Query gi|254780345|ref|YP_003064758.1| transcription antitermination protein NusB [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 170
No_of_seqs 111 out of 2231
Neff 7.9
Searched_HMMs 39220
Date Sun May 29 16:17:31 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780345.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01951 nusB transcription a 100.0 3.4E-37 8.7E-42 243.8 14.5 134 16-155 1-140 (140)
2 PRK00202 nusB transcription an 100.0 3.9E-35 1E-39 231.4 15.7 131 15-157 2-132 (132)
3 cd00619 Terminator_NusB Transc 100.0 1E-34 2.6E-39 228.9 15.2 130 16-157 1-130 (130)
4 COG0781 NusB Transcription ter 100.0 1.6E-33 4.1E-38 221.7 16.5 143 12-161 6-149 (151)
5 pfam01029 NusB NusB family. Th 100.0 6.1E-30 1.6E-34 200.1 15.2 125 18-155 2-126 (126)
6 cd00447 NusB_Sun RNA binding d 100.0 3.7E-29 9.4E-34 195.4 14.9 126 19-156 2-128 (129)
7 PRK09634 nusB transcription an 99.9 7.3E-25 1.9E-29 169.5 13.6 94 63-158 111-204 (206)
8 cd00620 Methyltransferase_Sun 99.9 2.8E-24 7.1E-29 165.9 14.3 124 18-156 2-125 (126)
9 PRK10901 16S rRNA methyltransf 99.9 2.2E-22 5.5E-27 154.6 14.2 128 16-159 3-130 (428)
10 TIGR00563 rsmB ribosomal RNA s 99.8 1.2E-19 3E-24 138.0 10.0 128 20-159 1-128 (487)
11 pfam09185 DUF1948 Domain of un 97.3 0.01 2.6E-07 35.9 12.4 133 15-153 2-139 (140)
12 pfam11573 Med23 Mediator compl 88.5 1.8 4.7E-05 22.3 8.1 84 62-149 1090-1179(1341)
13 TIGR02746 TraC-F-type type-IV 58.4 11 0.00027 17.7 3.0 140 21-170 621-778 (900)
14 pfam02284 COX5A Cytochrome c o 46.1 21 0.00054 15.9 4.0 54 102-155 23-77 (108)
15 TIGR01320 mal_quin_oxido malat 45.9 5.9 0.00015 19.2 0.0 41 109-149 52-107 (487)
16 PRK05590 hypothetical protein; 45.6 12 0.0003 17.4 1.5 58 107-166 29-88 (165)
17 cd00923 Cyt_c_Oxidase_Va Cytoc 45.4 22 0.00056 15.8 4.1 52 103-154 21-73 (103)
18 PRK05257 malate:quinone oxidor 42.5 8.3 0.00021 18.3 0.4 30 108-137 60-96 (499)
19 KOG4077 consensus 42.4 24 0.00062 15.5 4.2 57 102-158 62-119 (149)
20 pfam04271 consensus 41.2 25 0.00065 15.4 3.6 51 100-156 13-63 (73)
21 COG3935 DnaD Putative primosom 39.4 27 0.00069 15.2 3.5 51 99-155 141-191 (246)
22 KOG3583 consensus 32.1 33 0.00084 14.7 2.1 28 143-170 143-171 (279)
23 pfam07261 DnaB_2 Replication i 30.9 37 0.00095 14.4 3.5 51 100-156 13-63 (77)
24 PRK11001 mtlR mannitol repress 29.5 39 0.001 14.2 3.2 54 64-118 100-163 (170)
25 smart00550 Zalpha Z-DNA-bindin 27.1 43 0.0011 14.0 3.2 52 108-165 7-58 (68)
26 TIGR01446 DnaD_dom DnaD and ph 26.8 44 0.0011 13.9 3.4 53 99-157 13-65 (74)
27 pfam10752 DUF2533 Protein of u 25.3 47 0.0012 13.8 2.9 30 122-152 27-56 (84)
28 PRK05561 DNA topoisomerase IV 23.7 50 0.0013 13.6 6.1 128 18-150 316-495 (745)
29 TIGR01063 gyrA DNA gyrase, A s 21.9 55 0.0014 13.4 4.2 54 37-90 342-395 (864)
30 PRK13339 malate:quinone oxidor 21.0 57 0.0015 13.3 1.8 30 108-137 57-93 (497)
31 pfam06039 Mqo Malate:quinone o 20.8 58 0.0015 13.2 2.0 29 109-137 56-91 (489)
32 KOG1586 consensus 20.6 57 0.0015 13.3 1.6 52 105-156 196-247 (288)
No 1
>TIGR01951 nusB transcription antitermination factor NusB; InterPro: IPR011605 The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. The antitermination proteins of Escherichia coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle. The solution structure indicates that the protein folds into an alpha/alpha-helical topology consisting of six helices; the arginine-rich N-terminus appears to be disordered .; GO: 0003715 transcription termination factor activity, 0006353 transcription termination.
