Query gi|254781106|ref|YP_003065519.1| cell division protein MraZ [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 145
No_of_seqs 111 out of 1044
Neff 6.9
Searched_HMMs 39220
Date Mon May 30 04:41:57 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781106.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00326 cell division protein 100.0 8.1E-44 0 290.9 14.4 140 3-144 1-140 (147)
2 COG2001 Uncharacterized protei 100.0 1.8E-43 0 288.7 14.1 134 3-138 1-134 (146)
3 TIGR00242 TIGR00242 mraZ prote 99.9 1.1E-23 2.9E-28 166.8 8.5 136 3-138 1-136 (152)
4 pfam02381 MraZ MraZ protein. T 99.6 7.3E-15 1.9E-19 112.6 6.4 71 3-77 1-71 (72)
5 pfam02381 MraZ MraZ protein. T 99.5 8.8E-14 2.3E-18 106.0 6.5 58 79-136 1-58 (72)
6 PRK00326 cell division protein 97.3 0.0004 1E-08 46.5 5.1 50 82-131 4-56 (147)
7 COG2001 Uncharacterized protei 96.4 0.0062 1.6E-07 39.2 5.0 58 3-64 75-132 (146)
8 TIGR01439 lp_hng_hel_AbrB tran 95.5 0.011 2.7E-07 37.7 2.9 42 10-52 2-43 (44)
9 PRK08577 hypothetical protein; 94.8 0.034 8.5E-07 34.7 3.5 44 9-52 6-49 (135)
10 TIGR01439 lp_hng_hel_AbrB tran 94.4 0.069 1.8E-06 32.7 4.5 37 86-122 2-41 (44)
11 COG2002 AbrB Regulators of sta 94.3 0.044 1.1E-06 33.9 3.3 36 7-42 5-40 (89)
12 COG2002 AbrB Regulators of sta 93.9 0.1 2.6E-06 31.7 4.4 38 84-121 6-47 (89)
13 pfam04014 SpoVT_AbrB SpoVT / A 88.5 0.55 1.4E-05 27.2 3.5 41 11-52 2-42 (47)
14 PRK08577 hypothetical protein; 88.2 0.58 1.5E-05 27.0 3.4 38 84-121 5-44 (135)
15 TIGR00242 TIGR00242 mraZ prote 85.1 0.71 1.8E-05 26.5 2.5 51 82-132 4-58 (152)
16 TIGR02851 spore_V_T stage V sp 76.9 1.6 4.2E-05 24.3 2.0 47 9-56 6-55 (184)
17 TIGR02922 TIGR02922 conserved 75.3 0.63 1.6E-05 26.8 -0.5 17 10-26 29-45 (69)
18 pfam09558 DUF2375 Protein of u 65.3 2.3 5.8E-05 23.4 0.6 15 12-26 31-45 (71)
19 PRK08115 ribonucleotide-diphos 61.2 15 0.00038 18.3 4.2 91 17-113 93-186 (857)
20 PRK09974 putative regulator Pr 59.2 16 0.00042 18.1 5.2 28 7-34 9-36 (111)
21 COG5256 TEF1 Translation elong 44.4 28 0.00072 16.7 4.9 53 87-141 126-178 (428)
22 TIGR02733 desat_CrtD C-3',4' d 43.5 18 0.00045 17.9 2.2 16 125-140 394-409 (499)
23 pfam07656 KWG KWG Leptospira. 38.6 11 0.00027 19.3 0.4 17 11-27 4-20 (26)
24 cd05792 S1_eIF1AD_like S1_eIF1 30.7 14 0.00036 18.5 0.0 12 17-28 26-37 (78)
25 TIGR01425 SRP54_euk signal rec 28.5 25 0.00064 17.0 1.0 23 109-131 289-314 (453)
26 PRK13656 trans-2-enoyl-CoA red 27.4 33 0.00084 16.2 1.4 53 45-97 282-335 (400)
27 pfam11772 EpuA DNA-directed RN 26.9 30 0.00076 16.5 1.1 22 111-132 21-42 (47)
28 pfam02261 Asp_decarbox Asparta 23.8 62 0.0016 14.5 3.5 40 82-121 14-57 (116)
29 COG0172 SerS Seryl-tRNA synthe 23.7 60 0.0015 14.6 2.2 16 91-106 406-421 (429)
30 TIGR01660 narH nitrate reducta 23.4 32 0.00081 16.3 0.7 39 61-105 430-468 (495)
31 COG2072 TrkA Predicted flavopr 22.4 37 0.00095 15.9 0.9 28 91-118 158-186 (443)
32 TIGR01317 GOGAT_sm_gam glutama 22.3 18 0.00046 17.9 -0.7 31 88-118 283-319 (517)
33 PRK05449 aspartate alpha-decar 22.0 67 0.0017 14.3 3.5 40 83-122 15-58 (126)
34 TIGR02959 SigZ RNA polymerase 21.9 60 0.0015 14.6 1.9 59 20-95 101-163 (170)
35 cd06919 Asp_decarbox Aspartate 20.9 71 0.0018 14.2 3.5 39 83-121 14-56 (111)
No 1
>PRK00326 cell division protein MraZ; Reviewed
Probab=100.00 E-value=8.1e-44 Score=290.86 Aligned_cols=140 Identities=27% Similarity=0.493 Sum_probs=131.6
Q ss_pred CCCCCCCCEECCCCCEEECHHHHHHHHHCCCCCEEECCCCCCCEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 42221121056766271078899998524898499516566441304523678999998630688751379999986311
Q gi|254781106|r 3 RFLSNVTQKIDSKGRVSVPFVFRTILAQRCITDLYCFQDFFFPAISVGNSDLLEYFEQKIAEYNPFSIQANQLSLLVHGG 82 (145)
Q Consensus 3 ~F~G~~~~~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~~~w~~~~~~i~~l~~~~~~~~~~~r~~~~~ 82 (145)
||+|+|+|+||+||||+|||+||+.|...+...+++++. .++||++||++.|++++++|.+++.++++.+.+.|.++++
T Consensus 1 mF~G~~~~~iD~KGRislPa~fR~~L~~~~~~~~~~~~~-~~~cL~~y~~~~~~~~~~~i~~~~~~~~~~~~~~r~~~~~ 79 (147)
T PRK00326 1 MFRGAYAHNLDAKGRLSIPAKFRDVLLEEAGGRLVLTKG-QDGCLLLYPLPEWEKIEEKLAALPLTNPEARAFQRLLLGG 79 (147)
T ss_pred CCCCCCCCCCCCCCCEEECHHHHHHHHHCCCCEEEEEEC-CCCCEEEECHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf 915442166768875578899999997358985999958-9991798288899999999861288998999999998437
Q ss_pred HHHCCCCCCCEEECCHHHHHHCCCCCEEEEEECCCEEEECCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 11122178614751989998709985399994199899629899999999959999998843
