Query gi|254780713|ref|YP_003065126.1| 16S rRNA-processing protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 190
No_of_seqs 117 out of 1571
Neff 6.9
Searched_HMMs 39220
Date Sun May 29 19:39:18 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780713.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13828 rimM 16S rRNA-process 100.0 0 0 323.6 21.9 172 1-176 1-175 (177)
2 PRK00122 rimM 16S rRNA-process 100.0 0 0 307.5 20.0 164 4-169 1-168 (168)
3 TIGR02273 16S_RimM 16S rRNA pr 100.0 0 0 306.2 18.1 160 7-168 1-179 (179)
4 COG0806 RimM RimM protein, req 100.0 0 0 300.3 18.9 168 1-170 1-174 (174)
5 PRK13829 rimM 16S rRNA-process 100.0 0 0 298.5 20.0 167 6-176 6-177 (177)
6 pfam01782 RimM RimM N-terminal 99.8 2.4E-18 6.2E-23 123.1 9.1 79 9-87 1-84 (84)
7 pfam05239 PRC PRC-barrel domai 98.9 3.7E-09 9.4E-14 71.4 6.9 70 96-168 2-77 (77)
8 COG1873 Protein implicated in 96.4 0.014 3.5E-07 34.4 6.7 64 96-164 4-78 (87)
9 TIGR01150 puhA photosynthetic 95.0 0.052 1.3E-06 31.2 4.9 70 102-172 157-232 (264)
10 cd00226 PRCH Photosynthetic re 92.7 0.38 9.8E-06 26.3 5.9 61 102-167 147-211 (246)
11 COG2451 Ribosomal protein L35A 89.7 0.38 9.7E-06 26.4 3.3 30 55-84 23-52 (100)
12 COG3881 PRC-barrel domain cont 88.6 1.7 4.5E-05 22.6 6.1 68 48-123 39-107 (176)
13 COG3277 GAR1 RNA-binding prote 85.1 1.7 4.3E-05 22.7 4.4 35 102-136 25-59 (98)
14 PRK04337 50S ribosomal protein 83.8 1.1 2.8E-05 23.7 3.0 29 55-83 17-45 (87)
15 pfam01247 Ribosomal_L35Ae Ribo 82.6 1.5 3.9E-05 23.0 3.4 29 55-83 17-45 (94)
16 COG1588 POP4 RNase P/RNase MRP 70.9 8.3 0.00021 18.8 6.4 65 96-163 8-76 (95)
17 PRK06009 flgD flagellar basal 68.6 9.4 0.00024 18.5 5.2 75 59-143 54-128 (135)
18 KOG0887 consensus 64.0 4.6 0.00012 20.2 2.0 33 55-87 27-60 (111)
19 PRK13149 H/ACA RNA-protein com 63.7 12 0.0003 18.0 4.9 32 104-135 26-57 (73)
20 PRK11911 flgD flagellar basal 60.5 13 0.00034 17.6 5.2 50 100-154 88-140 (140)
21 TIGR02888 spore_YlmC_YmxH spor 59.5 14 0.00036 17.5 5.2 61 99-163 1-75 (76)
22 TIGR02408 ectoine_ThpD ectoine 57.2 5.5 0.00014 19.8 1.4 44 61-107 89-135 (278)
23 TIGR02225 recomb_XerD tyrosine 55.2 6 0.00015 19.6 1.3 83 59-152 98-190 (305)
24 PTZ00041 60S ribosomal protein 47.8 19 0.00047 16.8 2.8 29 57-85 46-75 (128)
25 pfam05935 Arylsulfotrans Aryls 41.7 28 0.0007 15.9 5.4 69 114-184 171-258 (459)
26 pfam12317 IFT46_B_C Intraflage 39.3 11 0.00028 18.1 0.6 29 142-170 38-66 (214)
27 TIGR00491 aIF-2 translation in 34.5 36 0.00092 15.2 2.9 60 105-167 1045-1105(1145)
28 KOG2356 consensus 29.2 42 0.0011 14.9 2.2 96 62-170 89-196 (366)
29 TIGR00635 ruvB Holliday juncti 28.2 30 0.00077 15.7 1.3 54 110-166 67-129 (305)
30 KOG3262 consensus 27.7 30 0.00076 15.7 1.3 33 105-137 80-112 (215)
31 COG4974 XerD Site-specific rec 25.7 52 0.0013 14.3 2.3 70 64-151 111-189 (300)
32 TIGR00580 mfd transcription-re 23.7 54 0.0014 14.2 2.0 46 92-146 382-432 (997)
33 KOG3041 consensus 22.6 56 0.0014 14.2 1.8 39 130-173 78-116 (225)
34 PTZ00223 40S ribosomal protein 21.4 63 0.0016 13.9 6.3 84 77-168 153-240 (273)
35 TIGR01173 glmU UDP-N-acetylglu 21.3 30 0.00076 15.7 0.2 51 60-110 157-214 (461)
36 PRK13559 hypothetical protein; 20.5 61 0.0016 14.0 1.7 32 93-124 127-161 (363)
37 KOG2090 consensus 20.0 65 0.0017 13.8 1.7 73 60-135 366-444 (704)
No 1
>PRK13828 rimM 16S rRNA-processing protein; Provisional
Probab=100.00 E-value=0 Score=323.57 Aligned_cols=172 Identities=30% Similarity=0.549 Sum_probs=158.7
Q ss_pred CCCCCCEEEEEEEECCCEEEEEEEEEECCCCHHHHHHCCEEC--CCCEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCC
Q ss_conf 998200799999944630505999994189977876301020--798379999999739979999638778455676349
Q gi|254780713|r 1 MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYS--NDNRELRILKMYRKNKRFIATFSGIDNIHSASELRD 78 (190)
Q Consensus 1 M~k~~~~i~iGkI~k~hGlkGevki~~~td~~~~~~~~~~~~--~~~~~~~i~~~~~~~~~~iikf~gi~s~~~A~~l~g 78 (190)
|| ++|+.||+|++|||+|||++|++||++|+++.++..+. ....++.++.++.++++++++|+||+||++|++|+|
T Consensus 1 M~--~d~i~iG~I~~~hGlkGevkv~~~td~p~~~~~~~~~~~~~~~~~~~i~~~r~~~~~~ivkf~gi~~r~~Ae~l~g 78 (177)
T PRK13828 1 MM--TDRICVGRIGGAHGVRGEVRLKSFTEDPLAIADYGPLTTEDGARSFTVALARPAKDGLVARLKGVATREEAEALRG 78 (177)
T ss_pred CC--CCEEEEEEEECCEEECEEEEEEECCCCHHHHHCCCEEEECCCCEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCC
T ss_conf 97--6649999994999356599999978997896067738936998889999999979989999878899899998569
Q ss_pred CEEEECHHHCCCCCCCCCCCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEECC-CCCEEEEECHHHHCCEEECCC
Q ss_conf 6877417778865564100214524011367525843119988665799508999749-982899875031001056339
Q gi|254780713|r 79 LKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNT-MEKTFLIPFTKFAVLEVNLQE 157 (190)
Q Consensus 79 ~~i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~-~~ke~lIP~v~~~I~~ID~~~ 157 (190)
+.+|++++.|| +++++||||+|||||+|+|.+|+.+|+|.+|+++||||+|+|+.. +++++||||+++||.+||+++
T Consensus 79 ~~i~i~~~~lp--~l~e~e~Y~~dLiGl~V~d~~g~~lG~V~~v~~~ga~dvl~V~~~~~~~~iLIP~v~~~V~~VD~~~ 156 (177)
T PRK13828 79 LELYVPRDRLP--SLDDDEFYHADLIGLAVVDTGGELLGRVKAVHNFGAGDILEITAPGGGPTLLLPFTRAVVPTVDLAG 156 (177)
T ss_pred CEEEEEHHHCC--CCCCCCEEHHHHCCCEEEECCCCEEEEEEEEECCCCCEEEEEEECCCCCEEEEECCCCCCCEEECCC
T ss_conf 86999878888--8757869648827969992899898999998428995299999889995899835831017797789
Q ss_pred CEEEEECCCCCCCCCCCCC
Q ss_conf 7999952810038886547
Q gi|254780713|r 158 NKILIDPIAAGLNNTTMKN 176 (190)
Q Consensus 158 k~I~v~~p~Glld~~~~~~ 176 (190)
|+|+|+||+||+|++.+..
