Query gi|254781208|ref|YP_003065621.1| hypothetical protein CLIBASIA_05575 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 578
No_of_seqs 170 out of 529
Neff 8.2
Searched_HMMs 39220
Date Mon May 30 07:14:50 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781208.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA00661 hypothetical protein 100.0 0 0 990.4 52.4 545 2-573 1-556 (734)
2 COG5308 NUP170 Nuclear pore co 71.3 6.2 0.00016 17.6 10.7 16 331-348 375-390 (1263)
3 TIGR01059 gyrB DNA gyrase, B s 70.3 4.2 0.00011 18.8 2.7 55 46-101 13-77 (818)
4 KOG0284 consensus 62.2 7 0.00018 17.2 2.6 30 333-362 225-255 (464)
5 pfam11134 Phage_stabilize Phag 60.0 10 0.00025 16.2 6.9 45 379-423 167-216 (468)
6 TIGR01058 parE_Gpos DNA topois 53.2 3.3 8.3E-05 19.5 -0.3 27 46-74 23-49 (655)
7 COG5156 DOC1 Anaphase-promotin 53.0 13 0.00033 15.4 4.6 107 407-518 27-140 (189)
8 PTZ00109 DNA gyrase subunit b; 51.2 14 0.00035 15.2 2.6 29 45-75 67-95 (941)
9 COG0187 GyrB Type IIA topoisom 48.3 14 0.00036 15.1 2.3 55 44-99 16-80 (635)
10 TIGR02854 spore_II_GA sigma-E 47.6 16 0.0004 14.8 4.9 37 65-101 255-294 (320)
11 TIGR02109 PQQ_syn_pqqE coenzym 46.9 11 0.00028 15.9 1.6 65 5-79 53-120 (363)
12 TIGR03470 HpnH hopanoid biosyn 44.6 15 0.00037 15.0 1.9 48 7-62 74-121 (318)
13 KOG1306 consensus 39.6 20 0.00052 14.0 2.3 48 6-56 106-153 (596)
14 KOG0973 consensus 37.0 22 0.00057 13.7 3.7 22 74-95 77-99 (942)
15 PRK08125 bifunctional UDP-gluc 36.7 23 0.00058 13.7 5.3 49 329-389 225-273 (660)
16 PRK05644 gyrB DNA gyrase subun 30.9 28 0.00071 13.1 5.0 52 46-99 23-84 (725)
17 PRK13775 formimidoylglutamase; 29.4 17 0.00044 14.5 0.3 12 17-28 9-20 (328)
18 cd01797 NIRF_N NIRF_N This 27.4 23 0.00058 13.7 0.6 10 339-348 41-50 (78)
19 cd01798 parkin_N parkin_N par 26.8 22 0.00057 13.7 0.5 11 339-349 37-47 (70)
20 pfam01375 Enterotoxin_a Heat-l 26.0 31 0.0008 12.7 1.1 19 313-331 181-199 (258)
21 cd00823 TopoIIB_Trans TopoIIB_ 25.6 16 0.00041 14.8 -0.5 36 46-81 7-42 (151)
22 TIGR02826 RNR_activ_nrdG3 anae 25.5 30 0.00077 12.8 1.0 49 9-60 73-127 (165)
23 KOG1034 consensus 24.0 37 0.00093 12.3 7.4 47 51-97 24-74 (385)
24 TIGR02160 PA_CoA_Oxy5 phenylac 21.0 42 0.0011 11.9 1.0 31 379-415 196-226 (371)
25 TIGR01072 murA UDP-N-acetylglu 20.3 18 0.00046 14.4 -1.0 12 337-348 339-350 (443)
No 1
>PHA00661 hypothetical protein
Probab=100.00 E-value=0 Score=990.38 Aligned_cols=545 Identities=20% Similarity=0.285 Sum_probs=443.4
Q ss_pred CEEEEEECCCCCCEECHHHHHCCCCHHHHHHHHHEEEEEEEEEECCCEECCCCCEEEECCCCCCCEEEEEEEECCCCEEE
Q ss_conf 61266521412420088784143358998768841531498341071427720210000578885379999956996599
Q gi|254781208|r 2 VNTTWTKHSFSAGELSPRLLQSRKDLSLHAQGVAKSRNLIPLRYGPLVSMPLMQEYRDCRLDPRSNRVFSFSIPDGGYAL 81 (578)
Q Consensus 2 a~~~~~q~~F~~GElsP~L~~gR~D~~ky~~g~~~~~N~i~~p~GGl~rRPGt~fv~~l~~s~~~~rlipF~fs~~e~Yi 81 (578)
+|++++|+||++|||||+| .||+|++||.+||++||||+++||||++|||||+||+++|++.+++|||||+||++|+||
T Consensus 1 ~~i~~~Q~~F~~GElsp~l-~gR~Dl~~Y~~g~~~~~N~~v~~~Gg~~rRpG~~fi~~~~~~~~~~rLiPF~fs~~q~yi 79 (734)
T PHA00661 1 SNVRVLQRSFGGGEISPEL-FGRIDDAKYQSGLAICRNFIVKPQGPAENRAGFRFVRAVKDSAKKVRLIPFTYSVTQTYV 79 (734)
T ss_pred CCCCCCCCCCCCCCCCHHH-CCCCCHHHHHHHHHHHCCCEECCCCCCEECCCCEEHHHCCCCCCCEEEEEEEECCCCEEE
T ss_conf 9630222475654238112-356368999989997208488243682047966423111587787799858967995899
Q ss_pred EEEECCEEEEEECCCCEEEEECCCEEEEEECCCCCCCEEEEEEEECCEEEEECCCCCEEEEEEECCCCCCEEEEEEEEEC
Q ss_conf 99979969999818827995036403677225665000279998355899982884227898521576313345443214
Q gi|254781208|r 82 LVFGDKKLQIVVVRSSTKWSPALFGKTYKTPYTFKDNKSLEYAVFGSTAVFVHKDHPPHHLLYIQDGDKISFTFDEIKFL 161 (578)
Q Consensus 82 l~f~~~~irV~~~~g~~~~~~~~~~~~~~tpy~~~~l~~l~~~QsaD~~fI~h~~~~p~~L~R~s~~~~~~w~l~~~~~~ 161 (578)
|||+++|||||+++|.+ .+++.++++++||++++|++|+|+|+||+||||||+||||||.|+++++ |+++++.|.
