Query gi|254781027|ref|YP_003065440.1| hypothetical protein CLIBASIA_04645 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 108
No_of_seqs 107 out of 854
Neff 6.7
Searched_HMMs 39220
Date Mon May 30 03:18:50 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781027.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09862 putative ATP-dependen 100.0 3E-31 7.6E-36 178.8 7.9 107 1-108 90-203 (506)
2 TIGR00368 TIGR00368 Mg chelata 100.0 4.2E-32 1.1E-36 183.1 2.7 107 1-108 85-206 (505)
3 COG0606 Predicted ATPase with 100.0 1.8E-30 4.7E-35 174.8 3.5 107 1-108 76-191 (490)
4 TIGR02902 spore_lonB ATP-depen 98.5 1.1E-07 2.8E-12 59.5 4.2 65 6-72 459-531 (532)
5 PRK11823 DNA repair protein Ra 98.3 5.3E-07 1.4E-11 56.0 4.4 60 12-74 386-453 (454)
6 COG1066 Sms Predicted ATP-depe 98.2 1.8E-06 4.6E-11 53.3 4.3 58 13-74 390-455 (456)
7 pfam05362 Lon_C Lon protease ( 98.2 2.3E-06 5.9E-11 52.8 4.6 61 12-72 130-202 (205)
8 TIGR00763 lon ATP-dependent pr 98.1 2.1E-06 5.5E-11 52.9 3.0 60 13-72 868-940 (941)
9 TIGR00416 sms DNA repair prote 97.8 1.4E-05 3.5E-10 48.8 2.3 56 13-69 418-481 (481)
10 PRK10787 DNA-binding ATP-depen 97.6 9.4E-05 2.4E-09 44.6 5.1 65 12-76 698-774 (784)
11 TIGR02903 spore_lon_C ATP-depe 97.4 9.7E-05 2.5E-09 44.5 2.9 62 11-72 546-615 (616)
12 COG0466 Lon ATP-dependent Lon 97.4 0.00032 8.3E-09 41.9 4.9 63 13-75 701-775 (782)
13 PRK13765 ATP-dependent proteas 97.3 0.00033 8.5E-09 41.8 4.7 69 3-73 523-602 (637)
14 KOG2004 consensus 96.8 0.0013 3.3E-08 38.8 3.4 63 12-74 824-898 (906)
15 COG1067 LonB Predicted ATP-dep 96.5 0.0064 1.6E-07 35.3 5.5 71 3-75 528-621 (647)
16 TIGR00764 lon_rel ATP-dependen 83.7 0.91 2.3E-05 24.4 2.5 68 5-74 570-648 (662)
17 TIGR02653 Lon_rel_chp conserve 83.6 1.1 2.7E-05 24.1 2.9 48 7-54 596-651 (677)
18 COG3480 SdrC Predicted secrete 77.7 3.2 8E-05 21.7 3.6 71 5-75 247-341 (342)
19 COG1223 Predicted ATPase (AAA+ 71.4 1.5 3.8E-05 23.4 0.7 17 91-107 116-132 (368)
20 PRK13228 consensus 56.5 18 0.00046 17.8 4.2 47 30-77 182-229 (232)
21 COG3050 HolD DNA polymerase II 40.0 8.8 0.00022 19.4 0.2 19 90-108 103-121 (133)
22 PRK05342 clpX ATP-dependent pr 38.4 8.3 0.00021 19.6 -0.2 13 96-108 72-84 (411)
23 COG1750 Archaeal serine protea 35.7 41 0.001 16.1 4.7 67 11-78 134-213 (579)
24 PRK06100 DNA polymerase III su 35.5 13 0.00032 18.6 0.4 21 88-108 104-124 (132)
25 TIGR00382 clpX ATP-dependent C 31.3 13 0.00034 18.5 -0.0 12 97-108 102-113 (452)
26 pfam03603 DNA_III_psi DNA poly 31.1 23 0.0006 17.3 1.2 21 88-108 101-121 (128)
27 COG1219 ClpX ATP-dependent pro 28.6 17 0.00045 17.9 0.2 12 97-108 62-73 (408)
28 PRK06856 DNA polymerase III su 25.4 25 0.00063 17.2 0.5 20 89-108 101-120 (127)
29 TIGR00010 TIGR00010 hydrolase, 24.6 42 0.0011 16.0 1.6 67 11-78 90-214 (269)
30 PRK08942 D,D-heptose 1,7-bisph 22.9 71 0.0018 14.9 3.2 42 30-73 133-177 (181)
31 TIGR01970 DEAH_box_HrpB ATP-de 20.4 59 0.0015 15.3 1.6 41 23-64 252-297 (858)
No 1
>PRK09862 putative ATP-dependent protease; Provisional
Probab=99.97 E-value=3e-31 Score=178.77 Aligned_cols=107 Identities=21% Similarity=0.323 Sum_probs=97.2
Q ss_pred CCCCCCCCHHHHCCEEEEEEECCCCC-------HHHHHHHHHCCCEEEEEHHHHHHHHHHCCCCEEEECCCHHHHHHHHC
Q ss_conf 95345888577356689985035775-------37999872039869983655045563128810751074999999970
Q gi|254781027|r 1 MASIQAISTESFSHYLAVGEINLDGS-------LPAAICAKNMNKDFICPQSCGSEAAWASDSLRIVAPSTLLELINHLN 73 (108)
Q Consensus 1 L~Asgqi~~~~l~~~~~iGELsLdG~-------Lp~al~a~~~~~~~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv~~l~ 73 (108)
|+|+|||+.+.+++|+|+|||||||+ ||++++|++.|+++|||.+|..|++++. +++||+++||.|+++|++
T Consensus 90 L~a~~qi~~~~l~~~~~~GEL~LdG~lr~v~G~lp~~l~a~~~g~~~ivp~~n~~ea~~v~-~~~v~~~~~L~e~~~~l~ 168 (506)
T PRK09862 90 LAASEQLTANKLDEYELVGELALTGALRGVPGAISSATEAIKSGRKIIVAKDNEDEVGLIN-GEGCLIADHLQAVCAFLE 168 (506)
T ss_pred HHHCCCCCHHHHCCEEEEEECCCCCEEECCCCHHHHHHHHHHCCCEEEECCCCHHHHCCCC-CCCEECCCCHHHHHHHHC
T ss_conf 9976999824430248885125586043065368999999975998995346456650569-982870325999999865
Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHCCHHHHHCCC
Q ss_conf 98646767754446765699876715846630029
Q gi|254781027|r 74 NKQLLPQPCKSTYKKRDNLPNFAEIKGQKTIKRAL 108 (108)
Q Consensus 74 g~~~~~~~~~~~~~~~~~~~Df~dV~GQ~~aKRAL 108 (108)
|...++.+.+..........||+||+||+.|||||
T Consensus 169 g~~~~~~~~~~~~~~~~~~~D~~dv~Gq~~akral 203 (506)
T PRK09862 169 GKHALERPKPTDAVSRALQHDLSDVVGQEQGKRGL 203 (506)
T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHCCCHHHHHHH
T ss_conf 98767888866556876656756536979999999
No 2
>TIGR00368 TIGR00368 Mg chelatase homolog; InterPro: IPR004482 This family of bacterial proteins are variously described as 'hypothetical protein yifB', 'competence protein', 'hypothetical protein' or 'Mg chelatase-related protein'. These proteins are a subset of the magnesium chelatase, ChlI subunit family and either belong to or show significant homology to the non-peptidase homologs of the MEROPS peptidase family S16 (lon protease family, clan SF), IPR001984 from INTERPRO. .
