~~~~~~~~n~d~ava~GAa~~aa 375 (602)
T PF00012_consen 330 DSVELVGGSSRIPAVQEMLEEYFGKKISKSLNPDEAVARGAAIQAA 375 (602)
T ss_dssp SEEEEE--ETTSHHHHHHHHHHT--EEB-SS-TTTTTT---HHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCH
T ss_conf 7999878864148999988741475422244445434557422010
No 8
>PF07318 DUF1464: Protein of unknown function (DUF1464); InterPro: IPR009927 This family consists of several hypothetical archaeal proteins of around 350 residues in length. The function of this family is unknown.
Probab=37.16 E-value=9 Score=15.04 Aligned_cols=255 Identities=14% Similarity=0.111 Sum_probs=114.5
Q ss_pred EEECCCHHHEEEEECC-CCEEEECCCCCCHHHCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCC-----
Q ss_conf 8862763146766407-8441200121002215875648999999986217898189975515512462378545-----
Q T0628 10 AIDWGSTNLRAWLYQG-EECLESRQSEAGVTRLNGRSPAAVLAEITQHWRDGATPVVMAGMVGSNVGWKIAPYLP----- 83 (295)
Q Consensus 10 aiDwGTtnlR~~l~~~-~~vl~~~~~~~Gv~~~~~~~f~~~l~~~~~~~~~~~~PVi~~GMigS~~Gw~Eapy~~----- 83 (295)
.||-||+++.+..+++ +.++-..+-+.-. +.+ .+..+.+.+.+....++=+.-||| -.+..++-.++
T Consensus 1 GIDpGT~s~dv~~~dd~G~v~~~~~ip~~e--v~~--~p~~il~~l~~~~~~DlIa~psGy---G~pl~~~~~it~~e~~ 73 (343)
T PF07318_consen 1 GIDPGTSSIDVCGVDDDGKVIFDFSIPREE--VAK--NPFIILELLEEFGRIDLIAGPSGY---GDPLKRIREITEREIF 73 (343)
T ss_pred CCCCCCCCEEEEEECCCCCEEEEEECCHHH--HHH--CCHHHHHHHHHCCCCCEEEECCCC---CCCCCCCCCCCHHHHH
T ss_conf 979998607899984788478986246888--641--817899998744897789744656---8754123423333422
Q ss_pred ------------CCCCHHHHHHHHHCCCCCEEEECCEECCC------------CCCCCCCCCHHHHHHHHHHC------C
Q ss_conf ------------78897886354204798668835410078------------88876522269999998723------8
Q T0628 84 ------------LPAAFSDIGQQLTAVGDNIWIIPGLCVSR------------DDNHNVMRGEETQLLGARAL------A 133 (295)
Q Consensus 84 ------------~Pa~l~~l~~~~~~~~~~v~iiPGl~~~~------------~~~~DVMRGEEtqi~G~l~~------~ 133 (295)
-+.++-.+-..+..-+.|++++|||-... -+.+|=| -+-.+++... .
T Consensus 74 l~tl~~~~~~g~~~~Glr~~~~~~~~~~l~~~~iPGVihL~tVP~~RK~N~IDmGTaDKv---a~a~l~i~~~~e~~gi~ 150 (343)
T PF07318_consen 74 LATLIEGSEEGRELGGLRRMVREMAESDLPAVFIPGVIHLPTVPAWRKINRIDMGTADKV---ASAVLAIHDSAERLGIP 150 (343)
T ss_pred CEEECCCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHCCCCCCCHHHH---HHHHHHHHHHHHHCCCC
T ss_conf 046303433344556289999999867997698266123777862654143246757889---99998643007551767
Q ss_pred C---CCEEEECCCC-CEEEEEECCEEEEEEC------------CCHHHHHHHHHCCCEECCCCCCCCCCHHHHHHHHHHH
Q ss_conf 8---9789844887-2168862886888630------------2018999998608500234787657989999999997
Q T0628 134 P---SSVYVMPGTH-CKWVLADRRQIHDFRT------------VLTGELHHLLLQLSLVGAGLPPQETSAAAFAAGLQRG 197 (295)
Q Consensus 134 ~---~~~icLPGTH-sKWv~v~~g~I~~f~T------------~mTGELf~~L~~~siL~~~~~~~~~d~~aF~~gv~~~ 197 (295)
. +-+++--|.- +--+.|++|+|++.-- +|-||+--++.+..-+.+ ...|..|+...