T Consensus 80 Lefg~~~irv~~~~~~~--~~~~~~~eiatPyt~a~L~~l~yaQSADVmyIvHp~~pPrkL~Rts~ts---WtL~~v~F~ 154 (734)
T PHA00661 80 LEFGAGYFRFHTNGGTL--LNGAVPYEIATPYAEADLFNIHYTQSADVLTLVHPNYPPRELRRLGATN---WQLATVTFT 154 (734)
T ss_pred EEEECCEEEEEECCCEE--ECCCCEEEEECCCCHHHHHCEEEEEECCEEEEECCCCCCEEEEECCCCC---EEEEEEECC
T ss_conf 99808799999689589--3188206986777366550042450057899968998858999837896---799987524
Q ss_pred CCCCCCCCEEEEECCCCCEEEECCCCCEEEEECCCCCCCCCCCCEEEEEECCC----CEEEEEEEEEEEEEEEECCCEEE
Q ss_conf 57742221144431564123201233125772157764521145089820356----42775356887667641562689
Q gi|254781208|r 162 PPPWLGDGMISGVKSNAKLSISQADTSTARITSDMKIFKPLDKGRSIRLGCHP----PEWAKNTNYSIGAYIVADDKVYR 237 (578)
Q Consensus 162 ~~p~~~~~~~~~~~~~~~~~~~~~~t~~~t~Tas~~~f~~~~vG~~~~~~~~~----~~~~~~~s~~v~~~~~~~~~~~~ 237 (578)
.+|+.+.|... ....++++.++.+|+|++++.|.+.++|+++++.... ..|........+.....+...|.
T Consensus 155 ~gPf~~~n~~~-----~~t~~asa~~g~iTlTaSa~vf~~~~vG~l~~l~~~~~~~~~~w~t~~~~~~~~~~~~~~~~~~ 229 (734)
T PHA00661 155 SGPFEDINVDT-----PVSVTASANTGGTTLTASASVFALDAVGKLFYLEQPAVDSVPVWETSTESAPSSARRCTNNLYT 229 (734)
T ss_pred CCCCCCCCCCC-----CEEECCCCCCCCEEEEEEEEEEECCCCCCEEEEECCCCCCCCCEEECCEEECCCCEECCCCEEE
T ss_conf 78864445788-----4256146778846788642344204577158850345554321020111302320102451564
Q ss_pred EEEECCCCCEECCCC-CCEEECCCCCCCCEEEEEEEEEEEEEECCEEEEEEEEEEEEEEECCCCCEEECCCCCCCCCCCC
Q ss_conf 985035201000122-2012204530011011000113455411216778754688544215630122135565334566
Q gi|254781208|r 238 SLTTGRSGDRFGYSK-GATYVKDNNITWITVLNLSSKTSRESASGAVAPYYVWGDIKDVSKDGRSISVAPQSQTLFQAGV 316 (578)
Q Consensus 238 ~~~~~~~~~~~~~~~-~~t~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~f~~~~ 316 (578)
....+........+. +..|....+......+....+..++...+.. .......+......+ +..........+....
T Consensus 230 ~~~~~~~~~~~~~~t~g~~w~~~~ga~~~~~y~~~gg~~~~i~~g~g-~~~I~~~~s~~~~~t-~~~~~~~~~~~~~~~~ 307 (734)
T PHA00661 230 NGGAGTIGTLRPSHTEGSAWDGSGGASRYNVYKEQGGEWEYIHSGTG-TSLIDDVIAPDLSVT-PPIYDAVPSQVVGTLN 307 (734)
T ss_pred ECCCCCCCCCCCCCCCCCEEEECCCCCCCEEECCCCCEEEEECCCEE-EEEEEEEECCCCCCC-CCCCCCCCCCEECCCC
T ss_conf 03444111114554355133202575321110235724888515504-899956653764327-7311354420001567
Q ss_pred CCCEEEEEECCCCCCCCEEEEEECCEEEEECCCCCCCEEEEECCCCHHHCCCCCCCCCCCCCCCEEEEECCCCCCEEEEE
Q ss_conf 66411110026888982067999582899647778637998314762200014335667775415898448863126878
Q gi|254781208|r 317 SVVSWFMSAWGEQEGYPSHVTFHNNRLLFSGSKGDELSVYLSSFGAFYDFSLDGEYGCYDPTKALTTAVTDFSASTIHWM 396 (578)
Q Consensus 317 ~t~~w~~~~~sdt~GyP~~v~F~~nRL~f~gt~~~P~~I~~S~~gd~~nF~~~~~~~~~~ddd~i~~~~~~~~~~~i~~~ 396 (578)
++++|++++||+++|||++|+||||||+|||+.++||+|||||+|||+||.+.++. .|||+|.++++++|+|+|+||
T Consensus 308 at~~w~~~~~s~~~gyP~~v~f~e~RL~f~gt~~~P~tiw~S~~g~~~nf~~~~~~---~dddai~~ti~~~qvn~I~~l 384 (734)
T PHA00661 308 ASYKWAKYAFNSAGGYPAAVSYFEQRLCFAGTTNKPQNIWMTRSGTESAMSYSLPV---RDDDRIAFRVAARQANAIRHI 384 (734)
T ss_pred CCCCCCCCCCCCCCCCCCEEEEEECCEEECCCCCCCCCEEEECCCCHHHCCCCCCC---CCCHHEEEEECCCCCEEEEEE
T ss_conf 65311214643778972078985151586267789864888732254214789888---886016998216630007877
Q ss_pred EECCCEEEEEECCCEEEECCC---CCCCCCEEEEEEEEECCCCCCEEEECCEEEEEECCCCEEEEEEEEEC-CCCCCCCC
Q ss_conf 771858999946817997478---88754126888764215664306676749999469958999999713-55455651
Q gi|254781208|r 397 HPFGEGVLVGCDTSLWLLSIS---LSKGLSIDFRRVSGSGVYACPPVSVGDCLVFVCGVGRRIKYISGSTE-QGFRFNEI 472 (578)