Probab=99.97 E-value=4.2e-32 Score=183.07 Aligned_cols=107 Identities=28% Similarity=0.468 Sum_probs=93.2
Q ss_pred CCCCCCCCHHHHCCEEEEEEECCCCC-------HHHHHHHHHCCCE-EEEEHHHHHHHHHHCCCCEEEECCCHHHHHHHH
Q ss_conf 95345888577356689985035775-------3799987203986-998365504556312881075107499999997
Q gi|254781027|r 1 MASIQAISTESFSHYLAVGEINLDGS-------LPAAICAKNMNKD-FICPQSCGSEAAWASDSLRIVAPSTLLELINHL 72 (108)
Q Consensus 1 L~Asgqi~~~~l~~~~~iGELsLdG~-------Lp~al~a~~~~~~-~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv~~l 72 (108)
|+||.|++...|.+|+|+|||+|||+ ||++..|++.++. +|||.+|+.||+|| ++.+||+++||+|||.||
T Consensus 85 laaseq~da~~L~~yl~lGEL~LdG~lR~i~gvlP~~~~A~k~~~~~~iVp~~N~~EaSlv-~G~~~y~~~~L~~vv~fl 163 (505)
T TIGR00368 85 LAASEQLDAKKLDEYLFLGELALDGKLRGIKGVLPAIALAQKSGRKFIIVPKENAEEASLV-DGLNVYGADHLKEVVKFL 163 (505)
T ss_pred HHHHHHHHHHCCCCEEEHHHHHHCCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCEEEE-CCCCEEHHHHHHHHHHHH
T ss_conf 9986333043144011001133247511045689999999865876776216675520266-387402047489999999
Q ss_pred C--CCCCCCCCCCCCC-----CCCCCCCCHHHHCCHHHHHCCC
Q ss_conf 0--9864676775444-----6765699876715846630029
Q gi|254781027|r 73 N--NKQLLPQPCKSTY-----KKRDNLPNFAEIKGQKTIKRAL 108 (108)
Q Consensus 73 ~--g~~~~~~~~~~~~-----~~~~~~~Df~dV~GQ~~aKRAL 108 (108)
. |...+++.+.... .+.....||+||+||++|||||
T Consensus 164 ~ql~~~~L~~~t~~~~~~~~~~s~~~~~DL~dv~GQ~~akRAl 206 (505)
T TIGR00368 164 EQLGSEKLPPRTNTKAKSIINVSLIIDLDLKDVKGQQHAKRAL 206 (505)
T ss_pred HHHCCCCCCCCCCCCCCHHHHHCCHHHCCCCCCCCHHHCCHHH
T ss_conf 7623101777545553103441320104432254510110267
No 3
>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=1.8e-30 Score=174.76 Aligned_cols=107 Identities=34% Similarity=0.538 Sum_probs=94.5
Q ss_pred CCCCCCCCHHHHCCEEEEEEECCCCC-------HHHHHHHHHCC-CEEEEEHHHHHHHHHHCCCCEEEECCCHHHHHHHH
Q ss_conf 95345888577356689985035775-------37999872039-86998365504556312881075107499999997
Q gi|254781027|r 1 MASIQAISTESFSHYLAVGEINLDGS-------LPAAICAKNMN-KDFICPQSCGSEAAWASDSLRIVAPSTLLELINHL 72 (108)
Q Consensus 1 L~Asgqi~~~~l~~~~~iGELsLdG~-------Lp~al~a~~~~-~~~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv~~l 72 (108)
|+|++||+.+.+.+|+|+|||+|||. ||+++.+++.+ +++|||.+|+.||+||+ +++||+++||.++++||
T Consensus 76 laa~~~~~~~~l~~~~~lGEL~LdG~l~~v~G~lp~~~~a~~~~~~~~i~p~~n~~Easli~-~~~v~~~~~l~ev~~~l 154 (490)
T COG0606 76 LAASGQLPADALILYEFLGELSLDGLLRPVGGVLPAALAAKEKGKRGLIVPKENAEEASLIG-GLPVYGARYLEEVVNFL 154 (490)
T ss_pred HHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCEECCHHCCCCCCCCC-CCCCCCHHHHHHHHHHH
T ss_conf 97426664134555776533411675225677115588875315782772411144034458-88725330299999986
Q ss_pred CCCCCCCCCCCCCCCCC-CCCCCHHHHCCHHHHHCCC
Q ss_conf 09864676775444676-5699876715846630029
Q gi|254781027|r 73 NNKQLLPQPCKSTYKKR-DNLPNFAEIKGQKTIKRAL 108 (108)
Q Consensus 73 ~g~~~~~~~~~~~~~~~-~~~~Df~dV~GQ~~aKRAL 108 (108)
+|...++.+.+...... ...+||+||+||++|||||
T Consensus 155 ~g~~~l~~~~~~~~~~~~~~~~D~~DV~GQ~~AKrAl 191 (490)
T COG0606 155 EGKLRLPIPIPSEVIESFSLAPDFKDVKGQEQAKRAL 191 (490)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHCCCHHHHHHH
T ss_conf 4886778778642113444576666643849999999
No 4
>TIGR02902 spore_lonB ATP-dependent protease LonB; InterPro: IPR014251 This entry represents LonB, a paralog of the ATP-dependent protease La (LonA, IPR004815 from INTERPRO). LonB proteins are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ) and are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore during sporulation, under control of sigmaF . The lonB gene, despite being located immediately upstream of lonA, was shown to be monocistronic. LonB appears to be involved in the post-translation control of sigmaH, but lonB mutation did not produce an obvious sporulation defect under the conditions tested . Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and these are excluded from this entry. .