Q gi|254781106|r 83 GIFLKMDSEGRILMTDFIRVFTGIENEVTFVGRGNYFQLWNPQTFRKLQEESRNEYCRQLLQ 144 (145)
Q Consensus 83 a~~~~~D~~GRi~ip~~lr~~agi~~ev~~vG~g~~fEIW~~~~~~~~~~~~~~~~~~~l~e 144 (145)
+.++++|+||||+||+.||++|||+++|+|||+|++||||+|++|+++.+++++++. +++|
T Consensus 80 a~~~~~D~~GRi~lP~~lr~~agi~~evv~vG~g~~~EIW~~~~~~~~~~~~~~~~~-~l~e 140 (147)
T PRK00326 80 AVEVELDKQGRILIPPNLREYAGLEKEVVLVGQGNKFEIWDPEAWEAYLAEAEEAFA-ALAE 140 (147)
T ss_pred CCEEEECCCCCEECCHHHHHHHCCCCEEEEEECCCEEEEECHHHHHHHHHHHHHHHH-HHHH
T ss_conf 705006798718689999998499870999947999999689999999987275199-9999
No 2
>COG2001 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=1.8e-43 Score=288.68 Aligned_cols=134 Identities=30% Similarity=0.554 Sum_probs=128.8
Q ss_pred CCCCCCCCEECCCCCEEECHHHHHHHHHCCCCCEEECCCCCCCEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 42221121056766271078899998524898499516566441304523678999998630688751379999986311
Q gi|254781106|r 3 RFLSNVTQKIDSKGRVSVPFVFRTILAQRCITDLYCFQDFFFPAISVGNSDLLEYFEQKIAEYNPFSIQANQLSLLVHGG 82 (145)
Q Consensus 3 ~F~G~~~~~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~~~w~~~~~~i~~l~~~~~~~~~~~r~~~~~ 82 (145)
||+|+|.++||+|||++|||+||..|...+.+ +|+++++ +.||.+||.++|++++++++++|.+++..|.|.|.++|+
T Consensus 1 MF~G~~~~~LD~KgRl~vPakfR~~L~~~~~~-~v~t~~~-~~~L~vyp~~ewe~~~~kl~~lp~~~~~aR~~~r~~~~~ 78 (146)
T COG2001 1 MFLGAYEHNLDSKGRLSVPAKFRAALGENAAG-LVVTRGI-DHCLEVYPLAEWERLEEKLSALPSTDPEARAFQRLLFGG 78 (146)
T ss_pred CCCCCCCCCCCCCCCEECCHHHHHHHHCCCCE-EEEECCC-CCCEEECCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCC
T ss_conf 97665566608767772459999998566750-8997257-688754599999999999972898987799999998457
Q ss_pred HHHCCCCCCCEEECCHHHHHHCCCCCEEEEEECCCEEEECCHHHHHHHHHHHHHHH
Q ss_conf 11122178614751989998709985399994199899629899999999959999
Q gi|254781106|r 83 GIFLKMDSEGRILMTDFIRVFTGIENEVTFVGRGNYFQLWNPQTFRKLQEESRNEY 138 (145)
Q Consensus 83 a~~~~~D~~GRi~ip~~lr~~agi~~ev~~vG~g~~fEIW~~~~~~~~~~~~~~~~ 138 (145)
|.+|++|+||||+||+.||+||+|+|||++||++++|||||+++|+++++++.+.+
T Consensus 79 a~e~elD~~GRi~ip~~Lr~~A~L~kevvlvG~~~~~EiW~~~~w~~~~~~~~~~~ 134 (146)
T COG2001 79 AVEVELDGAGRILIPQNLREYAGLEKEVVLVGQGDRFEIWDKQAWEAYQAEAEDAF 134 (146)
T ss_pred CEEEEECCCCCEECCHHHHHHHCCCCCEEEECCCCEEEECCHHHHHHHHHHHHHHH
T ss_conf 60776768888877999998738876289972778688748999999999888653
No 3
>TIGR00242 TIGR00242 mraZ protein; InterPro: IPR003444 This family is characterised by a 70 amino acid region and is found duplicated in a group of bacterial proteins. These proteins may be DNA-binding transcription factors, its members are probably enzymes containing a conserved DXXXR motif that probably forms part of the active site. .
Probab=99.90 E-value=1.1e-23 Score=166.82 Aligned_cols=136 Identities=24% Similarity=0.379 Sum_probs=128.1
Q ss_pred CCCCCCCCEECCCCCEEECHHHHHHHHHCCCCCEEECCCCCCCEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 42221121056766271078899998524898499516566441304523678999998630688751379999986311
Q gi|254781106|r 3 RFLSNVTQKIDSKGRVSVPFVFRTILAQRCITDLYCFQDFFFPAISVGNSDLLEYFEQKIAEYNPFSIQANQLSLLVHGG 82 (145)
Q Consensus 3 ~F~G~~~~~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~~~w~~~~~~i~~l~~~~~~~~~~~r~~~~~ 82 (145)
+|+|.+.+++|+|||+++|++||..+.....+..+++....++|+.+||...|+.+.+++..++..++..+.+.|.++++
T Consensus 1 ~~~g~~~~~~d~~~~~~~p~~~~~~~~~~~~g~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (152)
T TIGR00242 1 LFLGAFNVTLDAKGRLSLPAKYREGLLENSAGQLVCLNRGFENCLLLYPLPEWEKIEEKLNALPNTKPDTRRLKRLLFGG 80 (152)
T ss_pred CCCCCCHHCCCCCCCCCCHHHHHHHHHCCCCCCEEEEECCCHHHHHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf 95442000003456300103556553012356344431000013320561467899998862236652578888876326
Q ss_pred HHHCCCCCCCEEECCHHHHHHCCCCCEEEEEECCCEEEECCHHHHHHHHHHHHHHH
Q ss_conf 11122178614751989998709985399994199899629899999999959999
Q gi|254781106|r 83 GIFLKMDSEGRILMTDFIRVFTGIENEVTFVGRGNYFQLWNPQTFRKLQEESRNEY 138 (145)
Q Consensus 83 a~~~~~D~~GRi~ip~~lr~~agi~~ev~~vG~g~~fEIW~~~~~~~~~~~~~~~~ 138 (145)
+.+|++|++||+++|..++.+++++++++++|..+++|+|+...|+.+..+..+-.
T Consensus 81 ~~~~~~d~~g~~~~~~~~~~~~~~~~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~ 136 (152)
T TIGR00242 81 ATECELDGAGRVLIPGNLLNHAKLEKELVLVGQFNKLELWDKVLWEQYLAEDEDLE 136 (152)
T ss_pred CCCCCCCCCCCEECCHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 53000034572001202333200222144641232100111244555553223334
No 4
>pfam02381 MraZ MraZ protein. This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin).