Q Consensus 397 ~~~~~~l~~~t~~~~~~~~~~---~~~~~~~~~~~~s~~g~~~~~p~~~g~~~~fvq~~g~~vr~~~y~~~-d~y~~~dl 472 (578)
++.++ |++||+|+||.++++ +.||+|+++++||++||+.++|+.+|+++|||||+||+||||.|+++ |+|+++||
T Consensus 385 ~~~~~-L~i~T~ggE~~v~~~~~~~iTP~n~~~~~qt~~Gs~~v~P~~v~~~~lfvqr~g~~vre~~y~~~~d~y~~~dl 463 (734)
T PHA00661 385 VPLTS-LLLLTSGGEWVIASVNSDAVTPTTISVRPQSSVGSTDVQPVVVNNTTIFVQARGGHVRDLAYNFQADGYVTTDL 463 (734)
T ss_pred ECCCC-EEEEECCCEEEEECCCCCCCCCCCEEEEEEECCCCCCCCCEEECCEEEEEECCCCEEEEEEECCCCCCCCCCCH
T ss_conf 42895-89990673799706899875876268887301566776758888878999779973778875034565125224
Q ss_pred EEEEHHHCCC-CEEEEEEECCCCEEEEEEEECCCCCCEEEEEEEECCCCEEEEEEEEEEECCCEEEEEEEEECCCCCCCC
Q ss_conf 0241110388-636899607887189999706777756999999836541675358998579659999986226777761
Q gi|254781208|r 473 TQLADHLFNQ-RILQLVYQEEPHSIVWVVLEPKDNSFPRLLGCRFSAEGEGDFAWHTHMISDKHYVLSAASFPNDNRGGT 551 (578)
Q Consensus 473 t~la~hl~~~-~v~~~a~~~~p~~~~~~v~~~~~~~dg~l~~~ty~~~~q~v~~W~~~~t~g~~~~~~~~~~~~~~~~~d 551 (578)
|+||+||+++ +|++|||||+|++++|||++ ||.|++|||+|+| +|+|||||+|+|+|+++ ++|| ++.+|
T Consensus 464 s~la~Hl~~~~~i~~~a~q~~p~s~vw~v~~-----DG~l~~~ty~r~q-~V~gW~~h~t~G~f~sv--~~i~--~~~~D 533 (734)
T PHA00661 464 TLRAAHLFDNLDILDMCFAKAPQSIVWFIRS-----DGKLLGLTYVPEQ-QVGAWHQHDTAGVFESC--AVVA--EGNED 533 (734)
T ss_pred HHHHHHHCCCCCCEEEECCCCCCCEEEEECC-----CCEEEEEEECCHH-HEEEEEEEECCCEEEEE--EECC--CCCCE
T ss_conf 3414765268750241201598507999968-----9709999851625-16765786249827898--9827--89860
Q ss_pred EEEEEEEEC-CCEEEEEEEEECC
Q ss_conf 499999923-9836899998303
Q gi|254781208|r 552 SLWMLVALS-AGEERSFTVRLNL 573 (578)
Q Consensus 552 ~~~~~V~R~-~g~~~~y~e~~~~ 573 (578)
+||++|||+ ||.++||||||+.
T Consensus 534 ~vy~vVkRti~g~t~ryvE~l~~ 556 (734)
T PHA00661 534 RLYAVVRRTINGQTVRYVERLAS 556 (734)
T ss_pred EEEEEEEEECCCEEEEEEEECCC
T ss_conf 89999999629837999971165
No 2
>COG5308 NUP170 Nuclear pore complex subunit [Intracellular trafficking and secretion]
Probab=71.28 E-value=6.2 Score=17.61 Aligned_cols=16 Identities=13% Similarity=0.279 Sum_probs=7.3
Q ss_pred CCCEEEEEECCEEEEECC
Q ss_conf 982067999582899647
Q gi|254781208|r 331 GYPSHVTFHNNRLLFSGS 348 (578)
Q Consensus 331 GyP~~v~F~~nRL~f~gt 348 (578)
.||.- |+-+|++....
T Consensus 375 ~f~~n--l~~~~~~~lk~ 390 (1263)
T COG5308 375 DFYEN--LFLDRLVMLKR 390 (1263)
T ss_pred CCHHH--HCCCCCCHHCC
T ss_conf 63343--03356303205
No 3
>TIGR01059 gyrB DNA gyrase, B subunit; InterPro: IPR011557 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the B subunit (gyrB) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrB has two functional domains: an N-terminal ATPase and a C-terminal responsible for subunit interactions, the latter differing between subunit B and single polypeptide topoisomerase II . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=70.26 E-value=4.2 Score=18.80 Aligned_cols=55 Identities=7% Similarity=-0.070 Sum_probs=29.2
Q ss_pred CCCEECCCCCEEEECCCCCCCEEEEEEEEC--CCCEEE-------E-EEECCEEEEEECCCCEEEE
Q ss_conf 071427720210000578885379999956--996599-------9-9979969999818827995
Q gi|254781208|r 46 GPLVSMPLMQEYRDCRLDPRSNRVFSFSIP--DGGYAL-------L-VFGDKKLQIVVVRSSTKWS 101 (578)
Q Consensus 46 GGl~rRPGt~fv~~l~~s~~~~rlipF~fs--~~e~Yi-------l-~f~~~~irV~~~~g~~~~~ 101 (578)
.+++||||| ||+.+..-.|=+|||.=+.| -+|+-- + .-.|+-|.|-|++-++.+.