Probab=98.51 E-value=1.1e-07 Score=59.46 Aligned_cols=65 Identities=18% Similarity=0.284 Sum_probs=52.6
Q ss_pred CCCHHHHCCEEEEEEECCCCCHHH-------HHHHHHCC-CEEEEEHHHHHHHHHHCCCCEEEECCCHHHHHHHH
Q ss_conf 888577356689985035775379-------99872039-86998365504556312881075107499999997
Q gi|254781027|r 6 AISTESFSHYLAVGEINLDGSLPA-------AICAKNMN-KDFICPQSCGSEAAWASDSLRIVAPSTLLELINHL 72 (108)
Q Consensus 6 qi~~~~l~~~~~iGELsLdG~Lp~-------al~a~~~~-~~~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv~~l 72 (108)
-+|-+ ..+-|=||.||.|..-+ +-||++.| +++|+|++|..|.----++++|+||+++.|+++++
T Consensus 459 ~~PId--n~vAmTGEISL~G~VKPVGGV~~Ki~AA~~AGak~ViIP~eNwqe~~~~~~~I~vipVk~~~E~l~~~ 531 (532)
T TIGR02902 459 KVPID--NKVAMTGEISLNGLVKPVGGVVSKIEAAKKAGAKKVIIPYENWQESFESISGIKVIPVKNIDEVLEVA 531 (532)
T ss_pred CCCCC--CCEEEEEEEEEEEEEEECCCCCHHHHHHHHCCCCEEECCCCHHHHHHHHHCCEEEEECCCHHHHHHHH
T ss_conf 78887--72111333864010520178612689999749726534752078999855271586326389999883
No 5
>PRK11823 DNA repair protein RadA; Provisional
Probab=98.35 E-value=5.3e-07 Score=55.98 Aligned_cols=60 Identities=20% Similarity=0.305 Sum_probs=49.5
Q ss_pred HCCEEEEEEECCCCCHHH-------HHHHHHCC-CEEEEEHHHHHHHHHHCCCCEEEECCCHHHHHHHHCC
Q ss_conf 356689985035775379-------99872039-8699836550455631288107510749999999709
Q gi|254781027|r 12 FSHYLAVGEINLDGSLPA-------AICAKNMN-KDFICPQSCGSEAAWASDSLRIVAPSTLLELINHLNN 74 (108)
Q Consensus 12 l~~~~~iGELsLdG~Lp~-------al~a~~~~-~~~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv~~l~g 74 (108)
-.+++|+||+||+|.++. +-.|.+.| +++|||..|... .. ++++|++++++.|+++++.+
T Consensus 386 ~~~~~~~GEVGL~GEiR~V~~~~~Rl~EA~rlGf~~~ivP~~~~~~--~~-~~i~i~~v~~i~e~i~~l~~ 453 (454)
T PRK11823 386 PPDTVVFGEVGLSGEIRPVPRGEERLKEAAKLGFKRAIVPKANPKK--AP-EGIEVIGVKTLKEALELLFG 453 (454)
T ss_pred CCCCEEEEECCCCCEEECCCCHHHHHHHHHHCCCCEEEECCCCCCC--CC-CCCEEEEECCHHHHHHHHHC
T ss_conf 9882899941367034268988999999998699889957877767--99-99799995979999999758
No 6
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=98.19 E-value=1.8e-06 Score=53.29 Aligned_cols=58 Identities=21% Similarity=0.359 Sum_probs=48.4
Q ss_pred CCEEEEEEECCCCCHHHH-------HHHHHCC-CEEEEEHHHHHHHHHHCCCCEEEECCCHHHHHHHHCC
Q ss_conf 566899850357753799-------9872039-8699836550455631288107510749999999709
Q gi|254781027|r 13 SHYLAVGEINLDGSLPAA-------ICAKNMN-KDFICPQSCGSEAAWASDSLRIVAPSTLLELINHLNN 74 (108)
Q Consensus 13 ~~~~~iGELsLdG~Lp~a-------l~a~~~~-~~~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv~~l~g 74 (108)
.+++|+||+||+|+++.+ -.|.+.| ++.|+|..|.. ...+++++++++|.|+++++.+
T Consensus 390 ~~~v~~GEvgL~GeIR~V~~~~~RlkEA~klGFk~aivP~~~~~----~~~~~~~~~v~~l~~a~~~~~~ 455 (456)
T COG1066 390 QDTVVFGEVGLSGEIRPVPRGERRLKEAAKLGFKRAIVPKGNIP----LPEGIKVIGVSTLAEALEVVFD 455 (456)
T ss_pred CCEEEEEECCCCCEEEECCCHHHHHHHHHHCCCCEEECCCCCCC----CCCCCEEEEEECHHHHHHHHHC
T ss_conf 87189995035742542675889999999758977974687677----8888159985009999998744
No 7
>pfam05362 Lon_C Lon protease (S16) C-terminal proteolytic domain. The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.
Probab=98.18 E-value=2.3e-06 Score=52.76 Aligned_cols=61 Identities=25% Similarity=0.382 Sum_probs=49.5
Q ss_pred HCCEEEEEEECCCCC-HHH------HHHHHHCC-CEEEEEHHHHHHHHH----HCCCCEEEECCCHHHHHHHH
Q ss_conf 356689985035775-379------99872039-869983655045563----12881075107499999997
Q gi|254781027|r 12 FSHYLAVGEINLDGS-LPA------AICAKNMN-KDFICPQSCGSEAAW----ASDSLRIVAPSTLLELINHL 72 (108)
Q Consensus 12 l~~~~~iGELsLdG~-Lp~------al~a~~~~-~~~iiP~~N~~Ea~l----v~~~~~v~~~~~L~evv~~l 72 (108)
-.+..+-||++|.|. +|+ +++|++.| +++|+|.+|..+..- +.++++|++|+|+.|++++-
T Consensus 130 ~~~iAmTGEIsL~G~VlpIGGv~eKi~aA~raGik~ViiP~~N~~dl~~ip~~i~~~i~i~~V~~i~evl~~a 202 (205)
T pfam05362 130 RKDVAMTGEITLRGRVLPIGGLKEKLLAAHRAGIKTVIIPKENEKDLEEIPENVREGLEIIPVEHVDEVLKHA 202 (205)
T ss_pred CCCEEEEECCEEEEEEEEECCHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH
T ss_conf 7887996033135679984899999999999399889974777667998349997699999969399999997
No 8
>TIGR00763 lon ATP-dependent protease La; InterPro: IPR004815 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . 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. This signature defines the bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). This family of sequences does not include the archaeal lon homologs, IPR004663 from INTERPRO. In the eukaryotes the majority of the proteins are located in the mitochondrial matrix , . In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response .; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0006510 ATP-dependent proteolysis.
Probab=98.09 E-value=2.1e-06 Score=52.92 Aligned_cols=60 Identities=27% Similarity=0.367 Sum_probs=50.7
Q ss_pred CCEEEEEEECCCCC-HHH------HHHHHHCC-CEEEEEHHHH-HHH----HHHCCCCEEEECCCHHHHHHHH
Q ss_conf 56689985035775-379------99872039-8699836550-455----6312881075107499999997
Q gi|254781027|r 13 SHYLAVGEINLDGS-LPA------AICAKNMN-KDFICPQSCG-SEA----AWASDSLRIVAPSTLLELINHL 72 (108)
Q Consensus 13 ~~~~~iGELsLdG~-Lp~------al~a~~~~-~~~iiP~~N~-~Ea----~lv~~~~~v~~~~~L~evv~~l 72 (108)
.+.-+=||++|.|. ||+ ++||+..| +++|+|..|. .-- .-|..++++++|+|+.||..+.