T Consensus 151 y~~~nfIlvEiG~~~t~~iaV~~GkIvdG~ggt~g~pG~~~~G~lD~E~ay~i~~~~~~sK--------~~lFsgG~~~i 222 (343)
T PF07318_consen 151 YSTVNFILVEIGSNYTAAIAVKNGKIVDGIGGTIGFPGYLSHGALDGEVAYLIGNALEFSK--------NHLFSGGAAKI 222 (343)
T ss_pred CCCCEEEEEECCCCCEEEEEEECCEEEECCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCH--------HHHCCCCCEEE
T ss_conf 4434079997167836899998996870425534487554567564999998324554453--------22102672477
Q ss_pred HHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEEECC----HHHHHHHHHHHH-HCCC
Q ss_conf 40610588999999999842689878899999999-99999999973179963899848----589999999999-8098
Q T0628 198 INNPAVLPQLFEVRASHVLGALPREQVSEFLSGLL-IGAEVATLSDTFAGQQAISLVAG----SSLTSRYQQAFA-AIGR 271 (295)
Q Consensus 198 ~~~~~l~~~LF~~Ra~~L~~~~~~~~~~~~LsGlL-IG~Elaa~~~~~~~~~~v~LiG~----~~L~~~Y~~AL~-~~G~ 271 (295)
.... .+......+...++=.... +--+++++.+.-...+.|.|-|. ..+..-+...|+ .+..
T Consensus 223 a~~~------------e~~~~~~e~~~~a~~~~~e~v~k~V~sll~~~~~~~~IilSGr~~~~~e~~~~~~~~l~~~~~~ 290 (343)
T PF07318_consen 223 AGID------------EFAERADEDEKCAWEAMIEGVVKEVASLLPSVPDPREIILSGRLSRIPEFFKDLEDRLEEAFKI 290 (343)
T ss_pred ECCH------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 0417------------7776530214678999999999999987501479985999532157566899999999875265
Q ss_pred CEEECCH-----HHHHHHHHHHHHHHHCC
Q ss_conf 4343387-----99999999999999709
Q T0628 272 EVSAVAG-----DTAFQTGIRSIAYAVAN 295 (295)
Q Consensus 272 ~~~~~d~-----d~a~~~Gl~~ia~a~~~ 295 (295)
++....+ +++++ |..-||.++++
T Consensus 291 ~v~~l~~~~~~aKeaA~-G~A~IA~~i~g 318 (343)
T PF07318_consen 291 NVLKLEGLAGKAKEAAQ-GSAIIANGIAG 318 (343)
T ss_pred CEEECCCCCCCCHHHHH-HHHHHHHHHHC
T ss_conf 30102443332023310-28898776524
No 9
>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=35.49 E-value=9.5 Score=14.87 Aligned_cols=44 Identities=18% Similarity=0.174 Sum_probs=30.1
Q ss_pred EEEECCCHHHEEEEECCC-CEEEECCCCCCHHHCCCCC----HHHHHHHHHHHH
Q ss_conf 788627631467664078-4412001210022158756----489999999862
Q T0628 9 IAIDWGSTNLRAWLYQGE-ECLESRQSEAGVTRLNGRS----PAAVLAEITQHW 57 (295)
Q Consensus 9 IaiDwGTtnlR~~l~~~~-~vl~~~~~~~Gv~~~~~~~----f~~~l~~~~~~~ 57 (295)
|+||-|-||+-+-++|++ +++...+.+ +.+++ ....|..++..+
T Consensus 2 iGIDvGGTfTD~V~~d~~~~~i~~~K~~-----Tt~~d~~~gi~~al~~~~~~~ 50 (176)
T PF05378_consen 2 IGIDVGGTFTDAVLLDPDTGVIATAKVP-----TTPDDPSEGILNALEALLEQA 50 (176)
T ss_pred EEEECCCCCEEEEEEECCCCEEEEEECC-----CCCCCHHHHHHHHHHHHHHHC
T ss_conf 4386377867799992898789999868-----888688999999999987532
No 10
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VIIcolicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma urealyticum (Q9PQY7 from SWISSPROT, ). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase . This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC . ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0004518 nuclease activity, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus; PDB: 1vhx_B 1iv0_A 1ovq_A 1nmn_B 1nu0_A.