T Consensus 13 EAVRKRPGM-YIGdTg~G~GLHHlvyEVVDNaIDEAlAGyC~~I~v~i~~dgsv~V~DnGRGIPVd 77 (818)
T TIGR01059 13 EAVRKRPGM-YIGDTGEGTGLHHLVYEVVDNAIDEALAGYCDTINVTINDDGSVTVEDNGRGIPVD 77 (818)
T ss_pred CCCCCCCCC-EECCCCCCCCCEEEEEEEECCHHHHHHCCCCCEEEEEEECCCEEEEEECCCCCCCC
T ss_conf 775378883-01124878972389999843404420066124148999628769998588588743
No 4
>KOG0284 consensus
Probab=62.21 E-value=7 Score=17.24 Aligned_cols=30 Identities=27% Similarity=0.429 Sum_probs=18.5
Q ss_pred CEEEEEE-CCEEEEECCCCCCCEEEEECCCC
Q ss_conf 2067999-58289964777863799831476
Q gi|254781208|r 333 PSHVTFH-NNRLLFSGSKGDELSVYLSSFGA 362 (578)
Q Consensus 333 P~~v~F~-~nRL~f~gt~~~P~~I~~S~~gd 362 (578)
|++|-.| ++-|++-|++.++-.+|=-|+|.
T Consensus 225 VksvdWHP~kgLiasgskDnlVKlWDprSg~ 255 (464)
T KOG0284 225 VKSVDWHPTKGLIASGSKDNLVKLWDPRSGS 255 (464)
T ss_pred CCEECCCCCCCEEEECCCCCEEEEECCCCCC
T ss_conf 6112257754236773578536766588720
No 5
>pfam11134 Phage_stabilize Phage stabilisation protein. Phage stabilisation protein, also referred to as gp10 has a structure rich in beta sheets which spontaneously assembles into hexamers. Gp10 forms part of the baseplate of bacteriophage T4 and functions as a molecular lever that rotates and extends the hinged short tail fibers to facilitate cell attachment.
Probab=60.04 E-value=10 Score=16.17 Aligned_cols=45 Identities=4% Similarity=-0.039 Sum_probs=22.3
Q ss_pred CCEEEEE---CCCCCCEEEEEEECCCEEEEEECC--CEEEECCCCCCCCC
Q ss_conf 4158984---488631268787718589999468--17997478887541
Q gi|254781208|r 379 KALTTAV---TDFSASTIHWMHPFGEGVLVGCDT--SLWLLSISLSKGLS 423 (578)
Q Consensus 379 d~i~~~~---~~~~~~~i~~~~~~~~~l~~~t~~--~~~~~~~~~~~~~~ 423 (578)
+|+.+.. +-.|+..|.-+.++++.++.|-+. +.|.+.|+...|..
T Consensus 167 ~PdrY~a~yrAESqPDgIig~~~wRd~Iv~fGssTIEyFsltG~a~~~~~ 216 (468)
T pfam11134 167 HPDRYGAFYRAESQPDGIIGIDSWRDFIVCFGSSSIEYFSLTGAADFPQA 216 (468)
T ss_pred CCCCCCCCCCCCCCCCCEEECCEEEEEEEEECCCEEEEEECCCCCCCCCH
T ss_conf 74435644302259973650000010279813350240101377778726
No 6
>TIGR01058 parE_Gpos DNA topoisomerase IV, B subunit; InterPro: IPR005740 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit B (parE) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=53.15 E-value=3.3 Score=19.54 Aligned_cols=27 Identities=7% Similarity=-0.092 Sum_probs=18.2
Q ss_pred CCCEECCCCCEEEECCCCCCCEEEEEEEE
Q ss_conf 07142772021000057888537999995
Q gi|254781208|r 46 GPLVSMPLMQEYRDCRLDPRSNRVFSFSI 74 (578)
Q Consensus 46 GGl~rRPGt~fv~~l~~s~~~~rlipF~f 74 (578)
..++||||| ||+.. ++.+=+||++=+.
T Consensus 23 ~AVrKRPGM-YIGST-ds~GLHHl~wEIv 49 (655)
T TIGR01058 23 DAVRKRPGM-YIGST-DSKGLHHLVWEIV 49 (655)
T ss_pred HHHCCCCCC-EECCC-CCCCCHHHHHHHH
T ss_conf 000158984-12256-8785055678788
No 7
>COG5156 DOC1 Anaphase-promoting complex (APC), subunit 10 [Cell division and chromosome partitioning / Posttranslational modification, protein turnover, chaperones]
Probab=53.00 E-value=13 Score=15.40 Aligned_cols=107 Identities=18% Similarity=0.066 Sum_probs=70.6
Q ss_pred ECCCEEEECCCCC-CCCCEE--EEEEEEECCCCCCEEEECCEEEEEECCCCEEEEEEEEE--CCCCCCCCCEEEEHHHCC
Q ss_conf 4681799747888-754126--88876421566430667674999946995899999971--355455651024111038
Q gi|254781208|r 407 CDTSLWLLSISLS-KGLSID--FRRVSGSGVYACPPVSVGDCLVFVCGVGRRIKYISGST--EQGFRFNEITQLADHLFN 481 (578)
Q Consensus 407 t~~~~~~~~~~~~-~~~~~~--~~~~s~~g~~~~~p~~~g~~~~fvq~~g~~vr~~~y~~--~d~y~~~dlt~la~hl~~ 481 (578)
+.=.||.+++--. -|.-.. -...+++-+..++|-.+. +.|.-|.--.+..+..++ +++|...-+-+-|.|-+.