T Consensus 868 ~~~AMTGE~TLrG~VLpiGGlKEK~iAA~R~Gik~iilP~~N~e~Dl~elP~~v~e~L~~~~V~~~~ev~~~a 940 (941)
T TIGR00763 868 ADVAMTGEITLRGKVLPIGGLKEKTIAAKRAGIKTIILPEKNRERDLEELPENVKEGLEIHFVKHYDEVLKKA 940 (941)
T ss_pred CCCCCCCEEEECCCEEEECCHHHHHHHHHHHCEEEEECCCHHHCCCHHHHHHHHHHCCCEEEHHHHHHHHHHH
T ss_conf 5535510041023562005046888885350500777461200152662039887278411003278999982
No 9
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504 RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=97.76 E-value=1.4e-05 Score=48.82 Aligned_cols=56 Identities=14% Similarity=0.320 Sum_probs=44.7
Q ss_pred CCEEEEEEECCCCCHHHH-------HHHHHCC-CEEEEEHHHHHHHHHHCCCCEEEECCCHHHHH
Q ss_conf 566899850357753799-------9872039-86998365504556312881075107499999
Q gi|254781027|r 13 SHYLAVGEINLDGSLPAA-------ICAKNMN-KDFICPQSCGSEAAWASDSLRIVAPSTLLELI 69 (108)
Q Consensus 13 ~~~~~iGELsLdG~Lp~a-------l~a~~~~-~~~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv 69 (108)
.+.+|+||.||.|+++.| --|.+.| ++.|||++|.+.-.-. .+++||+|..+.+++
T Consensus 418 ~~~~~lGEVGL~G~ir~vp~~~~R~kEaak~GFkraIvP~~~~~~W~~~-~gi~~~~v~~v~~al 481 (481)
T TIGR00416 418 PDLVILGEVGLAGEIRPVPSLEERLKEAAKLGFKRAIVPKANLPKWTAP-EGIKVIGVKKVADAL 481 (481)
T ss_pred CCEEEEEEECCCCEEEECCCHHHHHHHHHHCCCCEEECCCCCCCCCCCC-CCCEEEEHHHHHHHC
T ss_conf 5638887643777040077631679999846863442147888875244-562476034465409
No 10
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=97.64 E-value=9.4e-05 Score=44.60 Aligned_cols=65 Identities=20% Similarity=0.239 Sum_probs=53.0
Q ss_pred HCCEEEEEEECCCCC-HHH------HHHHHHCC-CEEEEEHHHHHHHHH----HCCCCEEEECCCHHHHHHHHCCCC
Q ss_conf 356689985035775-379------99872039-869983655045563----128810751074999999970986
Q gi|254781027|r 12 FSHYLAVGEINLDGS-LPA------AICAKNMN-KDFICPQSCGSEAAW----ASDSLRIVAPSTLLELINHLNNKQ 76 (108)
Q Consensus 12 l~~~~~iGELsLdG~-Lp~------al~a~~~~-~~~iiP~~N~~Ea~l----v~~~~~v~~~~~L~evv~~l~g~~ 76 (108)
-.+..+-||++|.|. ||+ +++|+..| +++|+|.+|.....= |.++++++.|+|..||+++-....
T Consensus 698 ~~~~amTGEitL~G~VlpiGG~keK~laA~r~gi~~vi~P~~N~~d~~~ip~~v~~~l~~~~v~~~~ev~~~al~~~ 774 (784)
T PRK10787 698 RADVAMTGEITLRGQVLPIGGLKEKLLAAHRGGIKTVLIPFENKRDLEEIPDNVIADLDIHPVKRIEEVLTLALQNE 774 (784)
T ss_pred CCCCCEEEEEEECEEEEEECCHHHHHHHHHHCCCCEEEECHHHHHHHHHCCHHHHCCCEEEEECCHHHHHHHHHHCC
T ss_conf 99965556566020278207899999999984998999452123559874999886989999394999999997569
No 11
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family; InterPro: IPR014252 This entry shows some relation to the widely distributed ATP-dependent protease La, also called Lon or LonA (IPR004815 from INTERPRO), but is more closely related to LonB (IPR014251 from INTERPRO), a LonA paralog found only in endospore-forming bacteria. Proteins in this entry are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ). They are restricted to a subset of endospore-forming species, and probably participate in the program of endospore formation. We propose the designation LonC..
Probab=97.43 E-value=9.7e-05 Score=44.53 Aligned_cols=62 Identities=21% Similarity=0.275 Sum_probs=53.5
Q ss_pred HHCCEEEEEEECCCCCHHHH-------HHHHHCC-CEEEEEHHHHHHHHHHCCCCEEEECCCHHHHHHHH
Q ss_conf 73566899850357753799-------9872039-86998365504556312881075107499999997
Q gi|254781027|r 11 SFSHYLAVGEINLDGSLPAA-------ICAKNMN-KDFICPQSCGSEAAWASDSLRIVAPSTLLELINHL 72 (108)
Q Consensus 11 ~l~~~~~iGELsLdG~Lp~a-------l~a~~~~-~~~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv~~l 72 (108)
.=+|.-+-||.||-|.+.++ -.|+++| ++++||.+|..++---..+++|.+++|..|+++..
T Consensus 546 ~rQDvAiTGEiS~~G~ikpVGGi~EKIYGAk~~gi~~V~~P~~N~kdvPqg~~~I~v~~v~~iEE~~~iv 615 (616)
T TIGR02903 546 IRQDVAITGEISLRGKIKPVGGIFEKIYGAKRAGIKTVVIPEDNLKDVPQGLKGIEVKAVKTIEELLEIV 615 (616)
T ss_pred CEEEEEEEEEEEEECEEEECCCCCCCCHHHHHCCCCEEECCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
T ss_conf 3022565103886021651266333321455347435436730021356678871589705189899860
No 12
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=97.37 E-value=0.00032 Score=41.89 Aligned_cols=63 Identities=24% Similarity=0.292 Sum_probs=52.2
Q ss_pred CCEEEEEEECCCCC-HHH------HHHHHHCC-CEEEEEHHHHHHHHHH----CCCCEEEECCCHHHHHHHHCCC
Q ss_conf 56689985035775-379------99872039-8699836550455631----2881075107499999997098
Q gi|254781027|r 13 SHYLAVGEINLDGS-LPA------AICAKNMN-KDFICPQSCGSEAAWA----SDSLRIVAPSTLLELINHLNNK 75 (108)
Q Consensus 13 ~~~~~iGELsLdG~-Lp~------al~a~~~~-~~~iiP~~N~~Ea~lv----~~~~~v~~~~~L~evv~~l~g~ 75 (108)
.+.-+-||++|.|. ||+ +++|+..| +++|+|.+|..--.=+ .+++++++|++..||..+....