T Consensus 157 k~I~vd~PeGL~d~~~~~~ 175 (177)
T PRK13828 157 GRVVADPPAEIEGDDPEHS 175 (177)
T ss_pred CEEEEECCCCCCCCCCCCC
T ss_conf 9999989885468986667
No 2
>PRK00122 rimM 16S rRNA-processing protein; Provisional
Probab=100.00 E-value=0 Score=307.45 Aligned_cols=164 Identities=30% Similarity=0.492 Sum_probs=153.4
Q ss_pred CCCEEEEEEEECCCEEEEEEEEEECCCCHHHHHHCCEE----CCCCEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCCC
Q ss_conf 20079999994463050599999418997787630102----07983799999997399799996387784556763496
Q gi|254780713|r 4 LDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLY----SNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDL 79 (190)
Q Consensus 4 ~~~~i~iGkI~k~hGlkGevki~~~td~~~~~~~~~~~----~~~~~~~~i~~~~~~~~~~iikf~gi~s~~~A~~l~g~ 79 (190)
.+||+.||+|++|||+||+++++++|++|+.+.++..+ .....++.+++++.++++++++|++++||++|++|+|+
T Consensus 1 ~~d~i~iG~i~~~hGlkGevki~~~t~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~i~k~~~i~~re~Ae~l~g~ 80 (168)
T PRK00122 1 PEDLVVVGKIVSAHGIKGEVKVKSFTDFPERRFDYGPWLLKKDGEPRPVEIESGRVHKKFLIVKFEGVDDRNAAEALKGT 80 (168)
T ss_pred CCCEEEEEEECCCEEECEEEEEEECCCCHHHHCCCCEEEEECCCCEEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCCC
T ss_conf 98689999991988105799999987897995086729991699468998687999599999999588998999985398
Q ss_pred EEEECHHHCCCCCCCCCCCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEECCCCCEEEEECHHHHCCEEECCCCE
Q ss_conf 87741777886556410021452401136752584311998866579950899974998289987503100105633979
Q gi|254780713|r 80 KLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENK 159 (190)
Q Consensus 80 ~i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~~~ke~lIP~v~~~I~~ID~~~k~ 159 (190)
.+|+++++|| +++++||||+|||||+|+|.+|+.+|+|++|+++||||+|+|++.++||+||||+++||.+||.++|+
T Consensus 81 ~l~i~~~~lp--~l~~~e~y~~dLiG~~V~d~~~~~lG~V~~v~~~~a~d~l~i~~~~~ke~liP~~~~~i~~ID~~~k~ 158 (168)
T PRK00122 81 EIFVPRSQLP--ELEEDEYYWHDLIGLEVVTTEGEELGKVTDILETGANDVLVVKRPGGKERLIPFVEAVVKEVDLEAKR 158 (168)
T ss_pred EEEEEHHHCC--CCCCCCEEHHEECCCEEEECCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEECCHHCCCEEECCCCE
T ss_conf 7995288989--98788536212518699948996926999972169926999991899599997353100679778999
Q ss_pred EEEECCCCCC
Q ss_conf 9995281003
Q gi|254780713|r 160 ILIDPIAAGL 169 (190)
Q Consensus 160 I~v~~p~Gll 169 (190)
|+|+||+|||
T Consensus 159 I~v~~peGLl 168 (168)
T PRK00122 159 IVVDWPEGLL 168 (168)
T ss_pred EEEECCCCCC
T ss_conf 9997964249
No 3
>TIGR02273 16S_RimM 16S rRNA processing protein RimM; InterPro: IPR011961 This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterised in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. This entry represents the full-length model. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide .; GO: 0043022 ribosome binding, 0006364 rRNA processing, 0005840 ribosome.
Probab=100.00 E-value=0 Score=306.16 Aligned_cols=160 Identities=30% Similarity=0.552 Sum_probs=146.1
Q ss_pred EEEEEEEECCCEEEEEEEEEECCCCHHHHHHCCEE---CC----CC--EEEEEEEEEEECCEEEEEECCCCCHHHHHHHC
Q ss_conf 79999994463050599999418997787630102---07----98--37999999973997999963877845567634
Q gi|254780713|r 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLY---SN----DN--RELRILKMYRKNKRFIATFSGIDNIHSASELR 77 (190)
Q Consensus 7 ~i~iGkI~k~hGlkGevki~~~td~~~~~~~~~~~---~~----~~--~~~~i~~~~~~~~~~iikf~gi~s~~~A~~l~ 77 (190)
++.||+|++|||+||||||.|+||+++++.++..+ .. .. .+++..+.+.+++.++++|+||+|||+|++|+
T Consensus 1 ~~~~G~i~~~hG~~GevKv~~~Td~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fegi~~r~~Ae~L~ 80 (179)
T TIGR02273 1 LLVVGKIGGAHGIRGEVKVKSFTDFPESIFDYGPWLILKDSKSSQWKLVEVKVASVRKQKNKLIVKFEGIDDREAAEALK 80 (179)
T ss_pred CEEEEEEECCEECCEEEEEEECCCCHHHHCCCCCEEEEECCCCCCEEEEEEEEEEEEECCCEEEEEECCCCCHHHHHHHC
T ss_conf 97879993673200169998707985885388618999589887137999999999832885899966989979998636
Q ss_pred CCEEEECHHHCCCCCCC---CCCCCHHHHHCCEEE--EECCCEEEEEEEEEECCCCEEEEEEC----CCCCEEEEECHH-
Q ss_conf 96877417778865564---100214524011367--52584311998866579950899974----998289987503-
Q gi|254780713|r 78 DLKLYAKRQDFKDEELE---EDEFFNTDLEEMETF--DRQGKYWGQVCGVYNFGAGSILEIKN----TMEKTFLIPFTK- 147 (190)
Q Consensus 78 g~~i~i~~~~lp~~~l~---~~e~Y~~dLiG~~V~--d~~~~~iG~V~~v~~~~a~dil~V~~----~~~ke~lIP~v~- 147 (190)
|+.||+++++|| +|+ +|||||+|||||+|+ +++|+.||+|++|+++||||+|+|++ .+.+++||||++
T Consensus 81 g~~l~v~~~~lp--~l~~lkedEyY~~DLiGl~V~d~~~~G~~LG~V~~~~~tganDvlvv~~~~~~~~~~~~LiPf~~~ 158 (179)
T TIGR02273 81 GLELFVPREALP--ELEKLKEDEYYWTDLIGLEVVDVTTEGEELGKVVEILETGANDVLVVRSNVGKKGKKEVLIPFVEK 158 (179)
T ss_pred CCEEEEEHHHCC--CCCCCCCCCEEEEEEECCEEEECCCCCEEEEEEEEEEECCCCEEEEEECCCCCCCCCEEEEECCCC
T ss_conf 948989488848--755788975264303277898701589455689872555996599997478986771698655899
Q ss_pred HHCCEEECCCCEEEEECCCCC
Q ss_conf 100105633979999528100
Q gi|254780713|r 148 FAVLEVNLQENKILIDPIAAG 168 (190)
Q Consensus 148 ~~I~~ID~~~k~I~v~~p~Gl 168 (190)
++|++||+++|.|+|++|+||
T Consensus 159 ~~v~~id~~~k~i~v~~~~~~ 179 (179)
T TIGR02273 159 EIVKEIDLEKKIITVDWPEGL 179 (179)
T ss_pred CEEEEEECCCCEEEEEECCCC
T ss_conf 557765734778989617779
No 4
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=300.30 Aligned_cols=168 Identities=33% Similarity=0.549 Sum_probs=156.2
Q ss_pred CCCCCCEEEEEEEECCCEEEEEEEEEECCCCHHHHHHCCEECCCC-----EEEEEEEEEEECCEEEEEECCCCCHHHHHH
Q ss_conf 998200799999944630505999994189977876301020798-----379999999739979999638778455676
Q gi|254780713|r 1 MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDN-----RELRILKMYRKNKRFIATFSGIDNIHSASE 75 (190)
Q Consensus 1 M~k~~~~i~iGkI~k~hGlkGevki~~~td~~~~~~~~~~~~~~~-----~~~~i~~~~~~~~~~iikf~gi~s~~~A~~ 75 (190)
|++.++++.+|+|+++||++||+||+|+||+|+.+..+..+.... ..+.+.+++.+++.++++|+|+++|++|++
T Consensus 1 m~~~~~~~~vGkI~~t~Gi~GevrV~s~Td~~~~~~~~~~~~~~~~~~~~~~~~v~~~r~~~~~~i~kf~gi~dr~~ae~ 80 (174)
T COG0806 1 MTKPENLLLVGKIVSTHGIRGEVRVKSFTDFPESLFDYGPWLLLKPGGEWQELTVESVRKHKNLLILKFKGIDDRNAAEA 80 (174)
T ss_pred CCCCCCEEEEEEEEECCCCCEEEEEEECCCCHHHHCCCCCEEEECCCCCEEEEEEEEEEECCCEEEEEECCCCCHHHHHH
T ss_conf 99861028999997120434799999778898996286749994388853899999811159889999679799899997
Q ss_pred HCCCEEEECHHHCCCCCCCCCCCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEEC-CCCCEEEEECHHHHCCEEE
Q ss_conf 349687741777886556410021452401136752584311998866579950899974-9982899875031001056
Q gi|254780713|r 76 LRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKN-TMEKTFLIPFTKFAVLEVN 154 (190)