T Consensus 27 ~~La~w~~SSfK~g~p~r~~lddn~dtyWqsDg~qPH~i~--I~F~kr~~I~~v~lfls~t~DeSYtPs~i~v~aG~~~~ 104 (189)
T COG5156 27 THLAEWRLSSFKRGHPLRELLDDNMDTYWQSDGVQPHSIQ--ISFDKRRYIQSVQLFLSFTQDESYTPSKIGVRAGLTRE 104 (189)
T ss_pred HHHEEEEECCCCCCCCHHHHHHCCHHHHHCCCCCCCCEEE--EEEEEEEEEEEEHHHHHHHCCCCCCCCEEEEECCCCHH
T ss_conf 0010330020014885888763555665304898872699--99867776652122344321455482006785168865
Q ss_pred C-CEEEEEEECCCCEEEEE-EEECCCCCCEEEEEEEECC
Q ss_conf 8-63689960788718999-9706777756999999836
Q gi|254781208|r 482 Q-RILQLVYQEEPHSIVWV-VLEPKDNSFPRLLGCRFSA 518 (578)
Q Consensus 482 ~-~v~~~a~~~~p~~~~~~-v~~~~~~~dg~l~~~ty~~ 518 (578)
+ .++.+.--.+|+..+-+ |++.+. |+ |+.|-|.+
T Consensus 105 D~r~~~~vev~ep~Gwv~l~v~d~~~--d~-LL~c~~I~ 140 (189)
T COG5156 105 DVREISSVEVVEPEGWVTLSVADKRE--DD-LLKCIYIL 140 (189)
T ss_pred HHEEEEEEEEECCCCEEEEEECCCCC--CC-CEEEEEEE
T ss_conf 50547778997477569988021576--77-32479999
No 8
>PTZ00109 DNA gyrase subunit b; Provisional
Probab=51.25 E-value=14 Score=15.21 Aligned_cols=29 Identities=10% Similarity=-0.060 Sum_probs=19.7
Q ss_pred ECCCEECCCCCEEEECCCCCCCEEEEEEEEC
Q ss_conf 1071427720210000578885379999956
Q gi|254781208|r 45 YGPLVSMPLMQEYRDCRLDPRSNRVFSFSIP 75 (578)
Q Consensus 45 ~GGl~rRPGt~fv~~l~~s~~~~rlipF~fs 75 (578)
-.+++||||| ||+.. +..+-.+|+.=+.+
T Consensus 67 LEaVRKRPGM-YIG~T-d~~GlHHlv~EIvD 95 (941)
T PTZ00109 67 LEAVRKRPGM-YIGNT-DVKGLHQILFEIID 95 (941)
T ss_pred CHHHCCCCCC-EECCC-CCCCCCCEEEEEHH
T ss_conf 5321369974-45689-99863212210012
No 9
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=48.30 E-value=14 Score=15.09 Aligned_cols=55 Identities=5% Similarity=-0.097 Sum_probs=31.9
Q ss_pred EECCCEECCCCCEEEECCCCCCCEEEEEEEEC--CCCEEE-------EEE-ECCEEEEEECCCCEE
Q ss_conf 41071427720210000578885379999956--996599-------999-799699998188279
Q gi|254781208|r 44 RYGPLVSMPLMQEYRDCRLDPRSNRVFSFSIP--DGGYAL-------LVF-GDKKLQIVVVRSSTK 99 (578)
Q Consensus 44 p~GGl~rRPGt~fv~~l~~s~~~~rlipF~fs--~~e~Yi-------l~f-~~~~irV~~~~g~~~ 99 (578)
.-..++||||| ||+......+-.+|+.=+.+ -+|+-. +.+ .++.|.|.+++=+..
T Consensus 16 GLEaVRkRPGM-YIGst~~~~GLhHlv~EVvDNsiDEalaG~~~~I~V~l~~d~sisV~DnGRGIP 80 (635)
T COG0187 16 GLEAVRKRPGM-YIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRIDVTLHEDGSISVEDNGRGIP 80 (635)
T ss_pred CCHHHHCCCCC-EECCCCCCCCCEEEEEEEEECCHHHHHHCCCCEEEEEECCCCEEEEEECCCCCC
T ss_conf 74776459985-533689999650468676313074786386857899994798089987898776
No 10
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA; InterPro: IPR005081 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA . ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 sporulation (sensu Bacteria).
Probab=47.59 E-value=16 Score=14.83 Aligned_cols=37 Identities=16% Similarity=0.188 Sum_probs=30.2
Q ss_pred CCEEEEEEE-ECCCCEEEEEEECCEEEE--EECCCCEEEE
Q ss_conf 853799999-569965999997996999--9818827995
Q gi|254781208|r 65 RSNRVFSFS-IPDGGYALLVFGDKKLQI--VVVRSSTKWS 101 (578)
Q Consensus 65 ~~~rlipF~-fs~~e~Yil~f~~~~irV--~~~~g~~~~~ 101 (578)
.+.|+|||. .+.++.|+..|.+.++++ +..+....+.
T Consensus 255 ~r~~~IPf~~Vg~~~g~l~~ikPd~v~IrP~~~~~~~~v~ 294 (320)
T TIGR02854 255 SRIRLIPFRGVGGGSGFLLGIKPDRVKIRPRYEGEEIEVK 294 (320)
T ss_pred CCCCEEEEEEECCCCCCEEEEECCEEEEEEEECCCEEEEE
T ss_conf 3025524245658873147870666588464259747972
No 11
>TIGR02109 PQQ_syn_pqqE coenzyme PQQ biosynthesis protein E; InterPro: IPR011843 This entry describes coenzyme PQQ biosynthesis protein E, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.; GO: 0051539 4 iron 4 sulfur cluster binding, 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=46.94 E-value=11 Score=15.86 Aligned_cols=65 Identities=25% Similarity=0.195 Sum_probs=48.7
Q ss_pred EEEECCCCCCEECHHHHHCCCCHHHHHHHHHEE---EEEEEEEECCCEECCCCCEEEECCCCCCCEEEEEEEECCCCE
Q ss_conf 665214124200887841433589987688415---314983410714277202100005788853799999569965
Q gi|254781208|r 5 TWTKHSFSAGELSPRLLQSRKDLSLHAQGVAKS---RNLIPLRYGPLVSMPLMQEYRDCRLDPRSNRVFSFSIPDGGY 79 (578)
Q Consensus 5 ~~~q~~F~~GElsP~L~~gR~D~~ky~~g~~~~---~N~i~~p~GGl~rRPGt~fv~~l~~s~~~~rlipF~fs~~e~ 79 (578)
-..|-=||||| | + .|.||..+-..|+++ -|.|-+-.|.-..| +.+++..+-.+--|.|+=.+++.