Probab=100.00 E-value=3.4e-37 Score=243.84 Aligned_cols=134 Identities=31% Similarity=0.469 Sum_probs=120.9
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHC
Q ss_conf 46999999999999995699989999999985310013221120144343999999---999999989999999997410
Q gi|254780345|r 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRV---IIHGVMDRKQHIDLLISSCLT 92 (170)
Q Consensus 16 r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~---lv~~v~~~~~~id~~I~~~l~ 92 (170)
|+.+|+.|||+||++++++.+..++...+...... .-......+..|+.. ++.|+.+|..+||.+|.++|.
T Consensus 1 R~~aR~~a~q~Ly~~e~~~~~~~~~~~~~~~~~~~------e~~~~~~~~~~~~~~f~~l~~Gv~~~~~~iD~~I~~~La 74 (140)
T TIGR01951 1 RRKARELAFQALYQLELRGEDIDSLVEELALEEDD------EAEDIDKKDKEYAEKFAELVRGVLENLEEIDELIEKHLA 74 (140)
T ss_pred CHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHC------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 95888999999999852799888999999988731------689846466898999999998999999988999988863
Q ss_pred CCCCHHHCCCHHHHHHHHHHHHHHHCC-CCCCCC--HHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 357633235348999999999986435-578103--398899999983387723149999999995
Q gi|254780345|r 93 EKWSFSRLDMILCSILRAGVLELIECH-SVPVEV--IISEYVCIAHDFFYGDEPKFINAVLDKVSR 155 (170)
Q Consensus 93 ~~w~~~rl~~~~~~iLr~a~~El~~~~-~~p~~v--vInE~V~lak~f~~~~~~~fVNaVL~ki~k 155 (170)
++|+++||+.|||+|||+|+|||+|.. ++|.+| +|||||+|||.||+++++||||||||+|++
T Consensus 75 ~~W~l~RL~~VdraILRl~~yEl~~~~~D~P~~VA~~InEAielAK~ys~~~s~kFiNGvLd~i~~ 140 (140)
T TIGR01951 75 KDWTLERLSKVDRAILRLAAYELLYLKKDVPVKVAVVINEAIELAKKYSDDKSSKFINGVLDAIAK 140 (140)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCC
T ss_conf 479723512878999999999998636898940543257899999984268764137877664329
No 2
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=100.00 E-value=3.9e-35 Score=231.43 Aligned_cols=131 Identities=37% Similarity=0.565 Sum_probs=122.8
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 34699999999999999569998999999998531001322112014434399999999999998999999999741035
Q gi|254780345|r 15 RRGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEK 94 (170)
Q Consensus 15 ~r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~ 94 (170)
.|+.||+.|+|+||++++++.++++++.+|... ......|..|+++++.|+.+|+..||.+|.+++ ++
T Consensus 2 ~R~~aR~~A~q~Ly~~~~~~~~~~~il~~~~~~-----------~~~~~~d~~~~~~lv~gv~~~~~~iD~~I~~~l-~~ 69 (132)
T PRK00202 2 ARRKAREAAVQALYQWELSGNDIAEIEAEFLEE-----------QDGADADVAYFRELVSGVVENQEELDELISPHL-KD 69 (132)
T ss_pred CHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-----------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CC
T ss_conf 579999999999999985199999999999987-----------456557799999999999996999999999985-59
Q ss_pred CCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 763323534899999999998643557810339889999998338772314999999999523
Q gi|254780345|r 95 WSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKE 157 (170)
Q Consensus 95 w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~ 157 (170)
|+++|+++++++|||+|+|||++.+++|++|+|||||+|||.|+++++++|||||||+++|+.