Q Consensus 76 l~g~~i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~-~~~ke~lIP~v~~~I~~ID 154 (190)
|+|+.+|++++++| ++++|||||+||+||+|++.+|+.+|+|++++++||||+|+|+. ..+|++||||++++|++||
T Consensus 81 l~G~~i~v~~~~~p--~l~EdEfY~~DLiG~~V~~~~g~~lG~V~~i~~~Ga~Dvl~V~~~~~~k~~LIPf~~~~V~~Vd 158 (174)
T COG0806 81 LKGYEIFVDRSELP--ELEEDEFYYHDLIGLEVVTEDGELLGKVTEILETGANDVLVVKAKGGKKERLIPFVDAVVKEVD 158 (174)
T ss_pred HCCCEEEEEHHHCC--CCCCCCEEEEEECCCEEECCCCCEEEEEEEEEECCCCCEEEEEECCCCCEEEECCHHHEEEEEE
T ss_conf 26958997889989--9889968957415839993798388999898647995199999468995699506576020796
Q ss_pred CCCCEEEEECCCCCCC
Q ss_conf 3397999952810038
Q gi|254780713|r 155 LQENKILIDPIAAGLN 170 (190)
Q Consensus 155 ~~~k~I~v~~p~Glld 170 (190)
+++|+|.++|++||+|
T Consensus 159 ~~~k~I~v~~~~~ll~ 174 (174)
T COG0806 159 LEAKKIEVDPDEGLLD 174 (174)
T ss_pred CCCCEEEEECCCHHCC
T ss_conf 4887899724502039
No 5
>PRK13829 rimM 16S rRNA-processing protein; Provisional
Probab=100.00 E-value=0 Score=298.53 Aligned_cols=167 Identities=18% Similarity=0.322 Sum_probs=148.3
Q ss_pred CEEEEEEEECCCEEEEEEEEEECCCCHHHHHHC-CEECCCCEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCCCEEEEC
Q ss_conf 079999994463050599999418997787630-1020798379999999739979999638778455676349687741
Q gi|254780713|r 6 KLVLMATIGTTHGLNGEVYIDSYANNPIDLNRY-VLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAK 84 (190)
Q Consensus 6 ~~i~iGkI~k~hGlkGevki~~~td~~~~~~~~-~~~~~~~~~~~i~~~~~~~~~~iikf~gi~s~~~A~~l~g~~i~i~ 84 (190)
+++.||+|++|||+|||++++++||. ..+..+ .++......+.+..++.++++++++|++|+||++|++|+|+.+|++
T Consensus 6 dlv~IG~I~~~hGlkGevkv~~~tdp-~~~~~~~~~~~~~~~~~~v~~~~~~~~~~iv~~~gi~dr~~Ae~l~g~~l~i~ 84 (177)
T PRK13829 6 DLTRLGRFLGPHGVQGGLKFYVLGDP-VQVLALERVYVEGHGWLAIRRLERVGPELVLHLAGVTSRELAEALRGLRVYAE 84 (177)
T ss_pred CEEEEEEEECCEEECEEEEEEECCCH-HHHHCCCCEEECCCCEEEEEEEEEECCEEEEEECCCCCHHHHHHHCCCEEEEE
T ss_conf 58999999599925769999988893-89705674698489879999999989869999979799899997329999988
Q ss_pred HHHCCCCCCCCCCCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEECCCCCEEEEECHHHHCC----EEECCCCEE
Q ss_conf 7778865564100214524011367525843119988665799508999749982899875031001----056339799
Q gi|254780713|r 85 RQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVL----EVNLQENKI 160 (190)
Q Consensus 85 ~~~lp~~~l~~~e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~~~ke~lIP~v~~~I~----~ID~~~k~I 160 (190)
+++|| +|+++||||||||||+|+|.+|+.+|+|++++++||||+|||+.. ++|.||||+..||. ++|+..++|
T Consensus 85 ~~~LP--~l~e~EyY~~dLiGl~V~~~~g~~lG~V~~v~~~gA~DvlvV~~~-~~e~lIP~v~~~V~~~~~~~~~~~~~i 161 (177)
T PRK13829 85 DADLP--PLEEGRYYYHALRGLPVYGAEGRQLGEVVDVLDAGHQDLLVVRGV-GGERFVPLQAPYVRVEEGGGKPGAVHL 161 (177)
T ss_pred HHHCC--CCCCCCEEEHHCCCCEEECCCCCEEEEEEEECCCCCCEEEEEECC-CCEEEEECCCCEEEEEECCCCEEECEE
T ss_conf 88989--999997990453798999489979899979801799529999879-988999664266888704552000789
Q ss_pred EEECCCCCCCCCCCCC
Q ss_conf 9952810038886547
Q gi|254780713|r 161 LIDPIAAGLNNTTMKN 176 (190)
Q Consensus 161 ~v~~p~Glld~~~~~~ 176 (190)
+||||+||||++.+++
T Consensus 162 ~idpp~GL~dd~~~~~ 177 (177)
T PRK13829 162 TADAPAGLFGDGAAES 177 (177)
T ss_pred EEECCCCCCCCCCCCC
T ss_conf 9969796668765569
No 6
>pfam01782 RimM RimM N-terminal domain. The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. This N-terminal domain is found associated with a PRC-barrel domain.
Probab=99.76 E-value=2.4e-18 Score=123.07 Aligned_cols=79 Identities=30% Similarity=0.529 Sum_probs=69.3
Q ss_pred EEEEEECCCEEEEEEEEEECCCCHHHHHHCCEE---CC--CCEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCCCEEEE
Q ss_conf 999994463050599999418997787630102---07--9837999999973997999963877845567634968774
Q gi|254780713|r 9 LMATIGTTHGLNGEVYIDSYANNPIDLNRYVLY---SN--DNRELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYA 83 (190)
Q Consensus 9 ~iGkI~k~hGlkGevki~~~td~~~~~~~~~~~---~~--~~~~~~i~~~~~~~~~~iikf~gi~s~~~A~~l~g~~i~i 83 (190)
.||+|++|||+|||++|+++|++|+.+..+..+ .. ...++.++.++.++++++++|+||+||++|+.|+|+.||+
T Consensus 1 ~iG~I~~~hGlkG~vki~~~td~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~i~~~~gi~~re~A~~l~g~~i~i 80 (84)
T pfam01782 1 LVGKIVGTHGLKGEVKVKSFTDFPEAIFDYGPWFLLKKKGEWKPLTVESVRLHKKGLIVKFEGVDDRDAAEALKGAELYV 80 (84)
T ss_pred CEEEECCCCCCCEEEEEEECCCCHHHHCCCCCEEEECCCCCEEEEEEEEEEEECCEEEEEECCCCCHHHHHHHCCCEEEE
T ss_conf 98998775221288999975799899608671999869995788999999997999999977989989999737999999
Q ss_pred CHHH
Q ss_conf 1777
Q gi|254780713|r 84 KRQD 87 (190)
Q Consensus 84 ~~~~ 87 (190)
++++
T Consensus 81 ~r~~ 84 (84)
T pfam01782 81 PRSD 84 (84)
T ss_pred ECCC
T ss_conf 7899
No 7
>pfam05239 PRC PRC-barrel domain. The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain.
Probab=98.91 E-value=3.7e-09 Score=71.43 Aligned_cols=70 Identities=37% Similarity=0.643 Sum_probs=60.8
Q ss_pred CCCCHHHHHCCEEEEECCCEEEEEEEE-EECCCCEEEEEECCCC-----CEEEEECHHHHCCEEECCCCEEEEECCCCC
Q ss_conf 002145240113675258431199886-6579950899974998-----289987503100105633979999528100
Q gi|254780713|r 96 DEFFNTDLEEMETFDRQGKYWGQVCGV-YNFGAGSILEIKNTME-----KTFLIPFTKFAVLEVNLQENKILIDPIAAG 168 (190)
Q Consensus 96 ~e~Y~~dLiG~~V~d~~~~~iG~V~~v-~~~~a~dil~V~~~~~-----ke~lIP~v~~~I~~ID~~~k~I~v~~p~Gl 168 (190)
++||+++|+|++|++.+|+.+|+|.++ ++.+++.+..+.-..+ ++++||+.. ..++..++.|.++.++++
T Consensus 2 ~~~~~~~l~G~~V~~~~G~~lG~V~Dv~id~~~g~i~~i~~~~g~~~~~~~~~vP~~~---~~~~~~~~~i~v~~~~~~ 77 (77)
T pfam05239 2 DEFYASDLIGLEVYTEDGEKLGKVKDVVIDEGEGDVLYLVVSVGGFLGDKEVLIPFTK---LEVDLGKDRIIVDAPKEL 77 (77)
T ss_pred CCEEEEEEECCEEECCCCCEEEEEEEEEEECCCCCEEEEEECCCCCCCCEEEEECCCC---CEEECCCCEEEECCCCCC
T ss_conf 8279789748887999999998999999978999599999876887788249951116---669876999997999999
No 8
>COG1873 Protein implicated in RNA metabolism, contains PRC-barrel domain [General function prediction only]
Probab=96.41 E-value=0.014 Score=34.44 Aligned_cols=64 Identities=25% Similarity=0.365 Sum_probs=42.6
Q ss_pred CCCCHHHHHCCEEEEECCCEEEEEEEEE-ECCCC--EEEEEECC--------CCCEEEEECHHHHCCEEECCCCEEEEEC
Q ss_conf 0021452401136752584311998866-57995--08999749--------9828998750310010563397999952
Q gi|254780713|r 96 DEFFNTDLEEMETFDRQGKYWGQVCGVY-NFGAG--SILEIKNT--------MEKTFLIPFTKFAVLEVNLQENKILIDP 164 (190)
Q Consensus 96 ~e~Y~~dLiG~~V~d~~~~~iG~V~~v~-~~~a~--dil~V~~~--------~~ke~lIP~v~~~I~~ID~~~k~I~v~~ 164 (190)
..+++++|.|.+|++.+|..+|+|.++. +...+ .-|.|... .++.+.||| +.|..| ...|++..