Probab=99.56 E-value=7.3e-15 Score=112.63 Aligned_cols=71 Identities=18% Similarity=0.167 Sum_probs=61.1
Q ss_pred CCCCCCCCEECCCCCEEECHHHHHHHHHCCCCCEEECCCCCCCEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf 422211210567662710788999985248984995165664413045236789999986306887513799999
Q gi|254781106|r 3 RFLSNVTQKIDSKGRVSVPFVFRTILAQRCITDLYCFQDFFFPAISVGNSDLLEYFEQKIAEYNPFSIQANQLSL 77 (145)
Q Consensus 3 ~F~G~~~~~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~~~w~~~~~~i~~l~~~~~~~~~~~r 77 (145)
||.|+|+|+||+||||+||++||+.+. ....+++.+ .++||++||++.|+++++++.++|.++++.+.|.|
T Consensus 1 mf~G~~~~~lD~kGRi~iP~~lR~~~~---~~~~vv~~G-~~~~leiw~~~~w~~~~~k~~~~~~~~~~~r~~~R 71 (72)
T pfam02381 1 MFAGATEVELDSKGRIILPAKLREYAG---LEKECVTIG-QDNCLEIWPRAEWEQYEEKANEESFSAKDARAFLR 71 (72)
T ss_pred CCCCCCCCCCCCCCCEECCHHHHHHHC---CCCEEEEEC-CCCEEEECCHHHHHHHHHHHHHCCCCCHHHHHHCC
T ss_conf 988852167287873727999999867---998899978-88979986999999999999854437988996304
No 5
>pfam02381 MraZ MraZ protein. This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin).
Probab=99.47 E-value=8.8e-14 Score=105.96 Aligned_cols=58 Identities=24% Similarity=0.632 Sum_probs=54.4
Q ss_pred HHHHHHHCCCCCCCEEECCHHHHHHCCCCCEEEEEECCCEEEECCHHHHHHHHHHHHH
Q ss_conf 6311111221786147519899987099853999941998996298999999999599
Q gi|254781106|r 79 VHGGGIFLKMDSEGRILMTDFIRVFTGIENEVTFVGRGNYFQLWNPQTFRKLQEESRN 136 (145)
Q Consensus 79 ~~~~a~~~~~D~~GRi~ip~~lr~~agi~~ev~~vG~g~~fEIW~~~~~~~~~~~~~~ 136 (145)
+|+++.++++|++|||+||+.||++++++++|+++|++++||||+++.|+++.++..+
T Consensus 1 mf~G~~~~~lD~kGRi~iP~~lR~~~~~~~~vv~~G~~~~leiw~~~~w~~~~~k~~~ 58 (72)
T pfam02381 1 MFAGATEVELDSKGRIILPAKLREYAGLEKECVTIGQDNCLEIWPRAEWEQYEEKANE 58 (72)
T ss_pred CCCCCCCCCCCCCCCEECCHHHHHHHCCCCEEEEECCCCEEEECCHHHHHHHHHHHHH
T ss_conf 9888521672878737279999998679988999788897998699999999999985
No 6
>PRK00326 cell division protein MraZ; Reviewed
Probab=97.34 E-value=0.0004 Score=46.50 Aligned_cols=50 Identities=20% Similarity=0.306 Sum_probs=21.8
Q ss_pred HHHHCCCCCCCEEECCHHHHHHCCCC--CE-EEEEECCCEEEECCHHHHHHHH
Q ss_conf 11112217861475198999870998--53-9999419989962989999999
Q gi|254781106|r 82 GGIFLKMDSEGRILMTDFIRVFTGIE--NE-VTFVGRGNYFQLWNPQTFRKLQ 131 (145)
Q Consensus 82 ~a~~~~~D~~GRi~ip~~lr~~agi~--~e-v~~vG~g~~fEIW~~~~~~~~~ 131 (145)
+..+..+|+-|||.||..+|+...-. +. ++..|..+++++|.++.|++..
T Consensus 4 G~~~~~iD~KGRislPa~fR~~L~~~~~~~~~~~~~~~~cL~~y~~~~~~~~~ 56 (147)
T PRK00326 4 GAYAHNLDAKGRLSIPAKFRDVLLEEAGGRLVLTKGQDGCLLLYPLPEWEKIE 56 (147)
T ss_pred CCCCCCCCCCCCEEECHHHHHHHHHCCCCEEEEEECCCCCEEEECHHHHHHHH
T ss_conf 44216676887557889999999735898599995899917982888999999
No 7
>COG2001 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.44 E-value=0.0062 Score=39.16 Aligned_cols=58 Identities=14% Similarity=0.194 Sum_probs=42.4
Q ss_pred CCCCCCCCEECCCCCEEECHHHHHHHHHCCCCCEEECCCCCCCEEECCCHHHHHHHHHHHHC
Q ss_conf 42221121056766271078899998524898499516566441304523678999998630
Q gi|254781106|r 3 RFLSNVTQKIDSKGRVSVPFVFRTILAQRCITDLYCFQDFFFPAISVGNSDLLEYFEQKIAE 64 (145)
Q Consensus 3 ~F~G~~~~~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~~~w~~~~~~i~~ 64 (145)
+|-|.....+|+-|||.||+..|+-- +-..++++.. ..+++++|..+.|+...+...+
T Consensus 75 ~~~~a~e~elD~~GRi~ip~~Lr~~A--~L~kevvlvG--~~~~~EiW~~~~w~~~~~~~~~ 132 (146)
T COG2001 75 LFGGAVEVELDGAGRILIPQNLREYA--GLEKEVVLVG--QGDRFEIWDKQAWEAYQAEAED 132 (146)
T ss_pred HHCCCEEEEECCCCCEECCHHHHHHH--CCCCCEEEEC--CCCEEEECCHHHHHHHHHHHHH
T ss_conf 84576077676888887799999873--8876289972--7786887489999999998886
No 8
>TIGR01439 lp_hng_hel_AbrB transcriptional regulator, AbrB family; InterPro: IPR006339 This DNA-binding domain is found in proteins like AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. .
Probab=95.55 E-value=0.011 Score=37.72 Aligned_cols=42 Identities=19% Similarity=0.153 Sum_probs=26.3
Q ss_pred CEECCCCCEEECHHHHHHHHHCCCCCEEECCCCCCCEEECCCH
Q ss_conf 1056766271078899998524898499516566441304523
Q gi|254781106|r 10 QKIDSKGRVSVPFVFRTILAQRCITDLYCFQDFFFPAISVGNS 52 (145)
Q Consensus 10 ~~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~ 52 (145)
.++|.|||++||+..|+.|.-..+..+.+... .++-+.+.|.