T Consensus 53 GvlqlHfSGGE--P--~-aR~DL~eLv~~A~~LGlYtNLITSGvGLt~~r-----l~~L~~aGLDHvQlSfQ~vd~~~ 120 (363)
T TIGR02109 53 GVLQLHFSGGE--P--L-ARPDLVELVAHARRLGLYTNLITSGVGLTEAR-----LDALADAGLDHVQLSFQGVDEAL 120 (363)
T ss_pred CCEEEECCCCC--C--C-CCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHH-----HHHHHHCCCCEEEEEEECCCHHH
T ss_conf 90675130776--6--6-33577999999977587014677634567999-----99997579857887641478788
No 12
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=44.64 E-value=15 Score=15.01 Aligned_cols=48 Identities=19% Similarity=0.313 Sum_probs=31.1
Q ss_pred EECCCCCCEECHHHHHCCCCHHHHHHHHHEEEEEEEEEECCCEECCCCCEEEECCC
Q ss_conf 52141242008878414335899876884153149834107142772021000057
Q gi|254781208|r 7 TKHSFSAGELSPRLLQSRKDLSLHAQGVAKSRNLIPLRYGPLVSMPLMQEYRDCRL 62 (578)
Q Consensus 7 ~q~~F~~GElsP~L~~gR~D~~ky~~g~~~~~N~i~~p~GGl~rRPGt~fv~~l~~ 62 (578)
..-+|+||| | || |.|+...-..+++..=++...+-|+.-. +.+..++.
T Consensus 74 p~V~itGGE--P-LL--r~dl~eIv~~a~~~g~~v~l~TNG~Ll~---k~i~~~~~ 121 (318)
T TIGR03470 74 PVVSIPGGE--P-LL--HPEIDEIVRGLVARKKFVYLCTNALLLE---KKLDKFEP 121 (318)
T ss_pred CEEEECCCC--C-CC--CCCHHHHHHHHHHCCCEEEEECCHHHHH---HHHHHHHH
T ss_conf 789951887--4-55--6479999999997599799977552009---99999851
No 13
>KOG1306 consensus
Probab=39.55 E-value=20 Score=14.01 Aligned_cols=48 Identities=15% Similarity=0.112 Sum_probs=38.0
Q ss_pred EEECCCCCCEECHHHHHCCCCHHHHHHHHHEEEEEEEEEECCCEECCCCCE
Q ss_conf 652141242008878414335899876884153149834107142772021
Q gi|254781208|r 6 WTKHSFSAGELSPRLLQSRKDLSLHAQGVAKSRNLIPLRYGPLVSMPLMQE 56 (578)
Q Consensus 6 ~~q~~F~~GElsP~L~~gR~D~~ky~~g~~~~~N~i~~p~GGl~rRPGt~f 56 (578)
.-.|+|.+|+|.|.+ -++...|.--+.-..-+++-|.|-++|+++++-
T Consensus 106 ~~gn~f~agdLGPgT---IVGSAAfnlF~iiAVCv~vip~Ge~rki~~lrV 153 (596)
T KOG1306 106 FCGNEFQAGDLGPGT---IVGSAAFNLFEIIAVCVRVIPAGELRKIFHLRV 153 (596)
T ss_pred HHCCCCCCCCCCCCE---EECHHHHHHHHHEEEEEEECCCCCCCCCCCCEE
T ss_conf 713566326768723---761555421112278999837764112268608
No 14
>KOG0973 consensus
Probab=36.99 E-value=22 Score=13.74 Aligned_cols=22 Identities=18% Similarity=0.052 Sum_probs=8.0
Q ss_pred ECCCCEEEEEEEC-CEEEEEECC
Q ss_conf 5699659999979-969999818
Q gi|254781208|r 74 IPDGGYALLVFGD-KKLQIVVVR 95 (578)
Q Consensus 74 fs~~e~Yil~f~~-~~irV~~~~ 95 (578)
|+-+-+|+-.=++ .-|-||...
T Consensus 77 ~S~dG~~lAsGSDD~~v~iW~~~ 99 (942)
T KOG0973 77 FSPDGSYLASGSDDRLVMIWERA 99 (942)
T ss_pred ECCCCCEEEECCCCCEEEEEEEC
T ss_conf 87898768652686058886304
No 15
>PRK08125 bifunctional UDP-glucuronic acid decarboxylase/UDP-4-amino-4-deoxy-L-arabinose formyltransferase; Validated
Probab=36.67 E-value=23 Score=13.71 Aligned_cols=49 Identities=12% Similarity=0.190 Sum_probs=21.9
Q ss_pred CCCCCEEEEEECCEEEEECCCCCCCEEEEECCCCHHHCCCCCCCCCCCCCCCEEEEECCCC
Q ss_conf 8898206799958289964777863799831476220001433566777541589844886
Q gi|254781208|r 329 QEGYPSHVTFHNNRLLFSGSKGDELSVYLSSFGAFYDFSLDGEYGCYDPTKALTTAVTDFS 389 (578)
Q Consensus 329 t~GyP~~v~F~~nRL~f~gt~~~P~~I~~S~~gd~~nF~~~~~~~~~~ddd~i~~~~~~~~ 389 (578)
+++||.+=+|+.++-.. ||-|+.-.... ....|+....+|+.+..+.+.