Probab=33.64 E-value=9.8 Score=14.79 Aligned_cols=88 Identities=14% Similarity=0.229 Sum_probs=47.0
Q ss_pred CEEEEECCCHHHEEEEECCCCEEEECCCCCCHHH-CCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCC
Q ss_conf 4478862763146766407844120012100221-587564899999998621789818997551551246237854578
Q T0628 7 RYIAIDWGSTNLRAWLYQGEECLESRQSEAGVTR-LNGRSPAAVLAEITQHWRDGATPVVMAGMVGSNVGWKIAPYLPLP 85 (295)
Q Consensus 7 ~~IaiDwGTtnlR~~l~~~~~vl~~~~~~~Gv~~-~~~~~f~~~l~~~~~~~~~~~~PVi~~GMigS~~Gw~Eapy~~~P 85 (295)
.++++|+|+.+.=+-+.|....++. +.+... .+....-..|..++.+|... -++-|+.-.-.| -..|
T Consensus 2 ~iLgiD~G~kriGvAvsd~~~~~a~---pl~~i~~~~~~~~~~~l~~li~~~~~~---~iVvGlP~~~~G------~~~~ 69 (135)
T PF03652_consen 2 RILGIDYGTKRIGVAVSDPLGIIAS---PLETIPRKNDEKDWDELKKLIKEWQVD---GIVVGLPLNMDG------SEGE 69 (135)
T ss_dssp EEEE------EE-EEEE-TT--SEE---EEEEEEBTTHHCHHHHHHHHHHHCEEC---EEEE-EEBB--S------SC-T
T ss_pred EEEEEEECCCEEEEEEECCCCCEEE---EEEEEECCCCCHHHHHHHHHHHHHCCC---EEEEECCCCCCC------CCCH
T ss_conf 6999983799899999459997783---578898788867899999999984899---899957899998------8087
Q ss_pred C--CHHHHHHHHHC--CCCCEEEEC
Q ss_conf 8--97886354204--798668835
Q T0628 86 A--AFSDIGQQLTA--VGDNIWIIP 106 (295)
Q Consensus 86 a--~l~~l~~~~~~--~~~~v~iiP 106 (295)
. ....++..+.. ++.||+++=
T Consensus 70 ~~~~v~~fa~~L~~~~~~lpv~~~D 94 (135)
T PF03652_consen 70 QAKKVRKFAERLKKRFPGLPVYLVD 94 (135)
T ss_dssp THHHHHHHHHHHHHHH-TSEEEEEE
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEC
T ss_conf 9999999999999986499659860
No 11
>PF12534 DUF3733: Leucine-rich repeat containing protein 8
Probab=31.97 E-value=8.1 Score=15.32 Aligned_cols=19 Identities=21% Similarity=0.401 Sum_probs=13.2
Q ss_pred HHHHCCCCCEEEECCCCCE
Q ss_conf 9872388978984488721
Q T0628 128 GARALAPSSVYVMPGTHCK 146 (295)
Q Consensus 128 G~l~~~~~~~icLPGTHsK 146 (295)
|-+....|.++|+|.+-+|
T Consensus 43 ~~~q~~~~~~~clP~~~~~ 61 (65)
T PF12534_consen 43 GTFQFTQDKIVCLPCTSSK 61 (65)
T ss_pred HHHHHCCCCCEECCCCCCC
T ss_conf 6677415760376762110
No 12
>PF03490 Varsurf_PPLC: Variant-surface-glycoprotein phospholipase C; InterPro: IPR003633 Variant-surface-glycoprotein phospholipase C, by hydrolysis of the attached glycolipid, releases soluble variant surface glycoprotein containing phosphoinositol from the cell wall after lysis. It catalyses the conversion of variant-surface-glycoprotein 1,2 didecanoyl-SN-phosphatidylinositol and water to 1,2-didecanoylglycerol and the soluble variant-surface-glycoprotein. It also cleaves similar membrane anchors on some mammalian proteins.; GO: 0047396 glycosylphosphatidylinositol diacylglycerol-lyase activity, 0006650 glycerophospholipid metabolic process
Probab=30.29 E-value=6.1 Score=16.14 Aligned_cols=12 Identities=25% Similarity=0.495 Sum_probs=8.8
Q ss_pred CEEEECCCCCEE
Q ss_conf 789844887216
Q T0628 136 SVYVMPGTHCKW 147 (295)