T Consensus 2 v~v~~kG~i~IPK~iR~~lgl~eGd~l~~~~~-~d~~i~l~p~ 43 (44)
T TIGR01439 2 VKVTKKGQIVIPKEIREKLGLKEGDKLEVIRV-EDGEIILRPK 43 (44)
T ss_pred EEECCCCEEEECHHHHHHCCCCCCCEEEEEEE-CCCEEEEEEC
T ss_conf 57688762992738964069999987889882-7987989833
No 9
>PRK08577 hypothetical protein; Provisional
Probab=94.78 E-value=0.034 Score=34.67 Aligned_cols=44 Identities=27% Similarity=0.289 Sum_probs=28.7
Q ss_pred CCEECCCCCEEECHHHHHHHHHCCCCCEEECCCCCCCEEECCCH
Q ss_conf 21056766271078899998524898499516566441304523
Q gi|254781106|r 9 TQKIDSKGRVSVPFVFRTILAQRCITDLYCFQDFFFPAISVGNS 52 (145)
Q Consensus 9 ~~~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~ 52 (145)
.-++|+|||++||-.+|.+|.-..+-.+.+..+.+-+-+.+-|.
T Consensus 6 lVKVdskGritIPl~~r~~lgl~~G~y~LliaDtd~kEi~i~pi 49 (135)
T PRK08577 6 LVKVDSKGRITIPLEVRYALGLREGMYFLLIADTDKKEIHIEPI 49 (135)
T ss_pred EEEECCCCCEEEEHHHHHHHCCCCCCEEEEEEECCCCEEEEEEC
T ss_conf 99982688588628999984966685899997278764999972
No 10
>TIGR01439 lp_hng_hel_AbrB transcriptional regulator, AbrB family; InterPro: IPR006339 This DNA-binding domain is found in proteins like AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. .
Probab=94.43 E-value=0.069 Score=32.73 Aligned_cols=37 Identities=19% Similarity=0.332 Sum_probs=29.3
Q ss_pred CCCCCCCEEECCHHHHHHCCCC-C-EEEEE-ECCCEEEEC
Q ss_conf 2217861475198999870998-5-39999-419989962
Q gi|254781106|r 86 LKMDSEGRILMTDFIRVFTGIE-N-EVTFV-GRGNYFQLW 122 (145)
Q Consensus 86 ~~~D~~GRi~ip~~lr~~agi~-~-ev~~v-G~g~~fEIW 122 (145)
+.+|+.|||+||+..|+..||. + .+.+. =.+++++|-
T Consensus 2 v~v~~kG~i~IPK~iR~~lgl~eGd~l~~~~~~d~~i~l~ 41 (44)
T TIGR01439 2 VKVTKKGQIVIPKEIREKLGLKEGDKLEVIRVEDGEIILR 41 (44)
T ss_pred EEECCCCEEEECHHHHHHCCCCCCCEEEEEEECCCEEEEE
T ss_conf 5768876299273896406999998788988279879898
No 11
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=94.33 E-value=0.044 Score=33.92 Aligned_cols=36 Identities=25% Similarity=0.215 Sum_probs=26.4
Q ss_pred CCCCEECCCCCEEECHHHHHHHHHCCCCCEEECCCC
Q ss_conf 112105676627107889999852489849951656
Q gi|254781106|r 7 NVTQKIDSKGRVSVPFVFRTILAQRCITDLYCFQDF 42 (145)
Q Consensus 7 ~~~~~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~ 42 (145)
....++|.|||++||+.+|+.|.-.....+.+....
T Consensus 5 ~~~~kV~~~GqIvIPkeiR~~lgi~~Gd~lei~~~~ 40 (89)
T COG2002 5 MEVVKVDRKGQIVIPKEIREALGIKEGDVLEIIVDG 40 (89)
T ss_pred EEEEEECCCCEEEEEHHHHHHCCCCCCCEEEEEEEC
T ss_conf 059998879659955999998399989989999947
No 12
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=93.86 E-value=0.1 Score=31.68 Aligned_cols=38 Identities=29% Similarity=0.489 Sum_probs=27.4
Q ss_pred HHCCCCCCCEEECCHHHHHHCCCC-CE---EEEEECCCEEEE
Q ss_conf 112217861475198999870998-53---999941998996
Q gi|254781106|r 84 IFLKMDSEGRILMTDFIRVFTGIE-NE---VTFVGRGNYFQL 121 (145)
Q Consensus 84 ~~~~~D~~GRi~ip~~lr~~agi~-~e---v~~vG~g~~fEI 121 (145)
..+.+|..|||+||+.+|+..||+ ++ +...|-+.++-|
T Consensus 6 ~~~kV~~~GqIvIPkeiR~~lgi~~Gd~lei~~~~~~~~ivl 47 (89)
T COG2002 6 EVVKVDRKGQIVIPKEIREALGIKEGDVLEIIVDGDGGRIVL 47 (89)
T ss_pred EEEEECCCCEEEEEHHHHHHCCCCCCCEEEEEEECCCCEEEE
T ss_conf 599988796599559999983999899899999478867999
No 13
>pfam04014 SpoVT_AbrB SpoVT / AbrB like domain. One member of this family is AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator or the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. AbrB is thought to interact directly with the transcription initiation regions of genes under its control. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins. The product of the Bacillus subtilis gene spoVT is another member of this family and is also a transcriptional regulator. DNA binding activity in the Bacillus 0 AbrB homologue requires hexamerisation. Another family member has been isolated from the archaeon Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The E.coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as
Probab=88.50 E-value=0.55 Score=27.18 Aligned_cols=41 Identities=20% Similarity=0.134 Sum_probs=24.5
Q ss_pred EECCCCCEEECHHHHHHHHHCCCCCEEECCCCCCCEEECCCH
Q ss_conf 056766271078899998524898499516566441304523
Q gi|254781106|r 11 KIDSKGRVSVPFVFRTILAQRCITDLYCFQDFFFPAISVGNS 52 (145)
Q Consensus 11 ~lD~KGRi~iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~ 52 (145)
+++.+++++||+.||+.+.-..+..+.+.... ++.+.+.|.