T Consensus 70 w~~~rl~~v~~~ILr~a~yEl~~~~~~p~~v~InE~v~lak~~~~~~~~~fVNgVLd~i~r~l 132 (132)
T PRK00202 70 WTLERLDPVERAILRLAAYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKEL 132 (132)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHC
T ss_conf 996424689999999999999857577547799999999999778972133699999987529
No 3
>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.
Probab=100.00 E-value=1e-34 Score=228.87 Aligned_cols=130 Identities=35% Similarity=0.459 Sum_probs=121.1
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 46999999999999995699989999999985310013221120144343999999999999989999999997410357
Q gi|254780345|r 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKW 95 (170)
Q Consensus 16 r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w 95 (170)
|+.||+.|+|+|||+++++.+.++++..+.. .....+.|..|+++++.|+.++...||.+|.+++ ++|
T Consensus 1 R~~aRe~a~q~LYq~~~~~~~~~~i~~~~~~-----------~~~~~~~d~~f~~~l~~gv~~~~~~iD~~I~~~l-~~w 68 (130)
T cd00619 1 RRRARELAVQALYAWELAPEILAEVVSLLEL-----------LQYKSKKVLPFALKLVRGVLENIEEIDELIEKHL-RNW 68 (130)
T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH-----------HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCC
T ss_conf 9199999999999967079999999999987-----------5113346899999999999984999999999871-899
Q ss_pred CHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 63323534899999999998643557810339889999998338772314999999999523
Q gi|254780345|r 96 SFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKE 157 (170)
Q Consensus 96 ~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~ 157 (170)
+++|+++++++|||+|+||+++++++|++|+|||||+|||.|+++++++|||||||+++|+.
T Consensus 69 ~~~rl~~i~~~ILr~a~~El~~~~~~p~~v~InEavelak~f~~~~~~~fiNgVLd~i~k~l 130 (130)
T cd00619 69 SLDRLAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130 (130)
T ss_pred CHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHC
T ss_conf 96766799999999999999868676346799999999998577862044899999987519
No 4
>COG0781 NusB Transcription termination factor [Transcription]
Probab=100.00 E-value=1.6e-33 Score=221.67 Aligned_cols=143 Identities=37% Similarity=0.539 Sum_probs=120.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 132346999999999999995699-9899999999853100132211201443439999999999999899999999974
Q gi|254780345|r 12 LSHRRGIARLAAVQALYQIDIIGC-STTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSC 90 (170)
Q Consensus 12 ~~~~r~~aR~~aiq~Ly~~~~~~~-~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~ 90 (170)
+...|+.+|+.|||+||+|++++. ..+++.+.+..+.... +......+..|+..++.|+.+|...||.+|.++
T Consensus 6 ~~~~R~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~~~~~~~------d~~~~~~~~~~~~~lv~gv~~~~~~iD~~I~~~ 79 (151)
T COG0781 6 PKLTRRQARELAVQALYQWELSGSVSAEDILEDIEEEFVEN------ELDIELADSEYFRSLVKGVLENQEELDELISPH 79 (151)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHC------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 31258999999999999998658832567899999998621------210145349999999999999799999999998
Q ss_pred HCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 10357633235348999999999986435578103398899999983387723149999999995233320
Q gi|254780345|r 91 LTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKR 161 (170)
Q Consensus 91 l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~ 161 (170)
|.+ |+++|++.++|+|||+|+||+++.+++|.+|+|||||+|||.|+++++++|||||||++++..+..+
T Consensus 80 L~~-w~~~rL~~verAILRla~yEl~~~~dvP~~VvInEaielaK~f~~e~s~kFINgVLd~i~~~~~~~~ 149 (151)
T COG0781 80 LKK-WSLERLDLVERAILRLALYELLFRDDVPYKVVINEAIELAKKFSGEDSHKFVNGVLDKIAKKLRPKE 149 (151)
T ss_pred HCC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 806-9888823999999999999999647999751299999999996778733779999999998742202
No 5
>pfam01029 NusB NusB family. The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.