T Consensus 701 ~~vAMTGEITLrG~VLpIGGLKEKllAA~R~GIk~viiP~~N~~DleeiP~~vk~~l~i~~V~~~deVlk~al~~ 775 (782)
T COG0466 701 ADVAMTGEITLRGRVLPIGGLKEKLLAAHRGGIKTVIIPKDNERDLEEIPDNVKEGLEIHPVKTIDEVLKLALVG 775 (782)
T ss_pred CCCCCEEEEEEEEEEEECCCHHHHHHHHHHCCCCEEECCCCCCCCHHHCCHHHHCCCEEEEECCHHHHHHHHHCC
T ss_conf 885412457863024622559899999986598589646545014876779887497499925099999997168
No 13
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=97.34 E-value=0.00033 Score=41.82 Aligned_cols=69 Identities=23% Similarity=0.402 Sum_probs=52.5
Q ss_pred CCCCCCHHHHCCEEEEEEECCCCC-HHH------HHHHHHCC-CEEEEEHHHHHHHHH---HCCCCEEEECCCHHHHHHH
Q ss_conf 345888577356689985035775-379------99872039-869983655045563---1288107510749999999
Q gi|254781027|r 3 SIQAISTESFSHYLAVGEINLDGS-LPA------AICAKNMN-KDFICPQSCGSEAAW---ASDSLRIVAPSTLLELINH 71 (108)
Q Consensus 3 Asgqi~~~~l~~~~~iGELsLdG~-Lp~------al~a~~~~-~~~iiP~~N~~Ea~l---v~~~~~v~~~~~L~evv~~ 71 (108)
|...||-. +++.+-|.|+..|. +|+ +=+|.+.| +++|||+.|....-+ ..+.++|||++|+.|++++
T Consensus 523 AL~~iPi~--Q~~AvTGSl~q~G~VqpIGGVneKIEaa~~~G~k~ViIP~sN~~dv~~~~~~~~~i~iipv~~i~evl~~ 600 (637)
T PRK13765 523 ALENIPVD--QSVAMTGSLSVRGDVLPVGGVTYKIEAAAEAGIKKVIIPKSNEKDVLIEKEYEDKIEIIPVSTISEVLEH 600 (637)
T ss_pred HHHCCCCC--CCEEEEEEECCCCCEEECCCHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHCCCEEEEECCCHHHHHHH
T ss_conf 87479842--4435776423677345436707999999980886687240003434320765084699973739999998
Q ss_pred HC
Q ss_conf 70
Q gi|254781027|r 72 LN 73 (108)
Q Consensus 72 l~ 73 (108)
..
T Consensus 601 al 602 (637)
T PRK13765 601 AL 602 (637)
T ss_pred HH
T ss_conf 74
No 14
>KOG2004 consensus
Probab=96.78 E-value=0.0013 Score=38.84 Aligned_cols=63 Identities=21% Similarity=0.349 Sum_probs=52.3
Q ss_pred HCCEEEEEEECCCCC-HHH------HHHHHHCC-CEEEEEHHHHHH----HHHHCCCCEEEECCCHHHHHHHHCC
Q ss_conf 356689985035775-379------99872039-869983655045----5631288107510749999999709
Q gi|254781027|r 12 FSHYLAVGEINLDGS-LPA------AICAKNMN-KDFICPQSCGSE----AAWASDSLRIVAPSTLLELINHLNN 74 (108)
Q Consensus 12 l~~~~~iGELsLdG~-Lp~------al~a~~~~-~~~iiP~~N~~E----a~lv~~~~~v~~~~~L~evv~~l~g 74 (108)
-++.-+-||++|.|. ||+ +++|+..| +.+|.|.+|..+ +.-|..+++|..+.+..++.+..-+
T Consensus 824 r~d~AMTGEvTLtG~VLpiGGiKEK~iAA~RsG~k~ii~P~~N~~D~eelp~~vkegLev~~a~~yedv~~~aF~ 898 (906)
T KOG2004 824 RQDLAMTGEVTLTGKVLPVGGIKEKTIAARRSGVKTIIFPEANRRDFEELPENVKEGLEVHFAETYEDVFEAAFD 898 (906)
T ss_pred CCCCCCEEEEEEEEEEEECCCHHHHHHHHHHHCCEEEEECCCCHHHHHHHHHHHHHCCEEEEHHHHHHHHHHHHC
T ss_conf 555421235776444674276378899988728828972564366698745888706706638889999999727
No 15
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=96.52 E-value=0.0064 Score=35.32 Aligned_cols=71 Identities=20% Similarity=0.281 Sum_probs=52.2
Q ss_pred CCCCCCHHHHCCEEEEEEECCCCCH-H-------------HHHHHHHCC-CEEEEEHHHHHHHHHHCC--------CCEE
Q ss_conf 3458885773566899850357753-7-------------999872039-869983655045563128--------8107
Q gi|254781027|r 3 SIQAISTESFSHYLAVGEINLDGSL-P-------------AAICAKNMN-KDFICPQSCGSEAAWASD--------SLRI 59 (108)
Q Consensus 3 Asgqi~~~~l~~~~~iGELsLdG~L-p-------------~al~a~~~~-~~~iiP~~N~~Ea~lv~~--------~~~v 59 (108)
|...+|.. ++.-+-|++++.|.. | +.-++...| .++|||.+|..--.+-.+ .+.|
T Consensus 528 Al~~~Pv~--Q~iAiTGsi~q~G~VqpVGGV~eKIEgf~~~c~~~~~~G~q~ViIP~~N~~~l~l~~~v~~av~~g~f~I 605 (647)
T COG1067 528 ALSKIPVD--QDIAITGSIDQFGEVQPVGGVNEKIEGFFRVCQAAGLTGEQGVIIPKANVKDLSLSEDVVKAVKEGKFEI 605 (647)
T ss_pred HHHCCCCC--CCEEEEEEECCCCCEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHCCHHHHHHHHCCCEEE
T ss_conf 98548875--6346786333677245447730530004888888761588548833131866402387887754484699
Q ss_pred EECCCHHHHHHHHCCC
Q ss_conf 5107499999997098
Q gi|254781027|r 60 VAPSTLLELINHLNNK 75 (108)
Q Consensus 60 ~~~~~L~evv~~l~g~ 75 (108)
|||+|+.|++.++.+.
T Consensus 606 ~~V~~i~eal~~~~~~ 621 (647)
T COG1067 606 WPVETIDEALELLLGK 621 (647)
T ss_pred EEECCHHHHHHHHHCC
T ss_conf 9957299999998278
No 16
>TIGR00764 lon_rel ATP-dependent protease, putative; InterPro: IPR004663 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . 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. This signature defines the archaeal lon protease homologs, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein conserved region.; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0030163 protein catabolic process.
Probab=83.68 E-value=0.91 Score=24.44 Aligned_cols=68 Identities=22% Similarity=0.333 Sum_probs=51.8
Q ss_pred CCCCHHHHCCEEEEEEECCCCCH-H------HHHHHHHCC-CEEEEEHHHHHHHHHHC---CCCEEEECCCHHHHHHHHC
Q ss_conf 58885773566899850357753-7------999872039-86998365504556312---8810751074999999970
Q gi|254781027|r 5 QAISTESFSHYLAVGEINLDGSL-P------AAICAKNMN-KDFICPQSCGSEAAWAS---DSLRIVAPSTLLELINHLN 73 (108)
Q Consensus 5 gqi~~~~l~~~~~iGELsLdG~L-p------~al~a~~~~-~~~iiP~~N~~Ea~lv~---~~~~v~~~~~L~evv~~l~ 73 (108)
..||. -+++.+.|.|++.|.+ | -+-++.+.| +++++|..|..+.-+-. +.++++|++++.+++.+..