T Consensus 4 ~~~~~s~l~gk~V~~~~G~~vG~V~dv~ld~~~g~i~~l~v~~~~~~l~~~~k~~~v~IP~--~~V~aI---Gd~III~~ 78 (87)
T COG1873 4 EMMRLSELLGKEVITNDGKYVGTVSDVVLDIKEGKITGLLVIPTNKGLFLFGKGKEVIVPY--EYVKAI---GDIIIIKD 78 (87)
T ss_pred HHHEHHHHCCCEEECCCCEEEEEEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCEEEEEH--HHEEEE---CCEEEEEC
T ss_conf 1214877429689847884999997389984689389999956885200057796899754--575785---57999945
No 9
>TIGR01150 puhA photosynthetic reaction center H subunit; InterPro: IPR005652 The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors . LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) . Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP , , . The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits . RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain . In Blastochloris viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface. This entry describes the photosynthetic reaction centre H subunit, which has a single transmembrane helix and a large cytoplasmic domain . The core of the cytoplasmic domain has a PRC-barrel structure.; GO: 0045156 electron transporter transferring electrons within the cyclic electron transport pathway of photosynthesis activity, 0006118 electron transport, 0019684 photosynthesis light reaction, 0030077 plasma membrane light-harvesting complex.
Probab=94.97 E-value=0.052 Score=31.19 Aligned_cols=70 Identities=16% Similarity=0.308 Sum_probs=52.6
Q ss_pred HHHCCEEEEECCCEEEEEEEEE-ECCCCE--EEEEECCCC--CEEEEECHHHHCCEEECCCCEEEEECCC-CCCCCC
Q ss_conf 2401136752584311998866-579950--899974998--2899875031001056339799995281-003888
Q gi|254780713|r 102 DLEEMETFDRQGKYWGQVCGVY-NFGAGS--ILEIKNTME--KTFLIPFTKFAVLEVNLQENKILIDPIA-AGLNNT 172 (190)
Q Consensus 102 dLiG~~V~d~~~~~iG~V~~v~-~~~a~d--il~V~~~~~--ke~lIP~v~~~I~~ID~~~k~I~v~~p~-Glld~~ 172 (190)
|=.|+.|.+.++...|+|+|+. +.+.|- .|||+-..+ +..|+|+..-- .-++..+++|+|+-+- -++++-
T Consensus 157 dPrGLPV~~~d~~~aGkv~DlWvD~~e~~~RYLEvel~~~p~~~~LlP~~atr-i~~k~~s~~v~V~si~s~~Fa~v 232 (264)
T TIGR01150 157 DPRGLPVVAADGEVAGKVVDLWVDRPEQLIRYLEVELAAGPARKKLLPLAATR-IMVKVKSDRVTVNSILSDLFANV 232 (264)
T ss_pred CCCCCCEECCCEEEEEEEEEEEEECHHHCEEEEEEEEECCCCCCEECCCCCEE-EEEEEECCEEEEEEEEHHHHCCC
T ss_conf 88727534488047437988764015740154468750788751202411126-77787618789988603441478
No 10
>cd00226 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. Subunit H is positioned mainly in the cytoplasm with one transmembrane alpha helix. Provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Found in photosynthetic bacteria: alpha, beta, and gamma proteobacteria.
Probab=92.73 E-value=0.38 Score=26.32 Aligned_cols=61 Identities=18% Similarity=0.309 Sum_probs=45.6
Q ss_pred HHHCCEEEEECCCEEEEEEEEE-ECCCCE--EEEEECC-CCCEEEEECHHHHCCEEECCCCEEEEECCCC
Q ss_conf 2401136752584311998866-579950--8999749-9828998750310010563397999952810
Q gi|254780713|r 102 DLEEMETFDRQGKYWGQVCGVY-NFGAGS--ILEIKNT-MEKTFLIPFTKFAVLEVNLQENKILIDPIAA 167 (190)
Q Consensus 102 dLiG~~V~d~~~~~iG~V~~v~-~~~a~d--il~V~~~-~~ke~lIP~v~~~I~~ID~~~k~I~v~~p~G 167 (190)
|-.|+.|+-.+|+..|+|+++. +.+-|- +|||+.. .++.+|+|+.-.- | .++++.|+-+-|
T Consensus 147 DPrG~~V~g~Dg~v~G~V~D~WVDr~E~lvRYlEvel~~~g~~~LlP~~~a~---i--~~~~V~v~si~~ 211 (246)
T cd00226 147 DPRGLPVVGADGEVAGKVTDLWVDRPEQLFRYLEVELAGGGRTVLLPMGFAK---V--KSDRVKVTAILS 211 (246)
T ss_pred CCCCCEEECCCCCEEEEEEEEEECCHHHEEEEEEEEECCCCCEEEEEEEEEE---E--CCCEEEEEEECH
T ss_conf 9898975726886456899988887321245899996589966997621068---8--488189987616
No 11
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=89.69 E-value=0.38 Score=26.36 Aligned_cols=30 Identities=13% Similarity=0.150 Sum_probs=26.1
Q ss_pred EECCEEEEEECCCCCHHHHHHHCCCEEEEC
Q ss_conf 739979999638778455676349687741
Q gi|254780713|r 55 RKNKRFIATFSGIDNIHSASELRDLKLYAK 84 (190)
Q Consensus 55 ~~~~~~iikf~gi~s~~~A~~l~g~~i~i~ 84 (190)
.+.+..++|++|++|+++|..+.|..++..
T Consensus 23 q~P~~~liKi~gv~s~~eA~~y~gk~v~yk 52 (100)
T COG2451 23 QHPNVSLIKIEGVDSPEEAQFYLGKRVCYK 52 (100)
T ss_pred CCCCEEEEEEECCCCHHHHHHHHCCEEEEE
T ss_conf 699668999715799789876426279999
No 12
>COG3881 PRC-barrel domain containing protein [General function prediction only]
Probab=88.65 E-value=1.7 Score=22.62 Aligned_cols=68 Identities=19% Similarity=0.143 Sum_probs=43.4
Q ss_pred EEEEEEEEECCEEEEEECCCCCHHHHHHHCCCEEEECHHHCCCCCCCCCCCCHHHHHCCEEEE-ECCCEEEEEEEEE
Q ss_conf 999999973997999963877845567634968774177788655641002145240113675-2584311998866
Q gi|254780713|r 48 LRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFD-RQGKYWGQVCGVY 123 (190)
Q Consensus 48 ~~i~~~~~~~~~~iikf~gi~s~~~A~~l~g~~i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d-~~~~~iG~V~~v~ 123 (190)
+.+.+-.++.....+.+..+.|+-+- .--+++|-+.+- .+.+. +..++..++++. .+|+.||.|.+|+
T Consensus 39 flvnkggwfh~h~~lp~~~i~Sig~k----~Imi~vp~~~~~--~~~ns--~~ye~m~mk~~lt~dG~iLGmveDVy 107 (176)
T COG3881 39 FLVNKGGWFHKHCCLPVKNIVSIGSK----MIMIYVPYKGSF--IRFNS--FTYEIMNMKVILTYDGTILGMVEDVY 107 (176)
T ss_pred EEEECCCEEEEEEEEEECCEEEECCC----EEEEECCCCCEE--CCCCC--HHHHHHCCCEEECCCCCEEEEEEEEE
T ss_conf 99803857760001550556662244----489964665301--15670--65686467467414775766666888
No 13
>COG3277 GAR1 RNA-binding protein involved in rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=85.12 E-value=1.7 Score=22.71 Aligned_cols=35 Identities=17% Similarity=0.158 Sum_probs=29.2
Q ss_pred HHHCCEEEEECCCEEEEEEEEEECCCCEEEEEECC
Q ss_conf 24011367525843119988665799508999749
Q gi|254780713|r 102 DLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNT 136 (190)
Q Consensus 102 dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~ 136 (190)
--+|..|+|.+++.+|.|.+|+---.++.+.|+..
T Consensus 25 P~l~~~V~~~~~k~IG~V~dVfGPv~~PY~~Vkp~ 59 (98)
T COG3277 25 PPLNAPVYDANLKRIGKVVDVFGPVDEPYILVKPD 59 (98)
T ss_pred CCCCCEEEECCCCEEEEEEEEECCCCCCEEEEECC
T ss_conf 97998569448888888989875678877998154
No 14
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=83.80 E-value=1.1 Score=23.75 Aligned_cols=29 Identities=17% Similarity=0.202 Sum_probs=25.4
Q ss_pred EECCEEEEEECCCCCHHHHHHHCCCEEEE
Q ss_conf 73997999963877845567634968774
Q gi|254780713|r 55 RKNKRFIATFSGIDNIHSASELRDLKLYA 83 (190)
Q Consensus 55 ~~~~~~iikf~gi~s~~~A~~l~g~~i~i 83 (190)
.+.+..+++++|++++++|+.+.|+.+..
T Consensus 17 q~~n~~LlkieGV~~k~~a~~y~GKrv~y 45 (87)
T PRK04337 17 QYPRQVIIKPLGVNDREEAAKLIGRKVIW 45 (87)
T ss_pred CCCCEEEEEECCCCCHHHHHHHCCCEEEE
T ss_conf 65988999861868877847635746999
No 15
>pfam01247 Ribosomal_L35Ae Ribosomal protein L35Ae.
Probab=82.59 E-value=1.5 Score=22.95 Aligned_cols=29 Identities=7% Similarity=0.101 Sum_probs=25.1
Q ss_pred EECCEEEEEECCCCCHHHHHHHCCCEEEE
Q ss_conf 73997999963877845567634968774
Q gi|254780713|r 55 RKNKRFIATFSGIDNIHSASELRDLKLYA 83 (190)
Q Consensus 55 ~~~~~~iikf~gi~s~~~A~~l~g~~i~i 83 (190)
.+.+..+++++|++++++|+.+.|+.+..