Q Consensus 136 ~~icLPGTHsKW 147 (295)
..+|+||+|+--
T Consensus 25 ~~v~i~GsHns~ 36 (51)
T PF03490_consen 25 TQVCIPGSHNSA 36 (51)
T ss_pred HHEEECCCCCCC
T ss_conf 533401445642
No 13
>PF03309 Bvg_acc_factor: Bordetella pertussis Bvg accessory factor family; InterPro: IPR004619 This is a family of proteins found in a single copy in at least ten different early completed bacterial genomes. The only characterised member of the family is Bvg accessory factor (Baf), a protein required, in addition to the regulatory operon bvgAS, for heterologous transcription of the Bordetella pertussis toxin operon (ptx) in Escherichia coli . Pertussis toxin is an important virulence factor of Bordetella pertussis, the causative agent of pertussis or whooping cough. The BvgAS two-component system controls the expression of pertussis toxin and a number of other B. pertussis virulence factors. Baf acts with BvgAS to further activate ptx transcription in E. coli grown in minimal medium without affecting the growth rate, and functional Baf appears to be required for viability of B. pertussis.; GO: 0016563 transcription activator activity, 0045941 positive regulation of transcription; PDB: 2h3g_X 3djc_L 2gtd_E 3bex_D 3bf1_C 3bf3_F 2nrh_B 2f9w_B 2f9t_A.
Probab=24.64 E-value=15 Score=13.69 Aligned_cols=130 Identities=19% Similarity=0.257 Sum_probs=68.2
Q ss_pred EEEEECCCHHHEEEEECCCCEEE-ECCC-CCCHHHCCCCCHHHHHHHHHHHHCCCCC-CEEEECCCCCCCCCCCCCCCCC
Q ss_conf 47886276314676640784412-0012-1002215875648999999986217898-1899755155124623785457
Q T0628 8 YIAIDWGSTNLRAWLYQGEECLE-SRQS-EAGVTRLNGRSPAAVLAEITQHWRDGAT-PVVMAGMVGSNVGWKIAPYLPL 84 (295)
Q Consensus 8 ~IaiDwGTtnlR~~l~~~~~vl~-~~~~-~~Gv~~~~~~~f~~~l~~~~~~~~~~~~-PVi~~GMigS~~Gw~Eapy~~~ 84 (295)
++.||-|-|++..+++++++++. ..+- ..+-.....+.+...+...+..- .. .|++|-- +
T Consensus 1 ~L~iDiGNT~ik~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~v~isSV--------------~ 63 (206)
T PF03309_consen 1 ILLIDIGNTRIKWALFDGDKLISQSGRISHATALSHTSDELAALLWSLLPEP---KIEAVIISSV--------------V 63 (206)
T ss_dssp EEEEEE---EEEEEEEE---EEE-EEEE--EETCCSSCCCHHHHHHHHHHCC---CCGEEEEEES--------------S
T ss_pred CEEEEECCCEEEEEEEECCEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCC---CCCEEEEEEE--------------C
T ss_conf 9899965891699999899887523699705567678899999999861516---6881999992--------------6
Q ss_pred CCCHHHHHHHH-HCCCCCEEEE--C----CEECCCCCCCCCCCCHH--HHHHHHHHCCC-CCEEEECCCCCEEEEEE-CC
Q ss_conf 88978863542-0479866883--5----41007888876522269--99999872388-97898448872168862-88
Q T0628 85 PAAFSDIGQQL-TAVGDNIWII--P----GLCVSRDDNHNVMRGEE--TQLLGARALAP-SSVYVMPGTHCKWVLAD-RR 153 (295)
Q Consensus 85 Pa~l~~l~~~~-~~~~~~v~ii--P----Gl~~~~~~~~DVMRGEE--tqi~G~l~~~~-~~~icLPGTHsKWv~v~-~g 153 (295)
|.....+.... ..+. +++++ + |+++.. ..|.-+ |-. .-++|+.+..+ +-+++=-||-...=.|+ +|