T Consensus 2 k~g~s~~V~IPk~~r~~l~l~~Gd~v~~~~~~-~~~i~l~~~ 42 (47)
T pfam04014 2 KVGNSGAVTIPKEVRKALGIKEGDEVELEVDG-DGEIILRPK 42 (47)
T ss_pred CCCCCCEEECCHHHHHHCCCCCCCCEEEEECC-CCEEEEEEH
T ss_conf 31676469745999997099989957999789-975998545
No 14
>PRK08577 hypothetical protein; Provisional
Probab=88.16 E-value=0.58 Score=27.05 Aligned_cols=38 Identities=21% Similarity=0.352 Sum_probs=29.6
Q ss_pred HHCCCCCCCEEECCHHHHHHCCCCCE--EEEEECCCEEEE
Q ss_conf 11221786147519899987099853--999941998996
Q gi|254781106|r 84 IFLKMDSEGRILMTDFIRVFTGIENE--VTFVGRGNYFQL 121 (145)
Q Consensus 84 ~~~~~D~~GRi~ip~~lr~~agi~~e--v~~vG~g~~fEI 121 (145)
.-+.+|+.|||.||...|...||.+. +.+++.-++=||
T Consensus 5 elVKVdskGritIPl~~r~~lgl~~G~y~LliaDtd~kEi 44 (135)
T PRK08577 5 ELVKVDSKGRITIPLEVRYALGLREGMYFLLIADTDKKEI 44 (135)
T ss_pred EEEEECCCCCEEEEHHHHHHHCCCCCCEEEEEEECCCCEE
T ss_conf 9999826885886289999849666858999972787649
No 15
>TIGR00242 TIGR00242 mraZ protein; InterPro: IPR003444 This family is characterised by a 70 amino acid region and is found duplicated in a group of bacterial proteins. These proteins may be DNA-binding transcription factors, its members are probably enzymes containing a conserved DXXXR motif that probably forms part of the active site. .
Probab=85.10 E-value=0.71 Score=26.51 Aligned_cols=51 Identities=20% Similarity=0.238 Sum_probs=26.3
Q ss_pred HHHHCCCCCCCEEECCHHHHHHCCCCC----EEEEEECCCEEEECCHHHHHHHHH
Q ss_conf 111122178614751989998709985----399994199899629899999999
Q gi|254781106|r 82 GGIFLKMDSEGRILMTDFIRVFTGIEN----EVTFVGRGNYFQLWNPQTFRKLQE 132 (145)
Q Consensus 82 ~a~~~~~D~~GRi~ip~~lr~~agi~~----ev~~vG~g~~fEIW~~~~~~~~~~ 132 (145)
++..+.+|+.||+.+|..+|+..+-.. -++.-|..+++.+..+..|+.+.+
T Consensus 4 g~~~~~~d~~~~~~~p~~~~~~~~~~~~g~~~~~~~~~~~c~~~~~~~~~~~~~~ 58 (152)
T TIGR00242 4 GAFNVTLDAKGRLSLPAKYREGLLENSAGQLVCLNRGFENCLLLYPLPEWEKIEE 58 (152)
T ss_pred CCCHHCCCCCCCCCCHHHHHHHHHCCCCCCEEEEECCCHHHHHCCCCHHHHHHHH
T ss_conf 4200000345630010355655301235634443100001332056146789999
No 16
>TIGR02851 spore_V_T stage V sporulation protein T; InterPro: IPR014213 Members of this protein entry include the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB..
Probab=76.89 E-value=1.6 Score=24.27 Aligned_cols=47 Identities=19% Similarity=0.215 Sum_probs=30.5
Q ss_pred CCEECCCCCEEECHHHHHHHH--HCCCCCEEECCCCCCCEEECCCH-HHHH
Q ss_conf 210567662710788999985--24898499516566441304523-6789
Q gi|254781106|r 9 TQKIDSKGRVSVPFVFRTILA--QRCITDLYCFQDFFFPAISVGNS-DLLE 56 (145)
Q Consensus 9 ~~~lD~KGRi~iPa~fR~~L~--~~~~~~lv~~~~~~~~~l~~~~~-~~w~ 56 (145)
-++||+=|||.||-..|+.|- ++.+-++++-+.. +-.|.-|.+ .+..
T Consensus 6 VRRIDDLGRVViPKEIRRTLRIrEGDPLEIF~Dr~G-evILKKYSPI~EL~ 55 (184)
T TIGR02851 6 VRRIDDLGRVVIPKEIRRTLRIREGDPLEIFVDREG-EVILKKYSPIGELG 55 (184)
T ss_pred EEEEECCCCEEECCCCCCCCCCCCCCCCEEEEECCC-CEEEEECCCHHHHH
T ss_conf 775504686762643411010125997148880789-78987107803456
No 17
>TIGR02922 TIGR02922 conserved hypothetical protein TIGR02922; InterPro: IPR014271 Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by IPR013424 from INTERPRO..
Probab=75.28 E-value=0.63 Score=26.82 Aligned_cols=17 Identities=29% Similarity=0.630 Sum_probs=11.1
Q ss_pred CEECCCCCEEECHHHHH
Q ss_conf 10567662710788999
Q gi|254781106|r 10 QKIDSKGRVSVPFVFRT 26 (145)
Q Consensus 10 ~~lD~KGRi~iPa~fR~ 26 (145)
-.+.+-||+.||+.||+
T Consensus 29 ~~~~~~Grv~iP~eFk~ 45 (69)
T TIGR02922 29 FPVNESGRVVIPQEFKK 45 (69)
T ss_pred CCCCCCCCEECCCCCCC
T ss_conf 87666257760675668
No 18
>pfam09558 DUF2375 Protein of unknown function (DUF2375). Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by PEP_anchor (IPR013424).
Probab=65.26 E-value=2.3 Score=23.40 Aligned_cols=15 Identities=40% Similarity=0.776 Sum_probs=8.7
Q ss_pred ECCCCCEEECHHHHH
Q ss_conf 567662710788999
Q gi|254781106|r 12 IDSKGRVSVPFVFRT 26 (145)
Q Consensus 12 lD~KGRi~iPa~fR~ 26 (145)
+..-||++||+.||+
T Consensus 31 vs~~GrvmiPqeFrr 45 (71)
T pfam09558 31 VSETGRVMIPQEFRR 45 (71)
T ss_pred CCCCCCEECCHHHCC
T ss_conf 442565874058718
No 19
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=61.18 E-value=15 Score=18.33 Aligned_cols=91 Identities=15% Similarity=0.114 Sum_probs=66.5
Q ss_pred CEEECHHHHHHHHHCC--CCCEEE-CCCCCCCEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCE
Q ss_conf 2710788999985248--984995-1656644130452367899999863068875137999998631111122178614
Q gi|254781106|r 17 RVSVPFVFRTILAQRC--ITDLYC-FQDFFFPAISVGNSDLLEYFEQKIAEYNPFSIQANQLSLLVHGGGIFLKMDSEGR 93 (145)
Q Consensus 17 Ri~iPa~fR~~L~~~~--~~~lv~-~~~~~~~~l~~~~~~~w~~~~~~i~~l~~~~~~~~~~~r~~~~~a~~~~~D~~GR 93 (145)
++-+--.||..|.... ..+++. ..+.-+.-|++|.++.|++....|++.......++.+.-.|+..-....+=-.||
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~e~~~e~~~kr~a~~la~ve~~~~~~~~w~e~fy~~l~~~~fiPaGR 172 (857)
T PRK08115 93 QILIEEEYRPVLDDPEEAETGVVTRSLDVIEKPLEIFYEQIAKRNATGLAAVEKTEEKRKEWFEKFYKELASLNFIPAGR 172 (857)
T ss_pred EEEEHHHHHHHCCCHHHHCCCEEEEEHHHHCCCHHHHHHHHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf 98501433100168566427748831155315078789999998875631111399999999999999997458775410
Q ss_pred EECCHHHHHHCCCCCEEEEE
Q ss_conf 75198999870998539999
Q gi|254781106|r 94 ILMTDFIRVFTGIENEVTFV 113 (145)
Q Consensus 94 i~ip~~lr~~agi~~ev~~v 113 (145)
|+- -||-..+|++.