T Consensus 17 Q~~~~aLlkiegV~~~~~a~fylGKrvay 45 (94)
T pfam01247 17 QHPNTSLLKIEGVNTKEDAAFYLGKRVAY 45 (94)
T ss_pred CCCCEEEEEECCCCCHHHHHHHCCCEEEE
T ss_conf 66977999864826778967521667999
No 16
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=70.87 E-value=8.3 Score=18.81 Aligned_cols=65 Identities=20% Similarity=0.209 Sum_probs=40.3
Q ss_pred CCCCHHHHHCCEEEE---ECCCEEEEEEEEEECCCCEEEEEECCCCCEEEEECHHHHCCEEECCC-CEEEEE
Q ss_conf 002145240113675---25843119988665799508999749982899875031001056339-799995
Q gi|254780713|r 96 DEFFNTDLEEMETFD---RQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQE-NKILID 163 (190)
Q Consensus 96 ~e~Y~~dLiG~~V~d---~~~~~iG~V~~v~~~~a~dil~V~~~~~ke~lIP~v~~~I~~ID~~~-k~I~v~ 163 (190)
-..|+|+|||+.|.= .+-..+|.==-|.+-..| .|+|.+.+ ++..||-- ..+-++.... .++.|+
T Consensus 8 ~~i~~hEliGl~vrVv~s~~~s~vGI~G~VVdETkN-tLvi~t~~-~~~~VpK~-~~vfef~~~~G~~vkVd 76 (95)
T COG1588 8 RNIIRHELIGLEVRVVRSTNPSYVGIEGRVVDETKN-TLVIDTGS-REKVVPKD-GAVFEFEGPDGEKVKVD 76 (95)
T ss_pred CCCCHHHHCCCEEEEEECCCCCCCCEEEEEEEEECC-EEEEECCC-CEEEEECC-CEEEEEECCCCCEEEEC
T ss_conf 876837953719999726998723402799756210-89997799-66997567-47999984888689986
No 17
>PRK06009 flgD flagellar basal body rod modification protein; Reviewed
Probab=68.58 E-value=9.4 Score=18.52 Aligned_cols=75 Identities=13% Similarity=0.178 Sum_probs=45.3
Q ss_pred EEEEEECCCCCHHHHHHHCCCEEEECHHHCCCCCCCCCCCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEECCCC
Q ss_conf 79999638778455676349687741777886556410021452401136752584311998866579950899974998
Q gi|254780713|r 59 RFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTME 138 (190)
Q Consensus 59 ~~iikf~gi~s~~~A~~l~g~~i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~~~ 138 (190)
.++.++..+...|+...+....=-+-... .+.. -..|||-.|-..+|..=|+|..|.-...+.++++. +|
T Consensus 54 e~~~QlAqfs~lEq~~~~n~~l~~ll~~~----~l~q----A~~lIGktVt~~Dg~vtG~V~sV~~~~dg~~a~l~--dG 123 (135)
T PRK06009 54 QYMSQLATFSQVEQSVQTNSKLDTLLASS----SLSQ----AEGLIGRTVTSADGSITGVVKSVTIYSDGIIATLE--DG 123 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHH----HHHHHCEEEECCCCEEEEEEEEEEEECCCEEEEEE--CC
T ss_conf 99999999999999999999999999988----8887----88762807970797489999999993894499983--89
Q ss_pred CEEEE
Q ss_conf 28998
Q gi|254780713|r 139 KTFLI 143 (190)
Q Consensus 139 ke~lI 143 (190)
+++++
T Consensus 124 ~~v~~ 128 (135)
T PRK06009 124 KKVLL 128 (135)
T ss_pred CEEEE
T ss_conf 88983
No 18
>KOG0887 consensus
Probab=63.95 E-value=4.6 Score=20.24 Aligned_cols=33 Identities=12% Similarity=0.184 Sum_probs=28.1
Q ss_pred EECCEEEEEECCCCCHHHHHHHCCCE-EEECHHH
Q ss_conf 73997999963877845567634968-7741777
Q gi|254780713|r 55 RKNKRFIATFSGIDNIHSASELRDLK-LYAKRQD 87 (190)
Q Consensus 55 ~~~~~~iikf~gi~s~~~A~~l~g~~-i~i~~~~ 87 (190)
.+....+++++|++++|+|+-+.|+- +|+-++.
T Consensus 27 ~~~~t~llkiEGv~skeea~fYlGkR~~yvYKa~ 60 (111)
T KOG0887 27 QHPNTSLLKIEGVYSKEEASFYLGKRCVYVYKAK 60 (111)
T ss_pred CCCCCEEEEEECCCCHHHHHEEECCCEEEEEECC
T ss_conf 3787179999443664331024257089999548
No 19
>PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed
Probab=63.74 E-value=12 Score=17.97 Aligned_cols=32 Identities=16% Similarity=0.168 Sum_probs=27.0
Q ss_pred HCCEEEEECCCEEEEEEEEEECCCCEEEEEEC
Q ss_conf 01136752584311998866579950899974
Q gi|254780713|r 104 EEMETFDRQGKYWGQVCGVYNFGAGSILEIKN 135 (190)
Q Consensus 104 iG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~ 135 (190)
+|-.|+|+++..+|+|.+|+-.-.++.+-|+.
T Consensus 26 ~g~~V~d~~~~~VGkV~DvfGPV~~PY~~v~~ 57 (73)
T PRK13149 26 LNAVVVDKKLKKVGKIYDVFGPVKEPYVLVKS 57 (73)
T ss_pred CCCEEECCCCCEEEEEEEEECCCCCCEEEEEC
T ss_conf 99995967897968999977768987699884
No 20
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=60.55 E-value=13 Score=17.64 Aligned_cols=50 Identities=24% Similarity=0.365 Sum_probs=35.7
Q ss_pred HHHHHCCEEE--EECCCE-EEEEEEEEECCCCEEEEEECCCCCEEEEECHHHHCCEEE
Q ss_conf 4524011367--525843-119988665799508999749982899875031001056
Q gi|254780713|r 100 NTDLEEMETF--DRQGKY-WGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVN 154 (190)
Q Consensus 100 ~~dLiG~~V~--d~~~~~-iG~V~~v~~~~a~dil~V~~~~~ke~lIP~v~~~I~~ID 154 (190)
...|||-.|. +.+|+. -|+|..|.-...+.++++.. +++ .||. .+|.+|+
T Consensus 88 as~lIGK~V~~~d~dG~~~sG~V~sV~~~~~g~~l~l~d-g~~--~v~~--~~V~~V~ 140 (140)
T PRK11911 88 AVNFIGKDIKGVSLNGEVISGKVESVQQTTNGVMLKLKD-NDS--LVPM--TYVTEIN 140 (140)
T ss_pred HHHHCCCEEEEECCCCCEEEEEEEEEEEECCCEEEEEEC-CCE--EEEH--HHEEECC
T ss_conf 873338467887699988778889999828956999953-998--9885--7717549
No 21
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family; InterPro: IPR014238 Proteins in this entry belong to the broader family of PRC-barrel domain proteins, but are found only in endospore-forming bacteria within the Firmicutes (low-GC, Gram-positive bacteria). Most species encode two of these proteins, though their function is unknown. In Bacillus subtilis, which encodes YlmC and YmxH, YmxH is strongly induced by the mother cell-specific sigma-E factor ..
Probab=59.52 E-value=14 Score=17.54 Aligned_cols=61 Identities=23% Similarity=0.316 Sum_probs=38.7
Q ss_pred CHHHHHCCEEEE-ECCCEEEEE--EEEE-E-CCCC-EEEEEECC--------CCCEEEEECHHHHCCEEECCCCEEEEE
Q ss_conf 145240113675-258431199--8866-5-7995-08999749--------982899875031001056339799995
Q gi|254780713|r 99 FNTDLEEMETFD-RQGKYWGQV--CGVY-N-FGAG-SILEIKNT--------MEKTFLIPFTKFAVLEVNLQENKILID 163 (190)
Q Consensus 99 Y~~dLiG~~V~d-~~~~~iG~V--~~v~-~-~~a~-dil~V~~~--------~~ke~lIP~v~~~I~~ID~~~k~I~v~ 163 (190)
+++||-+.+|+| .+|..+|.| +|+. + ..++ .=|.|-.. .+.++.||+ +-|++| -...|.|+
T Consensus 1 rlSdL~~kEiInv~~G~rLG~~~~~D~~ID~~~G~I~~lIip~~g~~~glf~~~~~~~IpW--~~IkKI--G~dvILvd 75 (76)
T TIGR02888 1 RLSDLRAKEIINVNDGKRLGLIGNIDLEIDEEDGKIESLIIPGKGKKFGLFSKGEEIEIPW--KAIKKI--GSDVILVD 75 (76)
T ss_pred CCCCCCCCCEEECCCCEEEEEECCCCEEEECCCCEEEEEEECCCCEEEECEECCCCEEECC--HHCEEE--CCEEEEEE
T ss_conf 9422257767973569388733484579808999598988718970522100687548663--002780--79088974
No 22
>TIGR02408 ectoine_ThpD ectoine hydroxylase; InterPro: IPR012774 Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms.; GO: 0016725 oxidoreductase activity acting on CH or CH2 groups.