T Consensus 64 p~~~~~~~~~~~~~~~-~~~~v~~~~~~~~l~~~y-~~p~~L-G~DR~~a~~aA~~~~~~~~lVID~GTAiTiD~v~~~g 140 (206)
T PF03309_consen 64 PELTERLLEALLKRFF-KPHFVKSPDEKLGLKNAY-DDPEQL-GVDRWAAAVAARQLYGKPVLVIDAGTAITIDVVDADG 140 (206)
T ss_dssp GHHHHHHHHHHHHHCS---EEEE--GGC---EESS-SSGGG----HHHHHHHHHHHHCTSEEEEEEE---EEEEEEETTS
T ss_pred CHHHHHHHHHHHHHCC-CCEEEEECCCCCCCCCCC-CCCCCC-CHHHHHHHHHHHHHHCCCEEEEECCCCEEEEEECCCC
T ss_conf 8899999999999729-989998066467842568-881015-5899999999999819988999769611799986899
Q ss_pred EEEE
Q ss_conf 6888
Q T0628 154 QIHD 157 (295)
Q Consensus 154 ~I~~ 157 (295)
+..+
T Consensus 141 ~~lG 144 (206)
T PF03309_consen 141 RHLG 144 (206)
T ss_dssp EE--
T ss_pred CEEE
T ss_conf 1988
No 14
>PF00374 NiFeSe_Hases: Nickel-dependent hydrogenase; InterPro: IPR001501 Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes. There are various types of hydrogenases, but all of them seem to contain at least one iron-sulphur cluster. They can be broadly divided into two groups: hydrogenases containing nickel and, in some cases, also selenium (the [NiFe] and [NiFeSe] hydrogenases) and those lacking nickel (the [Fe] hydrogenases). The [NiFe] and [NiFeSe] hydrogenases are heterodimer that consist of a small subunit that contains a signal peptide and a large subunit. All the known large subunits seem to be evolutionary related ; they contain two Cys-x-x-Cys motifs; one at their N-terminal end; the other at their C-terminal end. These four cysteines are involved in the binding of nickel . In the [NiFeSe] hydrogenases the first cysteine of the C-terminal motif is a selenocysteine which has experimentally been shown to be a nickel ligand .; GO: 0008901 ferredoxin hydrogenase activity, 0016151 nickel ion binding, 0006118 electron transport; PDB: 1cc1_L 1yrq_J 3cus_Q 1yqw_Q 3cur_J 1frf_L 2frv_J 1frv_B 1yq9_I 1e3d_B ....
Probab=24.18 E-value=15 Score=13.63 Aligned_cols=17 Identities=12% Similarity=0.544 Sum_probs=6.5
Q ss_pred CCCEEEEEECCEEEEEE
Q ss_conf 87216886288688863
Q T0628 143 THCKWVLADRRQIHDFR 159 (295)
Q Consensus 143 THsKWv~v~~g~I~~f~ 159 (295)
+=.+|+.|++|+|+.++
T Consensus 436 ~L~H~~~i~dGkI~nyq 452 (507)
T PF00374_consen 436 ALGHWIRIEDGKIENYQ 452 (507)
T ss_dssp -BEEEEEEETTEEEEEE
T ss_pred CEEEEEEECCCEEEEEE
T ss_conf 43679998599388877
No 15
>PF11795 DUF3322: Uncharacterized protein conserved in bacteria N-term (DUF3322)
Probab=20.23 E-value=10 Score=14.62 Aligned_cols=21 Identities=10% Similarity=0.192 Sum_probs=10.0
Q ss_pred HHHHHHHHHCCCCEEECCHHH
Q ss_conf 999999998098434338799
Q T0628 260 SRYQQAFAAIGREVSAVAGDT 280 (295)
Q Consensus 260 ~~Y~~AL~~~G~~~~~~d~d~ 280 (295)
..|.+.+...|+..+-+..-+
T Consensus 161 g~~lR~l~i~GvdtK~iE~h~ 181 (190)
T PF11795_consen 161 GLYLRQLPIPGVDTKFIERHR 181 (190)
T ss_pred CCCHHHCCCCCCCHHHHHHHH
T ss_conf 874653786663158899888
Done!