T Consensus 173 il~------GAGt~~~vT~f 186 (857)
T PRK08115 173 VLY------GAGSKKEVTFF 186 (857)
T ss_pred EEE------CCCCCCEEEEE
T ss_conf 332------57888705798
No 20
>PRK09974 putative regulator PrlF; Provisional
Probab=59.17 E-value=16 Score=18.12 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=22.9
Q ss_pred CCCCEECCCCCEEECHHHHHHHHHCCCC
Q ss_conf 1121056766271078899998524898
Q gi|254781106|r 7 NVTQKIDSKGRVSVPFVFRTILAQRCIT 34 (145)
Q Consensus 7 ~~~~~lD~KGRi~iPa~fR~~L~~~~~~ 34 (145)
+-+.+|-+||-++||..-|++|.-....
T Consensus 9 e~estlT~kgQtTiP~~vR~aL~l~~gd 36 (111)
T PRK09974 9 ETESTLTDRYQTTVPAPVRKALKLGKRD 36 (111)
T ss_pred CCCEEECCCCCEECCHHHHHHHCCCCCC
T ss_conf 1113540588755789999985899998
No 21
>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
Probab=44.42 E-value=28 Score=16.66 Aligned_cols=53 Identities=15% Similarity=0.329 Sum_probs=41.4
Q ss_pred CCCCCCEEECCHHHHHHCCCCCEEEEEECCCEEEECCHHHHHHHHHHHHHHHHHH
Q ss_conf 2178614751989998709985399994199899629899999999959999998
Q gi|254781106|r 87 KMDSEGRILMTDFIRVFTGIENEVTFVGRGNYFQLWNPQTFRKLQEESRNEYCRQ 141 (145)
Q Consensus 87 ~~D~~GRi~ip~~lr~~agi~~ev~~vG~g~~fEIW~~~~~~~~~~~~~~~~~~~ 141 (145)
.++.+|-.-....|....||+.=++.|---|-.+ ||.++|++..++-.+ +.+.
T Consensus 126 g~~~~gQtrEH~~La~tlGi~~lIVavNKMD~v~-wde~rf~ei~~~v~~-l~k~ 178 (428)
T COG5256 126 GFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVS-WDEERFEEIVSEVSK-LLKM 178 (428)
T ss_pred CCCCCCCHHHHHHHHHHCCCCEEEEEEECCCCCC-CCHHHHHHHHHHHHH-HHHH
T ss_conf 4365875167899998569756999997156666-279999999999999-9997
No 22
>TIGR02733 desat_CrtD C-3',4' desaturase CrtD; InterPro: IPR014104 Members of this family are encoded by slr1293, a carotenoid biosynthesis protein which was shown to be the C-3',4' desaturase (CrtD) of myxoxanthophyll biosynthesis in Synechocystis sp. (strain PCC 6803), and close homologues (presumed to be functionally equivalent) from other cyanobacteria, where myxoxanthophyll biosynthesis is either known or expected. This enzyme can act on neurosporene and so presumably catalyses the first step that is committed to myxoxanthophyll..
Probab=43.51 E-value=18 Score=17.90 Aligned_cols=16 Identities=0% Similarity=0.115 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999999995999999
Q gi|254781106|r 125 QTFRKLQEESRNEYCR 140 (145)
Q Consensus 125 ~~~~~~~~~~~~~~~~ 140 (145)
+.|.+.+++......+
T Consensus 394 ~~Y~~~K~~y~~~~~~ 409 (499)
T TIGR02733 394 EDYTAKKKQYTETILE 409 (499)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 7899999999999999
No 23
>pfam07656 KWG KWG Leptospira. This motif occurs in multiple copies in Leptospira interrogans proteins.
Probab=38.63 E-value=11 Score=19.27 Aligned_cols=17 Identities=29% Similarity=0.600 Sum_probs=12.4
Q ss_pred EECCCCCEEECHHHHHH
Q ss_conf 05676627107889999
Q gi|254781106|r 11 KIDSKGRVSVPFVFRTI 27 (145)
Q Consensus 11 ~lD~KGRi~iPa~fR~~ 27 (145)
-||..|++.||++|...