Probab=57.21 E-value=5.5 Score=19.82 Aligned_cols=44 Identities=16% Similarity=0.353 Sum_probs=28.8
Q ss_pred EEEECCCCCHHHHHHHCCCEEEE--CHHHCCCCCCCCCCCCHH-HHHCCE
Q ss_conf 99963877845567634968774--177788655641002145-240113
Q gi|254780713|r 61 IATFSGIDNIHSASELRDLKLYA--KRQDFKDEELEEDEFFNT-DLEEME 107 (190)
Q Consensus 61 iikf~gi~s~~~A~~l~g~~i~i--~~~~lp~~~l~~~e~Y~~-dLiG~~ 107 (190)
+|+.+-+ ...|+++-|.+||| .|-++.+- ...-+|||| |-.-+=
T Consensus 89 lVRd~rv--~~~ARQiLGSdVYvHQsRiN~kPG-F~g~gFYWHSDFETWH 135 (278)
T TIGR02408 89 LVRDERV--VNAARQILGSDVYVHQSRINMKPG-FKGTGFYWHSDFETWH 135 (278)
T ss_pred HCCCHHH--HHHHHHHHCCCEEEEEEEECCCCC-CCCCCCEECCCCCCCC
T ss_conf 1130246--666656515612443211005878-8875442107732000
No 23
>TIGR02225 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011932 Proteins in this entry are part of the wider so-called "phage" integrase fmaily which describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This entry represents the chromosomally-encoded polypeptide XerD, which is closely related to, and interacts with, another chromosomally-encoded polypeptide, XerC (IPR011931 from INTERPRO). These proteins are site-specific tyrosine recombinases, which act by catalyzing the cutting and rejoining of the recombining DNA molecules . They form a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids. XerD is composed of two domains, an N-terminal alpha-helical domain, and a C-terminal domain composed mostly of alpha helices, with a three-stranded antiprallel beta sheet along one edge . The active site is found at the extreme C-terminal end of the polypeptide. Most of the C-terminal domain is structurally homologous to that of other "phage" integrases, but the active site regions of these enzymes are stucturally distinct.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division.
Probab=55.15 E-value=6 Score=19.62 Aligned_cols=83 Identities=14% Similarity=0.232 Sum_probs=42.1
Q ss_pred EEEEEECCCCCHHHHHHHCCCEEEECHHHCCCCC-----CCCCCCCHHHH---HCCEEEEECCCEEE-EEEEEEECCCCE
Q ss_conf 7999963877845567634968774177788655-----64100214524---01136752584311-998866579950
Q gi|254780713|r 59 RFIATFSGIDNIHSASELRDLKLYAKRQDFKDEE-----LEEDEFFNTDL---EEMETFDRQGKYWG-QVCGVYNFGAGS 129 (190)
Q Consensus 59 ~~iikf~gi~s~~~A~~l~g~~i~i~~~~lp~~~-----l~~~e~Y~~dL---iG~~V~d~~~~~iG-~V~~v~~~~a~d 129 (190)
+.--++-.+=|++++++|-..- ++.+. |. . += |.-- -|+ =||.| .|.+| ++.|| +.-.+-
T Consensus 98 K~~~~LP~vLt~~EV~~LL~~p--~~~~~-~~-g~kr~~lR-DrAm-LElLYATGlRV----SELv~L~~~d~-~l~~g~ 166 (305)
T TIGR02225 98 KVARKLPKVLTVEEVEALLAAP--IDVDT-PL-GGKRPALR-DRAM-LELLYATGLRV----SELVGLRLEDV-NLDEGV 166 (305)
T ss_pred CCCCCCCCCCCHHHHHHHHHHH--CCCCC-CC-CCCCHHHH-HHHH-HHHHHHCCCCE----EEEECCCHHHH-HCCCCE
T ss_conf 2245788837989999998500--24677-67-67640165-4799-99998648835----53305616652-002773
Q ss_pred -EEEEECCCCCEEEEECHHHHCCE
Q ss_conf -89997499828998750310010
Q gi|254780713|r 130 -ILEIKNTMEKTFLIPFTKFAVLE 152 (190)
Q Consensus 130 -il~V~~~~~ke~lIP~v~~~I~~ 152 (190)
+.+|.+.++||.|||+-+.-+.-
T Consensus 167 ~~~~v~GKG~KERlVP~G~~A~~~ 190 (305)
T TIGR02225 167 KVRKVRGKGSKERLVPLGEEAIEA 190 (305)
T ss_pred EEEEEEECCCCEEECCCHHHHHHH
T ss_conf 799986168841202202899999
No 24
>PTZ00041 60S ribosomal protein L35; Provisional
Probab=47.77 E-value=19 Score=16.84 Aligned_cols=29 Identities=10% Similarity=0.233 Sum_probs=24.2
Q ss_pred CCEEEEEECCCCCHHHHHHHCCCEE-EECH
Q ss_conf 9979999638778455676349687-7417
Q gi|254780713|r 57 NKRFIATFSGIDNIHSASELRDLKL-YAKR 85 (190)
Q Consensus 57 ~~~~iikf~gi~s~~~A~~l~g~~i-~i~~ 85 (190)
.+..+++++|++++++|+-+.|+.+ |+-+
T Consensus 46 ~ntaLlKIEGV~~k~e~~fYlGKRvayVYk 75 (128)
T PTZ00041 46 ENTALLKIEGVNTREDARFYLGKRVAYVYK 75 (128)
T ss_pred CCCEEEEEECCCCCCCCEEECCCEEEEEEE
T ss_conf 872789871657653324631557999998
No 25
>pfam05935 Arylsulfotrans Arylsulfotransferase (ASST). This family consists of several bacterial Arylsulfotransferase proteins. Arylsulfotransferase (ASST) transfers a sulfate group from phenolic sulfate esters to a phenolic acceptor substrate.
Probab=41.66 E-value=28 Score=15.88 Aligned_cols=69 Identities=14% Similarity=0.154 Sum_probs=38.4
Q ss_pred CEEEEEEEEEECC------CCEEEEEECCCCCEEEE-------------ECHHHHCCEEECCCCEEEEECCCCCCCCCCC
Q ss_conf 4311998866579------95089997499828998-------------7503100105633979999528100388865
Q gi|254780713|r 114 KYWGQVCGVYNFG------AGSILEIKNTMEKTFLI-------------PFTKFAVLEVNLQENKILIDPIAAGLNNTTM 174 (190)
Q Consensus 114 ~~iG~V~~v~~~~------a~dil~V~~~~~ke~lI-------------P~v~~~I~~ID~~~k~I~v~~p~Glld~~~~ 174 (190)
..+|+|......+ .||+++. ++|.-+++ .-+.+.|.+||...+.+.+=-..-+||....
T Consensus 171 D~lGkv~~~y~L~~g~~~~HHD~~e~--pnGN~L~l~~~~~~~~~~~~~~tveD~IieiD~tG~vv~~wDl~~iLd~yr~ 248 (459)
T pfam05935 171 DLLGRVIKNYRLPGGYIDFHHDIVEL--PNGNLLALVAESNYRGDGDGVDTVEDTIIEIDKTGEVVDVWDLFKILDPYRT 248 (459)
T ss_pred ECCCCEEEEEECCCCCCCCCCCEEEC--CCCCEEEEEECCCCCCCCCCCCEECEEEEEECCCCCEEEEECHHHHCCCCCC
T ss_conf 23563899998899887613121798--9998999974334236888767656099999999989899765786884224
Q ss_pred CCCCCCCCCC
Q ss_conf 4775447766
Q gi|254780713|r 175 KNPQYDCPLD 184 (190)
Q Consensus 175 ~~~~~~~~~~ 184 (190)
..+-.+.+..
T Consensus 249 ~~~~~~~~~~ 258 (459)
T pfam05935 249 TRPFGDIPGV 258 (459)
T ss_pred CCCCCCCCCC
T ss_conf 4646787788
No 26
>pfam12317 IFT46_B_C Intraflagellar transport complex B protein 46 C terminal. This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella.
Probab=39.25 E-value=11 Score=18.14 Aligned_cols=29 Identities=17% Similarity=0.074 Sum_probs=10.9
Q ss_pred EEECHHHHCCEEECCCCEEEEECCCCCCC
Q ss_conf 98750310010563397999952810038
Q gi|254780713|r 142 LIPFTKFAVLEVNLQENKILIDPIAAGLN 170 (190)
Q Consensus 142 lIP~v~~~I~~ID~~~k~I~v~~p~Glld 170 (190)
|-||+.+||..|---.-.|.|-.|+|..|
T Consensus 38 LkPFiPdyiPAVGdiDaFiKVprPD~~~d 66 (214)
T pfam12317 38 LKPFIPDYIPAVGDIDAFIKVPRPDGKPD 66 (214)
T ss_pred CCCCCCCCCCCCCCHHHHCCCCCCCCCCC
T ss_conf 57778101223457212111569999877
No 27
>TIGR00491 aIF-2 translation initiation factor aIF-2; InterPro: IPR004544 Initiation factor 2 (IF-2) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-2 promotes the GTP-dependent binding of the initiator tRNA to the small subunit of the ribosome. IF-2 is a protein of about 70 to 95 Kd which contains a central GTP-binding domain flanked by a highly variable N-terminal domain and a more conserved C-terminal domain. Some members of this family undergo protein self splicing that involves a post-translational excision of the intein followed by peptide ligation.; GO: 0003743 translation initiation factor activity, 0005525 GTP binding, 0006413 translational initiation, 0005622 intracellular.