T Consensus 570 ~~~p~--~~~~~~~g~l~~~g~~l~~gg~~~~~~~~~~~g~~~~~~p~~~~~d~~~~~~~~~~~~~~p~~~~~~~~~~~~ 647 (662)
T TIGR00764 570 EEIPV--DQDVALTGSLSLRGEVLPVGGVTEKIEAAIEAGLKKVIIPKSNLGDVLLDPETEGKIEIIPVETLDEVLEHVL 647 (662)
T ss_pred HHCCC--CCCEEEECCCCCCCCEEECCCCCHHHHHHHHCCCCEEECCCCCCCCEEECCCCCCCEEEECCHHHHHHHHHHH
T ss_conf 50664--2210100221125542321765235678875052034303544320022232347246630012334555443
Q ss_pred C
Q ss_conf 9
Q gi|254781027|r 74 N 74 (108)
Q Consensus 74 g 74 (108)
.
T Consensus 648 ~ 648 (662)
T TIGR00764 648 D 648 (662)
T ss_pred H
T ss_conf 0
No 17
>TIGR02653 Lon_rel_chp conserved hypothetical protein; InterPro: IPR013473 This entry describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to IPR008269 from INTERPRO, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of Escherichia coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST]..
Probab=83.63 E-value=1.1 Score=24.10 Aligned_cols=48 Identities=13% Similarity=0.233 Sum_probs=35.5
Q ss_pred CCHHHHCCEEEEEEECCCCCHHHH-------HHHHHCC-CEEEEEHHHHHHHHHHC
Q ss_conf 885773566899850357753799-------9872039-86998365504556312
Q gi|254781027|r 7 ISTESFSHYLAVGEINLDGSLPAA-------ICAKNMN-KDFICPQSCGSEAAWAS 54 (108)
Q Consensus 7 i~~~~l~~~~~iGELsLdG~Lp~a-------l~a~~~~-~~~iiP~~N~~Ea~lv~ 54 (108)
+....-+.++++|+|+|.|.+.++ --|.+.| |++++|-+|+..-.-|+
T Consensus 596 ~~~~vqeqmviLG~mtigG~i~~v~~La~~LQ~a~d~GAKr~liP~~sa~~i~~Vp 651 (677)
T TIGR02653 596 LKRPVQEQMVILGSMTIGGVIKPVQDLAGSLQLAMDSGAKRVLIPLSSARDILTVP 651 (677)
T ss_pred HCCCCCCCEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCC
T ss_conf 61688875189863132540043555468899998618754740300244546378
No 18
>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]
Probab=77.73 E-value=3.2 Score=21.70 Aligned_cols=71 Identities=24% Similarity=0.416 Sum_probs=45.4
Q ss_pred CCCCHHHHCCEEEE---EEECCCCCH-H------HHHHHHHCCCE-EEEEHHHHHHHH--------H-----HCCCCEEE
Q ss_conf 58885773566899---850357753-7------99987203986-998365504556--------3-----12881075
Q gi|254781027|r 5 QAISTESFSHYLAV---GEINLDGSL-P------AAICAKNMNKD-FICPQSCGSEAA--------W-----ASDSLRIV 60 (108)
Q Consensus 5 gqi~~~~l~~~~~i---GELsLdG~L-p------~al~a~~~~~~-~iiP~~N~~Ea~--------l-----v~~~~~v~ 60 (108)
.|+....+.+--|+ |-..-||+. | =+.+|.+.|.. |++|.+|..|+. + +.-.+.+.
T Consensus 247 ~qlt~~DL~~g~~IAGTGTI~~DG~VG~IGGI~qKvvAA~~AGA~vFf~P~~~~~e~~s~sny~~a~~~ak~l~t~mkiv 326 (342)
T COG3480 247 DQLTKGDLTGGRFIAGTGTIEVDGKVGPIGGIDQKVVAAAKAGADVFFVPADNCAEEMSDSNYDEALVAAEDLSTAMKIV 326 (342)
T ss_pred HHCCCCCCCCCEEEECCEEECCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCCHHHCCCCHHHHHHHHHHHCCCCEEE
T ss_conf 64053113586698411133468833574547677677876598599841876202201388888899887540362478
Q ss_pred ECCCHHHHHHHHCCC
Q ss_conf 107499999997098
Q gi|254781027|r 61 APSTLLELINHLNNK 75 (108)
Q Consensus 61 ~~~~L~evv~~l~g~ 75 (108)
|+.++++.+++|+..
T Consensus 327 pv~T~q~aldyl~~~ 341 (342)
T COG3480 327 PVKTLQEALDYLEKL 341 (342)
T ss_pred EECHHHHHHHHHHCC
T ss_conf 510003266675427
No 19
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=71.38 E-value=1.5 Score=23.36 Aligned_cols=17 Identities=24% Similarity=0.341 Sum_probs=14.4
Q ss_pred CCCCHHHHCCHHHHHCC
Q ss_conf 69987671584663002
Q gi|254781027|r 91 NLPNFAEIKGQKTIKRA 107 (108)
Q Consensus 91 ~~~Df~dV~GQ~~aKRA 107 (108)
...-|.||.||+.|||.
T Consensus 116 ~~it~ddViGqEeAK~k 132 (368)
T COG1223 116 SDITLDDVIGQEEAKRK 132 (368)
T ss_pred CCCCHHHHHCHHHHHHH
T ss_conf 36617664163988888
No 20
>PRK13228 consensus
Probab=56.47 E-value=18 Score=17.84 Aligned_cols=47 Identities=17% Similarity=0.137 Sum_probs=27.3
Q ss_pred HHHHHHCC-CEEEEEHHHHHHHHHHCCCCEEEECCCHHHHHHHHCCCCC
Q ss_conf 99872039-8699836550455631288107510749999999709864
Q gi|254781027|r 30 AICAKNMN-KDFICPQSCGSEAAWASDSLRIVAPSTLLELINHLNNKQL 77 (108)
Q Consensus 30 al~a~~~~-~~~iiP~~N~~Ea~lv~~~~~v~~~~~L~evv~~l~g~~~ 77 (108)
+.+|++.| +.+-|+++...+..+..-+.. +-+.|+.|+.+.|...+.