T Consensus 4 yID~~G~iVI~pqF~~~ 20 (26)
T pfam07656 4 YIDKSGKIVIPPQFXXX 20 (26)
T ss_pred CCCCCCCEECCCCCCCC
T ss_conf 17688979718622333
No 24
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=30.65 E-value=14 Score=18.50 Aligned_cols=12 Identities=42% Similarity=0.570 Sum_probs=9.8
Q ss_pred CEEECHHHHHHH
Q ss_conf 271078899998
Q gi|254781106|r 17 RVSVPFVFRTIL 28 (145)
Q Consensus 17 Ri~iPa~fR~~L 28 (145)
=+++|++||+.+
T Consensus 26 Lv~mP~KFRk~i 37 (78)
T cd05792 26 LVSMPTKFRKNI 37 (78)
T ss_pred EEEECHHHHCCE
T ss_conf 996013343168
No 25
>TIGR01425 SRP54_euk signal recognition particle protein SRP54; InterPro: IPR006325 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.; GO: 0005525 GTP binding, 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=28.50 E-value=25 Score=16.97 Aligned_cols=23 Identities=22% Similarity=0.647 Sum_probs=18.7
Q ss_pred EEEEEECCCE---EEECCHHHHHHHH
Q ss_conf 3999941998---9962989999999
Q gi|254781106|r 109 EVTFVGRGNY---FQLWNPQTFRKLQ 131 (145)
Q Consensus 109 ev~~vG~g~~---fEIW~~~~~~~~~ 131 (145)
=|+|||-|+| ||+.+++.|-+.+
T Consensus 289 PiiFIGTGEhv~d~E~F~~~~FvskL 314 (453)
T TIGR01425 289 PIIFIGTGEHVDDFEIFDAEPFVSKL 314 (453)
T ss_pred CEEEECCCCCCCCCCCCCCCCHHHHH
T ss_conf 77981377502760578997147754
No 26
>PRK13656 trans-2-enoyl-CoA reductase; Provisional
Probab=27.40 E-value=33 Score=16.24 Aligned_cols=53 Identities=17% Similarity=0.194 Sum_probs=30.0
Q ss_pred CEEECCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH-HCCCCCCCEEECC
Q ss_conf 4130452367899999863068875137999998631111-1221786147519
Q gi|254781106|r 45 PAISVGNSDLLEYFEQKIAEYNPFSIQANQLSLLVHGGGI-FLKMDSEGRILMT 97 (145)
Q Consensus 45 ~~l~~~~~~~w~~~~~~i~~l~~~~~~~~~~~r~~~~~a~-~~~~D~~GRi~ip 97 (145)
|.+-+|-.-.++.+-++=.-........|.|...++++.- .+.+|.+|||.+-
T Consensus 282 Pv~PLYislL~KVMKe~G~HEgcIeQ~~RLf~e~lY~~~~~~~~~D~~gRiR~D 335 (400)
T PRK13656 282 PVMPLYISLLFKVMKEKGTHEGCIEQIQRLFKERLYGADPAIPEVDEEGRLRLD 335 (400)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC
T ss_conf 764899999999998636886279999999997640589987773867871576
No 27
>pfam11772 EpuA DNA-directed RNA polymerase subunit beta. This short 60-residue long bacterial family is the beta subunit of the DNA-directed RNA polymerase, likely to be EC:2.7.7.6. It is membrane-bound and is referred to by the name EpuA.
Probab=26.89 E-value=30 Score=16.50 Aligned_cols=22 Identities=23% Similarity=0.634 Sum_probs=15.4
Q ss_pred EEEECCCEEEECCHHHHHHHHH
Q ss_conf 9994199899629899999999
Q gi|254781106|r 111 TFVGRGNYFQLWNPQTFRKLQE 132 (145)
Q Consensus 111 ~~vG~g~~fEIW~~~~~~~~~~ 132 (145)
-++|.|+-+.+-+|++|....+
T Consensus 21 gviG~G~p~dVl~~~tWq~Iid 42 (47)
T pfam11772 21 GVIGGGNPWDVLSPDTWQHIID 42 (47)
T ss_pred EEECCCCHHHHCCHHHHHHHHH
T ss_conf 2316998777549999999998
No 28
>pfam02261 Asp_decarbox Aspartate decarboxylase. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase EC:4.1.1.11 which requires a pyruvoyl group for its activity. It is synthesized initially as a proenzyme which is then proteolytically cleaved to an alpha (C-terminal) and beta (N-terminal) subunit and a pyruvoyl group. This family contains both chains of aspartate decarboxylase.
Probab=23.77 E-value=62 Score=14.55 Aligned_cols=40 Identities=20% Similarity=0.256 Sum_probs=29.4
Q ss_pred HHHHCCCCCCCEEECCHHHHHHCCCCC----EEEEEECCCEEEE
Q ss_conf 111122178614751989998709985----3999941998996
Q gi|254781106|r 82 GGIFLKMDSEGRILMTDFIRVFTGIEN----EVTFVGRGNYFQL 121 (145)
Q Consensus 82 ~a~~~~~D~~GRi~ip~~lr~~agi~~----ev~~vG~g~~fEI 121 (145)
....+++|=.|-|.|.+.|.+.|||-- +|+=+-.|.+|+=
T Consensus 14 ~VT~a~l~YeGSitID~~Lm~aagi~~~E~V~V~Nv~NG~R~~T 57 (116)
T pfam02261 14 TVTEADLNYEGSITIDEDLLDAAGILEYEKVQIVNVNNGERFET 57 (116)
T ss_pred EEECCCCCCEEEEEECHHHHHHCCCCCCCEEEEEECCCCCEEEE
T ss_conf 88055545217789889999875999898899998989968999
No 29
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=23.74 E-value=60 Score=14.62 Aligned_cols=16 Identities=19% Similarity=0.580 Sum_probs=11.8
Q ss_pred CCEEECCHHHHHHCCC
Q ss_conf 6147519899987099
Q gi|254781106|r 91 EGRILMTDFIRVFTGI 106 (145)
Q Consensus 91 ~GRi~ip~~lr~~agi 106 (145)
.|+|.||+.|+.|.|-
T Consensus 406 dG~v~IPevL~~y~gg 421 (429)
T COG0172 406 DGSVKIPEVLRPYMGG 421 (429)
T ss_pred CCCEECCHHHHHHCCC
T ss_conf 9986344788732785
No 30
>TIGR01660 narH nitrate reductase, beta subunit; InterPro: IPR006547 The nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and are b-type cytochromes that receive electrons from the quinone pool and transfers them to the beta subunit. The sequences in this family are the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for Gram-positive and Gram-negative bacteria. A few thermophiles and archaea also match the model. A number of the sequences in this set are experimentally characterised, these include: E.Coli NarH (P11349 from SWISSPROT) and NarY (P19318 from SWISSPROT) , , P42176 from SWISSPROT from Bacillus subtilis, and related proteins from Psuedomonas fluorescens, Paracoccus denitrificans, and Halomonas halodenitrificans.; GO: 0008940 nitrate reductase activity, 0042126 nitrate metabolic process, 0009325 nitrate reductase complex.
Probab=23.41 E-value=32 Score=16.33 Aligned_cols=39 Identities=10% Similarity=0.069 Sum_probs=24.4
Q ss_pred HHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEECCHHHHHHCC
Q ss_conf 863068875137999998631111122178614751989998709
Q gi|254781106|r 61 KIAEYNPFSIQANQLSLLVHGGGIFLKMDSEGRILMTDFIRVFTG 105 (145)
Q Consensus 61 ~i~~l~~~~~~~~~~~r~~~~~a~~~~~D~~GRi~ip~~lr~~ag 105 (145)
-++.......+.+.+-|+| +-|. =.-|++||..+||.+.