Probab=34.51 E-value=36 Score=15.22 Aligned_cols=60 Identities=13% Similarity=0.174 Sum_probs=33.1
Q ss_pred CCEEEEECCCEEEEEEEEEECCCCEEEEEECCCCCEEEEECHH-HHCCEEECCCCEEEEECCCC
Q ss_conf 1136752584311998866579950899974998289987503-10010563397999952810
Q gi|254780713|r 105 EMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTK-FAVLEVNLQENKILIDPIAA 167 (190)
Q Consensus 105 G~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~~~ke~lIP~v~-~~I~~ID~~~k~I~v~~p~G 167 (190)
|+..+..+|..+|.|..+.+.|-+ +.. +..|+++=|-.-+ ..+.+-=.+...+.|+.|+-
T Consensus 1045 g~~L~~~DG~~vG~V~~~qd~g~n--l~~-A~~g~~~aiAI~drvv~gr~~~egd~lYVdvPE~ 1105 (1145)
T TIGR00491 1045 GYPLIKEDGEKVGEVREIQDKGKN--LKS-ASAGKEVAIAIEDRVVLGRQVEEGDELYVDVPER 1105 (1145)
T ss_pred CCCCCHHCCCCCCCEEEEHHCCCC--CEE-CCCCCCCCEEECCCEEEEEEECCCCEEEEECCCH
T ss_conf 887611020002420010033773--000-1047866513427178810761786688815803
No 28
>KOG2356 consensus
Probab=29.16 E-value=42 Score=14.86 Aligned_cols=96 Identities=17% Similarity=0.161 Sum_probs=51.0
Q ss_pred EEECCCCCHHHHHHHCCCE-EEECHHHCCCCCCCCCCCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEECCCCCE
Q ss_conf 9963877845567634968-774177788655641002145240113675258431199886657995089997499828
Q gi|254780713|r 62 ATFSGIDNIHSASELRDLK-LYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTMEKT 140 (190)
Q Consensus 62 ikf~gi~s~~~A~~l~g~~-i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~~~ke 140 (190)
+..+.+.+++.|+.-.+.. ++-+.+.-|-.+..+.++-|.++.. |.+.+-.+.-.|-...+.+.+|..
T Consensus 89 l~l~~~~~~E~aela~~lS~p~e~e~s~pii~fed~~~~~~~m~n-----------~~~~n~~~~s~qk~~~~dGs~g~k 157 (366)
T KOG2356 89 LLLNNLKSREAAELALNLSIPSESESSEPIIEFEDSESLSNLMSN-----------GMINNWVRCSGQKPGIIDGSDGTK 157 (366)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEHHHCCHHHHHHH-----------HHHHHHHCCCCCCEEEEECCCCCE
T ss_conf 155565477766898753875200134520000320102888876-----------754313203433126860787616
Q ss_pred EEEECHHHHCC-EE----------ECCCCEEEEECCCCCCC
Q ss_conf 99875031001-05----------63397999952810038
Q gi|254780713|r 141 FLIPFTKFAVL-EV----------NLQENKILIDPIAAGLN 170 (190)
Q Consensus 141 ~lIP~v~~~I~-~I----------D~~~k~I~v~~p~Glld 170 (190)
++||.-.-|+. .| +.--..|++||| |.+
T Consensus 158 YyIPpkSsF~~gDv~~~~qll~~H~llpdlIIiDPP--W~N 196 (366)
T KOG2356 158 YYIPPKSSFHVGDVKDIEQLLRAHDLLPDLIIIDPP--WFN 196 (366)
T ss_pred EEECCCCCEECCCHHHHHHHHHHHHHCCCEEEECCC--CCC
T ss_conf 872785502115377788875777636876996799--877
No 29
>TIGR00635 ruvB Holliday junction DNA helicase RuvB; InterPro: IPR004605 All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.; GO: 0003677 DNA binding, 0005524 ATP binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=28.23 E-value=30 Score=15.66 Aligned_cols=54 Identities=15% Similarity=0.227 Sum_probs=38.7
Q ss_pred EECCCEEEEEEEEEECCCCEEEEEECC-----CCCEEEEECHHHHCCEE----ECCCCEEEEECCC
Q ss_conf 525843119988665799508999749-----98289987503100105----6339799995281
Q gi|254780713|r 110 DRQGKYWGQVCGVYNFGAGSILEIKNT-----MEKTFLIPFTKFAVLEV----NLQENKILIDPIA 166 (190)
Q Consensus 110 d~~~~~iG~V~~v~~~~a~dil~V~~~-----~~ke~lIP~v~~~I~~I----D~~~k~I~v~~p~ 166 (190)
..-|...|.+++..+ +|||-|.-- .=.|+|.|+-++|-.+| ++.+|.|.+++|+
T Consensus 67 ~kPgDlaaiLt~L~~---gDVLFIDEIHRL~p~~EE~LYpAMEDF~lDi~IG~Gp~Ar~v~ldLpP 129 (305)
T TIGR00635 67 EKPGDLAAILTNLEE---GDVLFIDEIHRLSPAIEELLYPAMEDFRLDIVIGKGPSARSVRLDLPP 129 (305)
T ss_pred CCHHHHHHHHHHCCC---CCEEECCHHHHCCHHHHHHCCCCCCCEEEEEEEECCCCCCEEEECCCC
T ss_conf 475789999970568---963101256504833453105300121787787128985257606869
No 30
>KOG3262 consensus
Probab=27.70 E-value=30 Score=15.68 Aligned_cols=33 Identities=12% Similarity=0.096 Sum_probs=23.7
Q ss_pred CCEEEEECCCEEEEEEEEEECCCCEEEEEECCC
Q ss_conf 113675258431199886657995089997499
Q gi|254780713|r 105 EMETFDRQGKYWGQVCGVYNFGAGSILEIKNTM 137 (190)
Q Consensus 105 G~~V~d~~~~~iG~V~~v~~~~a~dil~V~~~~ 137 (190)
...||++|.+.||+|.+|.-.-..-.+-|+..+
T Consensus 80 NAPIylenk~qIGKVDEIfG~i~d~~fsIK~~d 112 (215)
T KOG3262 80 NAPIYLENKEQIGKVDEIFGPINDVHFSIKPSD 112 (215)
T ss_pred CCCEEECCHHHHCCHHHHCCCCCCCEEEEECCC
T ss_conf 885121163021316653066331179885378
No 31
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=25.68 E-value=52 Score=14.34 Aligned_cols=70 Identities=19% Similarity=0.240 Sum_probs=37.2
Q ss_pred ECCCCCHHHHHHHCCCEEEECHHHCCCCCCCC---------CCCCHHHHHCCEEEEECCCEEEEEEEEEECCCCEEEEEE
Q ss_conf 63877845567634968774177788655641---------002145240113675258431199886657995089997
Q gi|254780713|r 64 FSGIDNIHSASELRDLKLYAKRQDFKDEELEE---------DEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIK 134 (190)
Q Consensus 64 f~gi~s~~~A~~l~g~~i~i~~~~lp~~~l~~---------~e~Y~~dLiG~~V~d~~~~~iG~V~~v~~~~a~dil~V~ 134 (190)
+-.+=++++++.|.. .+..+-|. .|-+ -=--++|++|+.+.|-+ .-.+ .+.|.
T Consensus 111 LPk~Ls~~eve~Ll~----~~~~~~p~-~LRdrAmlELLYATGlRVSElv~L~l~dv~------------~~~~-~v~V~ 172 (300)
T COG4974 111 LPKFLSEEEVEALLE----APDEDTPL-GLRDRAMLELLYATGLRVSELVGLTLSDVD------------LRQG-VVRVR 172 (300)
T ss_pred CCCCCCHHHHHHHHH----CCCCCCCH-HHHHHHHHHHHHHCCCHHHHHHCCCHHHHC------------CCCC-EEEEE
T ss_conf 776259999999981----88889807-579999999999827759998567576513------------2468-68997
Q ss_pred CCCCCEEEEECHHHHCC
Q ss_conf 49982899875031001
Q gi|254780713|r 135 NTMEKTFLIPFTKFAVL 151 (190)
Q Consensus 135 ~~~~ke~lIP~v~~~I~ 151 (190)
+.++||.+||+-...+.
T Consensus 173 GKG~KeR~VP~g~~A~~ 189 (300)
T COG4974 173 GKGNKERLVPFGEEAVE 189 (300)
T ss_pred CCCCCEEEEECHHHHHH
T ss_conf 15882555213399999
No 32
>TIGR00580 mfd transcription-repair coupling factor; InterPro: IPR004576 All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by TcrF, which releases RNAP and the truncated transcript. The TcrF may replace RNAP at the lesion site and then recruit the UvrA/B/C repair system.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=23.66 E-value=54 Score=14.23 Aligned_cols=46 Identities=17% Similarity=0.237 Sum_probs=32.8
Q ss_pred CCCCCCCCHHHHHCCEEEEEC---CCEEEEEE-EEEECCCCEEEEEECCCCCE-EEEECH
Q ss_conf 564100214524011367525---84311998-86657995089997499828-998750
Q gi|254780713|r 92 ELEEDEFFNTDLEEMETFDRQ---GKYWGQVC-GVYNFGAGSILEIKNTMEKT-FLIPFT 146 (190)
Q Consensus 92 ~l~~~e~Y~~dLiG~~V~d~~---~~~iG~V~-~v~~~~a~dil~V~~~~~ke-~lIP~v 146 (190)
+|.+|+| |++.+ |.++|-.. -=...-..|.|++...++.. ++||.-
T Consensus 382 ~L~~Gd~---------VVH~~hGIG~F~~l~~~~~~~g~~~DYL~l~Ya~~~k~LyvPve 432 (997)
T TIGR00580 382 ELKPGDY---------VVHKDHGIGKFLGLEKKLKVLGIERDYLVLEYAGEDKKLYVPVE 432 (997)
T ss_pred CCCCCCE---------EEECCCCCCEEHHHHHHHHHCCCCCCEEEEEECCCCCEEEECCC
T ss_conf 3799887---------77533585021422321442476524124440277866860331
No 33
>KOG3041 consensus
Probab=22.56 E-value=56 Score=14.17 Aligned_cols=39 Identities=23% Similarity=0.222 Sum_probs=24.7
Q ss_pred EEEEECCCCCEEEEECHHHHCCEEECCCCEEEEECCCCCCCCCC
Q ss_conf 89997499828998750310010563397999952810038886
Q gi|254780713|r 130 ILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLNNTT 173 (190)
Q Consensus 130 il~V~~~~~ke~lIP~v~~~I~~ID~~~k~I~v~~p~Glld~~~ 173 (190)
+|-+-..+|+- +|=++ +++-..-+++.+.+|.||+|...