T Consensus 182 i~aA~~AGi~~i~V~~G~~~~~~l~~~~ad-~vv~~l~el~~lL~~~~~ 229 (232)
T PRK13228 182 VIAARAAGCPVFCVPYGYADGHGLAALDCD-AIVDSLPEAYALLTPQRN 229 (232)
T ss_pred HHHHHHCCCEEEEECCCCCCHHHHHHCCCC-EEECCHHHHHHHHHHCCC
T ss_conf 999999599399987999997789878999-999999999999751614
No 21
>COG3050 HolD DNA polymerase III, psi subunit [DNA replication, recombination, and repair]
Probab=39.96 E-value=8.8 Score=19.43 Aligned_cols=19 Identities=21% Similarity=0.548 Sum_probs=16.8
Q ss_pred CCCCCHHHHCCHHHHHCCC
Q ss_conf 5699876715846630029
Q gi|254781027|r 90 DNLPNFAEIKGQKTIKRAL 108 (108)
Q Consensus 90 ~~~~Df~dV~GQ~~aKRAL 108 (108)
...+-++|+++..+|||||
T Consensus 103 ~~Spa~s~~~~N~~arrAL 121 (133)
T COG3050 103 AHSPALSQLRANHQARRAL 121 (133)
T ss_pred HCCHHHHHHHCCHHHHHHH
T ss_conf 7390477653478999999
No 22
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=38.36 E-value=8.3 Score=19.57 Aligned_cols=13 Identities=31% Similarity=0.452 Sum_probs=10.2
Q ss_pred HHHCCHHHHHCCC
Q ss_conf 6715846630029
Q gi|254781027|r 96 AEIKGQKTIKRAL 108 (108)
Q Consensus 96 ~dV~GQ~~aKRAL 108 (108)
.-|.||+.|||+|
T Consensus 72 ~yVIGQ~~AKk~l 84 (411)
T PRK05342 72 QYVIGQERAKKVL 84 (411)
T ss_pred HHHCCCHHHHHHH
T ss_conf 1402848888999
No 23
>COG1750 Archaeal serine proteases [General function prediction only]
Probab=35.72 E-value=41 Score=16.07 Aligned_cols=67 Identities=25% Similarity=0.248 Sum_probs=51.3
Q ss_pred HHCCEEEEEEECCCCCHHH-------HHHHHHCC-CEEEEEHHHHH-----HHHHHCCCCEEEECCCHHHHHHHHCCCCC
Q ss_conf 7356689985035775379-------99872039-86998365504-----55631288107510749999999709864
Q gi|254781027|r 11 SFSHYLAVGEINLDGSLPA-------AICAKNMN-KDFICPQSCGS-----EAAWASDSLRIVAPSTLLELINHLNNKQL 77 (108)
Q Consensus 11 ~l~~~~~iGELsLdG~Lp~-------al~a~~~~-~~~iiP~~N~~-----Ea~lv~~~~~v~~~~~L~evv~~l~g~~~ 77 (108)
...++++-|=.-=||.+-+ +-+|.+.| +-+.+|.++.. |=+ ...+++|+.+.++-+.+-+|.|.+.
T Consensus 134 ~~~~v~mTG~I~PDgsigpVGGi~~K~~AA~~~g~kifLIP~Gq~~~~d~~~Y~-k~~gl~vieV~~~~~aiyy~tg~~~ 212 (579)
T COG1750 134 IRKDVMMTGMINPDGSIGPVGGILEKLEAAAKAGAKIFLIPVGQRIVVDLVEYG-KSLGLKVIEVGTLEDAAYYLTGPQI 212 (579)
T ss_pred CCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHH-HHCCEEEEEEECHHHHHHHHCCCCC
T ss_conf 546705652355887433454458889999857985999605544453078777-6426479997002210345416667
Q ss_pred C
Q ss_conf 6
Q gi|254781027|r 78 L 78 (108)
Q Consensus 78 ~ 78 (108)
.
T Consensus 213 e 213 (579)
T COG1750 213 E 213 (579)
T ss_pred C
T ss_conf 8
No 24
>PRK06100 DNA polymerase III subunit psi; Provisional
Probab=35.48 E-value=13 Score=18.63 Aligned_cols=21 Identities=33% Similarity=0.537 Sum_probs=17.6
Q ss_pred CCCCCCCHHHHCCHHHHHCCC
Q ss_conf 765699876715846630029
Q gi|254781027|r 88 KRDNLPNFAEIKGQKTIKRAL 108 (108)
Q Consensus 88 ~~~~~~Df~dV~GQ~~aKRAL 108 (108)
..-..|.+++++|-..|||||
T Consensus 104 ~~L~SP~L~el~~n~~aKRaL 124 (132)
T PRK06100 104 KQLQSPLLSDIDGNNEHRRAL 124 (132)
T ss_pred CEEECCCHHHHHCCHHHHHHH
T ss_conf 767284889882698999999
No 25
>TIGR00382 clpX ATP-dependent Clp protease, ATP-binding subunit ClpX; InterPro: IPR004487 ClpX is a member of the HSP (heat-shock protein) 100 family. Gel filtration and electron microscopy showed that ClpX subunits associate to form a six-membered ring that is stabilized by binding of ATP or nonhydrolyzable analogs of ATP . It functions as an ATP-depedent molecular chaperone and is the regulatory subunit of the ClpXP protease . ClpXP is involved in DNA damage repair, stationary-phase gene expression, and ssrA-mediated protein quality control. To date more than 50 proteins include transcription factors, metabolic enzymes, and proteins involved in the starvation and oxidative stress responses have been identified as substrates . The N-terminal domain of ClpX is a C4-type zinc binding domain (ZBD) involved in substrate recognition. ZBD forms a very stable dimer that is essential for promoting the degradation of some typical ClpXP substrates such as lO and MuA . ; GO: 0005515 protein binding, 0005524 ATP binding, 0016887 ATPase activity, 0015031 protein transport.
Probab=31.33 E-value=13 Score=18.53 Aligned_cols=12 Identities=33% Similarity=0.501 Sum_probs=10.0
Q ss_pred HHCCHHHHHCCC
Q ss_conf 715846630029
Q gi|254781027|r 97 EIKGQKTIKRAL 108 (108)
Q Consensus 97 dV~GQ~~aKRAL 108 (108)
-|.||+.||..|
T Consensus 102 YVIGQe~AKKVL 113 (452)
T TIGR00382 102 YVIGQEQAKKVL 113 (452)
T ss_pred CCCCCCCCCEEE
T ss_conf 612310105254
No 26
>pfam03603 DNA_III_psi DNA polymerase III psi subunit.
Probab=31.12 E-value=23 Score=17.28 Aligned_cols=21 Identities=33% Similarity=0.593 Sum_probs=17.8
Q ss_pred CCCCCCCHHHHCCHHHHHCCC
Q ss_conf 765699876715846630029
Q gi|254781027|r 88 KRDNLPNFAEIKGQKTIKRAL 108 (108)
Q Consensus 88 ~~~~~~Df~dV~GQ~~aKRAL 108 (108)
..-..+.++++++-..|||||
T Consensus 101 ~~l~SP~L~~l~~n~~aKRaL 121 (128)
T pfam03603 101 KQLQSPSLSDLDGNAQAKRAL 121 (128)
T ss_pred CEECCCCHHHHHCCHHHHHHH
T ss_conf 421593999881487999999
No 27
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=28.57 E-value=17 Score=17.93 Aligned_cols=12 Identities=33% Similarity=0.501 Sum_probs=8.5
Q ss_pred HHCCHHHHHCCC
Q ss_conf 715846630029
Q gi|254781027|r 97 EIKGQKTIKRAL 108 (108)
Q Consensus 97 dV~GQ~~aKRAL 108 (108)
-|.||+.|||.|
T Consensus 62 YVIGQe~AKKvL 73 (408)
T COG1219 62 YVIGQEQAKKVL 73 (408)
T ss_pred HEECCHHHHCEE
T ss_conf 432625431034
No 28
>PRK06856 DNA polymerase III subunit psi; Validated
Probab=25.35 E-value=25 Score=17.19 Aligned_cols=20 Identities=35% Similarity=0.547 Sum_probs=17.3
Q ss_pred CCCCCCHHHHCCHHHHHCCC
Q ss_conf 65699876715846630029
Q gi|254781027|r 89 RDNLPNFAEIKGQKTIKRAL 108 (108)
Q Consensus 89 ~~~~~Df~dV~GQ~~aKRAL 108 (108)
.-..+.++++++-..|||||
T Consensus 101 ~l~Sp~L~~L~~n~~aKRaL 120 (127)
T PRK06856 101 QVQSPALTELRANPTAKRAL 120 (127)
T ss_pred EECCCCHHHHHCCHHHHHHH
T ss_conf 67581899883697999999
No 29
>TIGR00010 TIGR00010 hydrolase, TatD family; InterPro: IPR015991 Escherichia coli TatD (synonym MttC) has been shown experimentally to be a DNase . On the basis of operon structure, it was originally thought to be involved in the Sec-independent export of protein precursors bearing twin arginine signal peptides by the Tat system . This alternative membrane targeting and translocation system (Mtt), also called twin arginine translocase (Tat) (MttA1A2BC or TatABCD), has been shown to transport fully folded proteins to, or across, the membrane , . However, it was later determined that TatD is not required for this translocation process , . Furthermore, it was noted that no exact correlation exists between the ability of an organism to synthesise a TatD-like protein and whether that organism has a Tat protein transport pathway . Also, with the exception of Escherichia coli , the genetic linkage between TatD and other Tat genes (operon structure) is not maintained. Members of this group may be distantly related to a large 3D fold-based domain superfamily of metalloenzymes . The description of this fold superfamily was based on an analysis of conservation patterns in three dimensions, and the discovery that the same active-site architecture occurs in a large set of enzymes involved primarily in nucleotide metabolism. The group is thought to include urease, dihydroorotase, allantoinase, hydantoinase, AMP-, adenine- and cytosine- deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolase, formylmethanofuran dehydrogenase, and other enzymes ..