T Consensus 225 T~PyPGAFTy~ggkKii---------IWsa~~~~~~~---~~~PGtVls~~Pl~iacg~ga 273 (660)
T PRK08125 225 TDPWPGAFSYVGEQKFT---------IWSSRVHPHAS---GAQPGTVISVAPLRIACGDGA 273 (660)
T ss_pred CCCCCCEEEEECCEEEE---------EEEECCCCCCC---CCCCCEEEECCCEEEEECCCC
T ss_conf 99989725998996899---------99811015665---689953884175699945971
No 16
>PRK05644 gyrB DNA gyrase subunit B; Validated
Probab=30.95 E-value=28 Score=13.09 Aligned_cols=52 Identities=8% Similarity=-0.056 Sum_probs=30.5
Q ss_pred CCCEECCCCCEEEECCCCCCCEEEEEEEEC--CCCEEE-------EE-EECCEEEEEECCCCEE
Q ss_conf 071427720210000578885379999956--996599-------99-9799699998188279
Q gi|254781208|r 46 GPLVSMPLMQEYRDCRLDPRSNRVFSFSIP--DGGYAL-------LV-FGDKKLQIVVVRSSTK 99 (578)
Q Consensus 46 GGl~rRPGt~fv~~l~~s~~~~rlipF~fs--~~e~Yi-------l~-f~~~~irV~~~~g~~~ 99 (578)
.+++||||| ||+.. +..+-.+|+.-+.+ -+|+-. +. ..++.|-|++++-+..
T Consensus 23 e~VRkRPgM-YiG~t-~~~glhhlv~EvvDNsiDEa~aG~~~~I~V~i~~DgsitV~DnGRGIP 84 (725)
T PRK05644 23 EAVRKRPGM-YIGDT-GGRGLHHLVYEVVDNSIDEALAGYCDEIEVTIHADGSVSVTDNGRGIP 84 (725)
T ss_pred HHHCCCCCC-EECCC-CCCCCEEEEEEEEHHHHHHHHCCCCCEEEEEECCCCEEEEEECCCCCC
T ss_conf 755059864-65669-998766889864214787986389967999996898299998997677
No 17
>PRK13775 formimidoylglutamase; Provisional
Probab=29.42 E-value=17 Score=14.50 Aligned_cols=12 Identities=8% Similarity=0.033 Sum_probs=8.2
Q ss_pred CHHHHHCCCCHH
Q ss_conf 887841433589
Q gi|254781208|r 17 SPRLLQSRKDLS 28 (578)
Q Consensus 17 sP~L~~gR~D~~ 28 (578)
.|.|++||+|..
T Consensus 9 ~~~~w~gr~dd~ 20 (328)
T PRK13775 9 TTSYYHGGIDDD 20 (328)
T ss_pred CHHHCCCCCCCC
T ss_conf 835407776776
No 18
>cd01797 NIRF_N NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=27.40 E-value=23 Score=13.71 Aligned_cols=10 Identities=30% Similarity=0.720 Sum_probs=7.9
Q ss_pred ECCEEEEECC
Q ss_conf 9582899647
Q gi|254781208|r 339 HNNRLLFSGS 348 (578)
Q Consensus 339 ~~nRL~f~gt 348 (578)
-||||.|+|-
T Consensus 41 dqQRLifaGK 50 (78)
T cd01797 41 ECQRLFYRGK 50 (78)
T ss_pred HHEEEEECCC
T ss_conf 6745664450
No 19
>cd01798 parkin_N parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=26.76 E-value=22 Score=13.73 Aligned_cols=11 Identities=27% Similarity=0.709 Sum_probs=8.4
Q ss_pred ECCEEEEECCC
Q ss_conf 95828996477
Q gi|254781208|r 339 HNNRLLFSGSK 349 (578)
Q Consensus 339 ~~nRL~f~gt~ 349 (578)
-||||.|+|-.
T Consensus 37 ~qqRLIFaGkq 47 (70)
T cd01798 37 DQLRVIFAGKE 47 (70)
T ss_pred HHEEEEECCCC
T ss_conf 89688878818
No 20
>pfam01375 Enterotoxin_a Heat-labile enterotoxin alpha chain.
Probab=26.04 E-value=31 Score=12.74 Aligned_cols=19 Identities=11% Similarity=0.214 Sum_probs=12.2
Q ss_pred CCCCCCCEEEEEECCCCCC
Q ss_conf 4566664111100268889
Q gi|254781208|r 313 QAGVSVVSWFMSAWGEQEG 331 (578)
Q Consensus 313 ~~~~~t~~w~~~~~sdt~G 331 (578)
.+....+.|++..|....+
T Consensus 181 gFp~~~PaW~~~~~~~fap 199 (258)
T pfam01375 181 GFPPDFPAWREEPWRHFAP 199 (258)
T ss_pred CCCCCCCCCCCCCCCCCCC
T ss_conf 7999993302467766687
No 21
>cd00823 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Probab=25.55 E-value=16 Score=14.76 Aligned_cols=36 Identities=14% Similarity=-0.081 Sum_probs=25.6
Q ss_pred CCCEECCCCCEEEECCCCCCCEEEEEEEECCCCEEE
Q ss_conf 071427720210000578885379999956996599
Q gi|254781208|r 46 GPLVSMPLMQEYRDCRLDPRSNRVFSFSIPDGGYAL 81 (578)
Q Consensus 46 GGl~rRPGt~fv~~l~~s~~~~rlipF~fs~~e~Yi 81 (578)
-||+|.-.-+|++.+.-.+.-.+-+||+....-+|=
T Consensus 7 kGl~k~~~peF~a~vtR~p~vy~G~PF~VEvgiayG 42 (151)
T cd00823 7 KGLKKELNPDFVAAVTRKPKVYRGHPFIVEVGIAYG 42 (151)
T ss_pred HHHHHHCCCEEEEEECCCCCEECCCCEEEEEEEECC
T ss_conf 999874285079996259833279987999860006
No 22
>TIGR02826 RNR_activ_nrdG3 anaerobic ribonucleoside-triphosphate reductase activating protein; InterPro: IPR014191 Members of this entry represent a set of proteins related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR, see IPR012837 from INTERPRO). Members of this entry are found paired with members of a similarly divergent set of anaerobic ribonucleoside-triphosphate reductases. Identification of these proteins as RNR activating proteins is partly from pairing with the candidate RNR and further supported by the finding that upstream of these operons are examples of a conserved regulatory element that is found in nearly all bacteria and that occurs specifically upstream of operons for all three classes of RNR genes ..