T Consensus 78 Il~il~~dG~~-~ivL~----kQfRpP~Gk~ciElPAGLiD~ge 116 (225)
T KOG3041 78 ILAILESDGKP-YIVLV----KQFRPPTGKICIELPAGLIDDGE 116 (225)
T ss_pred EEEEEECCCCE-EEEEE----EEECCCCCCEEEECCCCCCCCCC
T ss_conf 99998048968-99997----75048977478972355434897
No 34
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=21.40 E-value=63 Score=13.86 Aligned_cols=84 Identities=11% Similarity=0.117 Sum_probs=50.8
Q ss_pred CCCEEEECHHHCCCCCCCCCCCCHHHHHCCEEEEEC---CCEEEEEEEEEECC-CCEEEEEECCCCCEEEEECHHHHCCE
Q ss_conf 496877417778865564100214524011367525---84311998866579-95089997499828998750310010
Q gi|254780713|r 77 RDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQ---GKYWGQVCGVYNFG-AGSILEIKNTMEKTFLIPFTKFAVLE 152 (190)
Q Consensus 77 ~g~~i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d~~---~~~iG~V~~v~~~~-a~dil~V~~~~~ke~lIP~v~~~I~~ 152 (190)
+|-.+.++ +|.-+.. +|+-++ .|-.|+-.. -+.+|+|.++..++ +-|+..|+...|.++---. .+|--
T Consensus 153 ~~Dtv~i~---l~~~kI~--d~ikfe-~G~l~~itgG~n~GrvG~I~~ie~~~gs~~iv~i~D~~g~~F~T~~--~~vFv 224 (273)
T PTZ00223 153 RGDTLVYN---VKEKKVV--DLIKNR-NGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRA--ANIFV 224 (273)
T ss_pred CCCEEEEE---CCCCCEE--EEEECC-CCCEEEEECCCCCCEEEEEEEEEECCCCCCEEEEEECCCCEEEEEE--EEEEE
T ss_conf 59989996---7986123--787338-9989999898325517899889864898767999978999788865--04999
Q ss_pred EECCCCEEEEECCCCC
Q ss_conf 5633979999528100
Q gi|254780713|r 153 VNLQENKILIDPIAAG 168 (190)
Q Consensus 153 ID~~~k~I~v~~p~Gl 168 (190)
|-...+...|++|.|=
T Consensus 225 IGk~~~~~~isLp~~k 240 (273)
T PTZ00223 225 IGKDMNSVPVTLPKQQ 240 (273)
T ss_pred EECCCCCCEEECCCCC
T ss_conf 9258985238763888
No 35
>TIGR01173 glmU UDP-N-acetylglucosamine pyrophosphorylase; InterPro: IPR005882 N-Acetylglucosamine-1-PO(4) uridyltransferase (GlmU, 2.7.7.23 from EC) is a trimeric bifunctional enzyme that catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-GlcNAc. The X-ray crystal structure of Escherichia coli GlmU in complex with UDP-GlcNAc and CoA has been determined to 2.1 A resolution and reveals a two-domain architecture that is responsible for these two reactions . The C-terminal domain is responsible for the CoA-dependent acetylation of Glc-1-PO(4) to GlcNAc-1-PO(4) and displays the longest left-handed parallel beta-helix observed to date. The acetyltransferase active site defined by the binding site for CoA makes use of residues from all three subunits and is positioned beneath an open cavity large enough to accommodate the Glc-1-PO(4) acetyl acceptor. The N-terminal domain catalyzes uridyl transfer from UTP to GlcNAc-1-PO(4) to form the final products UDP-GlcNAc and pyrophosphate. This domain is composed of a central seven-stranded beta-sheet surrounded by six alpha-helices in a Rossmann fold-like topology. ; GO: 0003977 UDP-N-acetylglucosamine diphosphorylase activity, 0009103 lipopolysaccharide biosynthetic process.
Probab=21.34 E-value=30 Score=15.69 Aligned_cols=51 Identities=16% Similarity=0.190 Sum_probs=31.1
Q ss_pred EEEEECCCCCHHHHHHHCCCEEEEC-HHHCC------CCCCCCCCCCHHHHHCCEEEE
Q ss_conf 9999638778455676349687741-77788------655641002145240113675
Q gi|254780713|r 60 FIATFSGIDNIHSASELRDLKLYAK-RQDFK------DEELEEDEFFNTDLEEMETFD 110 (190)
Q Consensus 60 ~iikf~gi~s~~~A~~l~g~~i~i~-~~~lp------~~~l~~~e~Y~~dLiG~~V~d 110 (190)
-||-.+.-+..+.+=.=+|+=+|+- ...|+ ...-..+|||+.|+|.+-.-+
T Consensus 157 ~IVE~KDA~~eqk~I~eiNtG~y~~~~~~L~~~L~~l~n~NaqgEYYLTD~ia~a~~~ 214 (461)
T TIGR01173 157 AIVEEKDANEEQKAIKEINTGVYVFDGAALKRWLPKLSNNNAQGEYYLTDVIALAVAD 214 (461)
T ss_pred EEECCCCCCHHHHCCCEEEEEEEEECHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCC
T ss_conf 9973359886980352788879998328999888762877044431478999998508
No 36
>PRK13559 hypothetical protein; Provisional
Probab=20.46 E-value=61 Score=13.95 Aligned_cols=32 Identities=22% Similarity=0.284 Sum_probs=24.3
Q ss_pred CCCCCCCHHHHHCCEEEEECCCEE---EEEEEEEE
Q ss_conf 641002145240113675258431---19988665
Q gi|254780713|r 93 LEEDEFFNTDLEEMETFDRQGKYW---GQVCGVYN 124 (190)
Q Consensus 93 l~~~e~Y~~dLiG~~V~d~~~~~i---G~V~~v~~ 124 (190)
-++|+.||..|--..|+|.+|+.+ |...+|-+
T Consensus 127 rKDGs~fwn~l~isPV~D~~G~v~~fig~q~DvTd 161 (363)
T PRK13559 127 RKDGSPFWNALHLGPIYDEDGKLLYFFGSQWDVTD 161 (363)
T ss_pred CCCCCEEEEEEEEEEEECCCCCEEEEEEEEEEECC
T ss_conf 26998247768988879899979999999985155
No 37
>KOG2090 consensus
Probab=20.04 E-value=65 Score=13.79 Aligned_cols=73 Identities=16% Similarity=0.289 Sum_probs=44.8
Q ss_pred EEEEECCCCCHHH-HHHHCCCEEEECHHHCCCCCCCCCCCCHHHHHCCEEEEECCCEEEEE-EEEEECC---CCE-EEEE
Q ss_conf 9999638778455-67634968774177788655641002145240113675258431199-8866579---950-8999
Q gi|254780713|r 60 FIATFSGIDNIHS-ASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQV-CGVYNFG---AGS-ILEI 133 (190)
Q Consensus 60 ~iikf~gi~s~~~-A~~l~g~~i~i~~~~lp~~~l~~~e~Y~~dLiG~~V~d~~~~~iG~V-~~v~~~~---a~d-il~V 133 (190)
.+..|..+.+.=+ -..|.....-|.-. +..+.+||-+..|+--+.|++++.+.+|.| .|+.+.+ .|| -+-|
T Consensus 366 i~~~fFslg~~ieGLs~L~~~LyGirl~---~~~l~pGE~WhpdV~KL~vv~E~eg~lG~IY~Dlf~R~gK~~g~aHFTI 442 (704)
T KOG2090 366 IYSPFFSLGSCIEGLSTLFQRLYGIRLI---PEPLAPGEVWHPDVRKLNVVHEQEGLLGYIYCDLFERPGKTVGDAHFTI 442 (704)
T ss_pred EEECCCCHHHHHHHHHHHHHHHHCEEEE---CCCCCCCCCCCCHHHHHEEECCCCCCEEEEEEEEECCCCCCCCCCEEEE
T ss_conf 0103441788998899999997571500---0589986546820144301347778046999872124799998803886
Q ss_pred EC
Q ss_conf 74
Q gi|254780713|r 134 KN 135 (190)
Q Consensus 134 ~~ 135 (190)
++
T Consensus 443 r~ 444 (704)
T KOG2090 443 RG 444 (704)
T ss_pred EC
T ss_conf 33
Done!