Probab=24.62 E-value=42 Score=15.98 Aligned_cols=67 Identities=22% Similarity=0.337 Sum_probs=38.3
Q ss_pred HHCCEEEEEEECCC-------C-C------------------HHHH-------------HHH---HH-CC-CEEE-EEHH
Q ss_conf 73566899850357-------7-5------------------3799-------------987---20-39-8699-8365
Q gi|254781027|r 11 SFSHYLAVGEINLD-------G-S------------------LPAA-------------ICA---KN-MN-KDFI-CPQS 45 (108)
Q Consensus 11 ~l~~~~~iGELsLd-------G-~------------------Lp~a-------------l~a---~~-~~-~~~i-iP~~ 45 (108)
...+...|||-||| . . +|.+ +.. .. .. ..++ |=-+
T Consensus 90 ~~~~v~AiGE~GLDY~~~~~~~e~~~Q~e~F~~q~~lA~~~~~P~iiH~RdA~~d~~~iL~~~y~~~~~~~~g~~HCftg 169 (269)
T TIGR00010 90 AHPKVVAIGETGLDYYKADEKKERRRQKEVFRAQLQLAEELNLPVIIHARDAEEDVLDILREYYAEKAPKVGGVLHCFTG 169 (269)
T ss_pred HCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHHCCCCCCCEEEEECCC
T ss_conf 06954798510440430687521789999999999999971996899788457999999999984278778757981488
Q ss_pred HHHHHHHHCCCCE---EEE----------CCCHHHHHHHHCCCCCC
Q ss_conf 5045563128810---751----------07499999997098646
Q gi|254781027|r 46 CGSEAAWASDSLR---IVA----------PSTLLELINHLNNKQLL 78 (108)
Q Consensus 46 N~~Ea~lv~~~~~---v~~----------~~~L~evv~~l~g~~~~ 78 (108)
...+|....+ .. +|- +++|++++..+--++.+
T Consensus 170 ~~E~a~~~ld-~gd~~~yiSisG~vTFknA~~l~~~v~~iP~e~LL 214 (269)
T TIGR00010 170 DAELAKKLLD-LGDLLFYISISGIVTFKNAKSLREVVKKIPLERLL 214 (269)
T ss_pred CHHHHHHHHC-CCCEEEEEECCCCEEEECCHHHHHHHHHCCCCCCE
T ss_conf 8899999960-69879999728602210626789999745964323
No 30
>PRK08942 D,D-heptose 1,7-bisphosphate phosphatase; Validated
Probab=22.93 E-value=71 Score=14.86 Aligned_cols=42 Identities=12% Similarity=0.053 Sum_probs=17.8
Q ss_pred HHHHHHCC-CEEEEEHHHHHHH--HHHCCCCEEEECCCHHHHHHHHC
Q ss_conf 99872039-8699836550455--63128810751074999999970
Q gi|254781027|r 30 AICAKNMN-KDFICPQSCGSEA--AWASDSLRIVAPSTLLELINHLN 73 (108)
Q Consensus 30 al~a~~~~-~~~iiP~~N~~Ea--~lv~~~~~v~~~~~L~evv~~l~ 73 (108)
..+|++.| +++.|--++..+- .-+ ....+-+.+|.+++++++
T Consensus 133 i~aa~~aG~k~ILV~TG~G~~~~~~~~--~~~~~i~~~l~d~~~~~~ 177 (181)
T PRK08942 133 LQAAAAAGVTPVLVRTGKGVKTLAEGA--APGTWVLDSLADVPAALK 177 (181)
T ss_pred HHHHHHCCCEEEEECCCCCCEEHHHCC--CCCCEEECCHHHHHHHHH
T ss_conf 999998799089977899720074459--998873318999999998
No 31
>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB; InterPro: IPR010225 This entry represents HrpB, one of two related predicted DEAH-box ATP-dependent helicases of unknown function found in many proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti, designated HelO, has been studied but is not essential for growth and mutants have no obvious phenotype . HrpB is typically about 800 residues in length, while its paralog HrpA (IPR010222 from INTERPRO), also uncharacterised, is about 1300 amino acids long. Related characterised eukaryotic proteins are RNA helicases associated with pre-mRNA processing ..
Probab=20.43 E-value=59 Score=15.27 Aligned_cols=41 Identities=20% Similarity=0.245 Sum_probs=30.2
Q ss_pred CCCCHHH-----HHHHHHCCCEEEEEHHHHHHHHHHCCCCEEEECCC
Q ss_conf 5775379-----99872039869983655045563128810751074
Q gi|254781027|r 23 LDGSLPA-----AICAKNMNKDFICPQSCGSEAAWASDSLRIVAPST 64 (108)
Q Consensus 23 LdG~Lp~-----al~a~~~~~~~iiP~~N~~Ea~lv~~~~~v~~~~~ 64 (108)
|-|.|+. |+.....|++=||=+-|-.|.||..+||+|+- .+
T Consensus 252 LYG~L~~~aQ~~AI~P~a~GrRKVVLATNiAEtSLTIeGvRvVi-Ds 297 (858)
T TIGR01970 252 LYGELELAAQDRAIKPAAAGRRKVVLATNIAETSLTIEGVRVVI-DS 297 (858)
T ss_pred CCCCCCHHHHHHHCCCCCCCCCEEEEEHHHHHHHEEECCEEEEE-EC
T ss_conf 67888978999870877466734342000122210017635887-15
Done!