Probab=25.54 E-value=30 Score=12.83 Aligned_cols=49 Identities=18% Similarity=0.136 Sum_probs=34.3
Q ss_pred CCCCCCE-ECHHHHHCCCCHHHHHHHHHEE-EEEEEEEECCCEECC----CCCEEEEC
Q ss_conf 1412420-0887841433589987688415-314983410714277----20210000
Q gi|254781208|r 9 HSFSAGE-LSPRLLQSRKDLSLHAQGVAKS-RNLIPLRYGPLVSMP----LMQEYRDC 60 (578)
Q Consensus 9 ~~F~~GE-lsP~L~~gR~D~~ky~~g~~~~-~N~i~~p~GGl~rRP----Gt~fv~~l 60 (578)
-.|.||| |.| + .+.++.++..-+++- .+..+-.+=|..--+ ....+.++
T Consensus 73 v~FlGGEPLAP--w-~~~~l~~Ll~~~k~~~~~L~v~LYTG~~~~~ive~~~~~~~~l 127 (165)
T TIGR02826 73 VLFLGGEPLAP--W-EPEALLSLLKLVKEEHAGLKVCLYTGREHLDIVEIPLELVQHL 127 (165)
T ss_pred EEECCCCCCCC--C-CHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHCCHHHHCCC
T ss_conf 20047898873--3-7689999999999753886688850885454432132232003
No 23
>KOG1034 consensus
Probab=23.99 E-value=37 Score=12.26 Aligned_cols=47 Identities=11% Similarity=0.082 Sum_probs=22.9
Q ss_pred CCCCCEEEECCCCC-CCEEEEEEE-EC--CCCEEEEEEECCEEEEEECCCC
Q ss_conf 77202100005788-853799999-56--9965999997996999981882
Q gi|254781208|r 51 MPLMQEYRDCRLDP-RSNRVFSFS-IP--DGGYALLVFGDKKLQIVVVRSS 97 (578)
Q Consensus 51 RPGt~fv~~l~~s~-~~~rlipF~-fs--~~e~Yil~f~~~~irV~~~~g~ 97 (578)
++..++.+.++-+. .+-.-+.|+ |. ++..-..-.|...+-+|...+.
T Consensus 24 k~~yk~t~~l~ed~~~~I~gv~fN~~~~~~e~~vfatvG~~rvtiy~c~~d 74 (385)
T KOG1034 24 KRSYKYTNHLKEDHNKPIFGVAFNSFLGCDEPQVFATVGGNRVTIYECPGD 74 (385)
T ss_pred CCCEEEEEEHHCCCCCCCCEEEEEHHCCCCCCCEEEEECCCEEEEEEECCC
T ss_conf 666476400111689765346620101788776699817967999997786
No 24
>TIGR02160 PA_CoA_Oxy5 phenylacetate-CoA oxygenase/reductase, PaaK subunit; InterPro: IPR011884 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA . .
Probab=21.01 E-value=42 Score=11.87 Aligned_cols=31 Identities=6% Similarity=-0.009 Sum_probs=15.4
Q ss_pred CCEEEEECCCCCCEEEEEEECCCEEEEEECCCEEEEC
Q ss_conf 4158984488631268787718589999468179974
Q gi|254781208|r 379 KALTTAVTDFSASTIHWMHPFGEGVLVGCDTSLWLLS 415 (578)
Q Consensus 379 d~i~~~~~~~~~~~i~~~~~~~~~l~~~t~~~~~~~~ 415 (578)
+-+.=.|.+.+++. | -+.||=+-.-.||-|=
T Consensus 196 ~ll~GRlD~ekl~~---L---~~~li~~~~~deaFlC 226 (371)
T TIGR02160 196 PLLSGRLDGEKLRA---L---LDSLIDVDEVDEAFLC 226 (371)
T ss_pred CCCCCCCCHHHHHH---H---HHHHCCHHHCCEEEEC
T ss_conf 41024227899998---8---5320021002400111
No 25
>TIGR01072 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase; InterPro: IPR005750 The bacterial enzyme UDP-N-acetylglucosamine (UDP-GlcNAc) enolpyruvyltransferase (MurA) catalyzes the transfer of enolpyruvate from phosphoenolpyruvate to uridine diphospho-N-acetylglucosamine, which is the first committed step of bacterial cell wall biosynthesis. Experimental evidence suggests that binding of substrates to the enzyme does not exclusively follow an ordered mechanism with UDP-GlcNAc binding first, although binding of UDP-GlcNAc to free enzyme is preferred and possibly influenced by pyruvate-P. The reaction thus appears to follow an induced-fit mechanism, in which the binding site for fosfomycin, and presumably also for pyruvate-P, is created by the interaction of free enzyme with the sugar nucleotide. ; GO: 0016740 transferase activity, 0019277 UDP-N-acetylgalactosamine biosynthetic process.
Probab=20.32 E-value=18 Score=14.36 Aligned_cols=12 Identities=25% Similarity=0.443 Sum_probs=9.5
Q ss_pred EEECCEEEEECC
Q ss_conf 999582899647
Q gi|254781208|r 337 TFHNNRLLFSGS 348 (578)
Q Consensus 337 ~F~~nRL~f~gt 348 (578)
+.|||||-|..-
T Consensus 339 tvFEnRf~Hv~E 350 (443)
T TIGR01072 339 TVFENRFMHVDE 350 (443)
T ss_pred CCCCCHHHHHHH
T ss_conf 775224566689
Done!