T Consensus 430 ~~~~VGLt~~Q~~~MYr~L-A~A~-----YeDRFViP~~HRE~~~ 468 (495)
T TIGR01660 430 VLEDVGLTEQQIEEMYRYL-AIAN-----YEDRFVIPSSHREIAS 468 (495)
T ss_pred HHHHCCCCHHHHHHHHHHH-HHCC-----CCCCEECCCCHHHHHH
T ss_conf 9976288888999999997-4115-----5774332774077899
No 31
>COG2072 TrkA Predicted flavoprotein involved in K+ transport [Inorganic ion transport and metabolism]
Probab=22.41 E-value=37 Score=15.91 Aligned_cols=28 Identities=25% Similarity=0.326 Sum_probs=18.0
Q ss_pred CCEEECCHHHHHHCCCC-CEEEEEECCCE
Q ss_conf 61475198999870998-53999941998
Q gi|254781106|r 91 EGRILMTDFIRVFTGIE-NEVTFVGRGNY 118 (145)
Q Consensus 91 ~GRi~ip~~lr~~agi~-~ev~~vG~g~~ 118 (145)
+|+++=|...++...+. |.|++||+|+.
T Consensus 158 ~g~~~HS~~~~~~~~~~GKrV~VIG~GaS 186 (443)
T COG2072 158 KGRILHSADWPNPEDLRGKRVLVIGAGAS 186 (443)
T ss_pred CCCEECCCCCCCHHHCCCCEEEEECCCCC
T ss_conf 86344410169613427887999898703
No 32
>TIGR01317 GOGAT_sm_gam glutamate synthases, NADH/NADPH, small subunit; InterPro: IPR006005 One pathway for the assimilation of ammonia and glutamate biosynthesis involves glutamate synthase (1.4.1.13 from EC) which transfers the amide group of glutamine to 2-oxoglutarate to yield two molecules of glutamate. 2 L-glutamate + NADP^+ = L-glutamine + 2-oxoglutarate + NADPH + H^+. This describes a family in several archaeal and deeply branched bacterial lineages of a homotetrameric form of the NADPH-dependent or NADH-dependent glutamate synthase (1.4.1.13 from EC and 1.4.1.14 from EC respectively) small subunit. There is no corresponding large subunit. ; GO: 0016639 oxidoreductase activity acting on the CH-NH2 group of donors NAD or NADP as acceptor, 0006537 glutamate biosynthetic process.
Probab=22.26 E-value=18 Score=17.88 Aligned_cols=31 Identities=19% Similarity=0.303 Sum_probs=18.0
Q ss_pred CCCCCEEECCHHHHHHC---CCC---CEEEEEECCCE
Q ss_conf 17861475198999870---998---53999941998
Q gi|254781106|r 88 MDSEGRILMTDFIRVFT---GIE---NEVTFVGRGNY 118 (145)
Q Consensus 88 ~D~~GRi~ip~~lr~~a---gi~---~ev~~vG~g~~ 118 (145)
|..+-|+.+-+.+++.- .|+ |+||+||-||+
T Consensus 283 L~~~tk~~l~~~~k~~~GqP~I~akGK~VvvIGGGDT 319 (517)
T TIGR01317 283 LTLNTKALLDDDFKDKDGQPFIKAKGKKVVVIGGGDT 319 (517)
T ss_pred HHHHHHHHCCCCCCCCCCCCCEEECCCEEEEECCCCC
T ss_conf 4675485608853666788735422867899757875
No 33
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=22.02 E-value=67 Score=14.34 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=29.2
Q ss_pred HHHCCCCCCCEEECCHHHHHHCCCCC----EEEEEECCCEEEEC
Q ss_conf 11122178614751989998709985----39999419989962
Q gi|254781106|r 83 GIFLKMDSEGRILMTDFIRVFTGIEN----EVTFVGRGNYFQLW 122 (145)
Q Consensus 83 a~~~~~D~~GRi~ip~~lr~~agi~~----ev~~vG~g~~fEIW 122 (145)
...+++|=.|-|.|.+.|.+.|||-- +|+=+-.|.+|+-.
T Consensus 15 VT~a~l~YeGSitID~~Lm~aagi~~~E~V~V~Nv~NG~Rf~TY 58 (126)
T PRK05449 15 VTEADLNYEGSITIDEDLLDAAGILENEKVDIVNVNNGARFETY 58 (126)
T ss_pred EECCCCCCEEEEEECHHHHHHCCCCCCCEEEEEECCCCCEEEEE
T ss_conf 80455452177898899998759998988999989899589999
No 34
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304 This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded..
Probab=21.89 E-value=60 Score=14.65 Aligned_cols=59 Identities=10% Similarity=0.120 Sum_probs=32.1
Q ss_pred ECHHHHHHHHHCCCCCEEECCCCCCCEEECCCHHHHHHHHHHHH-CCCCCCH---HHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf 07889999852489849951656644130452367899999863-0688751---3799999863111112217861475
Q gi|254781106|r 20 VPFVFRTILAQRCITDLYCFQDFFFPAISVGNSDLLEYFEQKIA-EYNPFSI---QANQLSLLVHGGGIFLKMDSEGRIL 95 (145)
Q Consensus 20 iPa~fR~~L~~~~~~~lv~~~~~~~~~l~~~~~~~w~~~~~~i~-~l~~~~~---~~~~~~r~~~~~a~~~~~D~~GRi~ 95 (145)
||-++|.+|. ++ + |++.|..++ +++|- +++.... ..|...|.++.++=.+++|..|+|.
T Consensus 101 LP~~~r~a~~--------L~----e--l~G~sQ~e~---A~kLGlSlSGaKSRVQRGR~~Lk~~L~~CC~~e~D~~G~~~ 163 (170)
T TIGR02959 101 LPDEYREAIR--------LT----E--LEGLSQKEI---AEKLGLSLSGAKSRVQRGRKKLKELLEDCCHLELDRVGNLI 163 (170)
T ss_pred CCHHHHHHHH--------HH----H--CCCCCHHHH---HHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCCCCEE
T ss_conf 6986788988--------87----5--079982799---87617533515678899999999877420100046876466
No 35
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=20.88 E-value=71 Score=14.19 Aligned_cols=39 Identities=23% Similarity=0.219 Sum_probs=28.9
Q ss_pred HHHCCCCCCCEEECCHHHHHHCCCCC----EEEEEECCCEEEE
Q ss_conf 11122178614751989998709985----3999941998996
Q gi|254781106|r 83 GIFLKMDSEGRILMTDFIRVFTGIEN----EVTFVGRGNYFQL 121 (145)
Q Consensus 83 a~~~~~D~~GRi~ip~~lr~~agi~~----ev~~vG~g~~fEI 121 (145)
..++++|=.|-|.|.+.|.+.|||-- +|+=+-.|.+|+=
T Consensus 14 VT~a~l~YeGSitID~~Lm~aa~i~~~E~V~V~N~~NG~Rf~T 56 (111)
T cd06919 14 VTEADLNYEGSITIDEDLLEAAGILPYEKVLVVNVNNGARFET 56 (111)
T ss_pred EECCCCCCEEEEEECHHHHHHCCCCCCCEEEEEECCCCCEEEE
T ss_conf 8055545217789889999875999898899998989947899
Done!