Probab=99.97 E-value=6.1e-30 Score=200.09 Aligned_cols=125 Identities=32% Similarity=0.460 Sum_probs=115.9
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf 99999999999999569998999999998531001322112014434399999999999998999999999741035763
Q gi|254780345|r 18 IARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSF 97 (170)
Q Consensus 18 ~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w~~ 97 (170)
.+|+.|+|+||+++.++.+.+++++.+.. ....+.|+.|++.++.|+.++...+|.+|.+++ ++|++
T Consensus 2 ~aR~~a~q~L~~~~~~~~~~~~~l~~~~~------------~~~~~~d~~~~~~l~~gv~~~~~~id~~i~~~~-~~~~~ 68 (126)
T pfam01029 2 NARELALQALYAVEERGASLNELLDKLLE------------ADLDERDRAFATELVYGVLRNLEELDALIAKLL-ENWPL 68 (126)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHH------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCH
T ss_conf 49999999999998609899999999987------------189889999999999999998999999999885-59996
Q ss_pred HHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 3235348999999999986435578103398899999983387723149999999995
Q gi|254780345|r 98 SRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSR 155 (170)
Q Consensus 98 ~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k 155 (170)
+++++++++|||+|+||+++.+++|++++|||||+|||.|++++++||||||||+++|
T Consensus 69 ~~l~~~~~~iLr~a~~El~~~~~~p~~~~InE~v~lak~~~~~~~~~fvNaVL~~i~r 126 (126)
T pfam01029 69 ERLDPVDRAILRLAAYELLYLDDIPPHVAINEAVELAKKFGGEKSAGFVNGVLRKIAR 126 (126)
T ss_pred HHCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHC
T ss_conf 6659999999999999998578998244589999999987788643028999887549
No 6
>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the
Probab=99.97 E-value=3.7e-29 Score=195.38 Aligned_cols=126 Identities=33% Similarity=0.425 Sum_probs=117.3
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf 99999999999995699989999999985310013221120144343999999999999989999999997410357633
Q gi|254780345|r 19 ARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFS 98 (170)
Q Consensus 19 aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w~~~ 98 (170)
||..|+|+||+++.++....+++.++.. ...+.+.|++|++++++|+.+++..+|.+|.+++ ++|+++
T Consensus 2 AR~~a~~~L~~~~~~~~~~~~~l~~~~~-----------~~~l~~~d~~~~~~lv~gv~~~~~~ld~~i~~~l-~~~~~~ 69 (129)
T cd00447 2 AREIAFQALYQVEIRNGISLEAVLSALE-----------KLQLAKKDRPFALELVYGVLRNLPELDDIISPLL-KKWLLD 69 (129)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHH-----------HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHH
T ss_conf 8999999999998209999999999998-----------7789778999999999999996999999999982-788031
Q ss_pred HCCCHHHHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 235348999999999986435-5781033988999999833877231499999999952
Q gi|254780345|r 99 RLDMILCSILRAGVLELIECH-SVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK 156 (170)
Q Consensus 99 rl~~~~~~iLr~a~~El~~~~-~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~ 156 (170)
++++++++|||+|+||++++. ++|++++|||||+|||.|++++++||||||||+++|+
T Consensus 70 ~~~~i~~~iLrl~~~el~~~~~~ip~~~~InE~v~lak~~~~~~~~~fvNavLr~i~r~ 128 (129)
T cd00447 70 RLDKVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKE 128 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf 10088899999999999985058985167899999999867886320079997798734
No 7
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=99.93 E-value=7.3e-25 Score=169.47 Aligned_cols=94 Identities=27% Similarity=0.365 Sum_probs=87.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCC
Q ss_conf 34399999999999998999999999741035763323534899999999998643557810339889999998338772
Q gi|254780345|r 63 HVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDE 142 (170)
Q Consensus 63 ~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~ 142 (170)
...+.|+.+++..+.+|...||..|.+++ ++|+++|++.+|++|||+|+||++|. ++|.+|+|||||+|||.|+++++
T Consensus 111 ~~VR~~a~~~i~~v~~~~~eID~~i~~~~-~~W~l~Rl~~iDr~ILRlAv~El~~~-d~P~~VaInEAVELAk~ys~~~s 188 (206)
T PRK09634 111 EEVREYALERVGLVIRNRDEIDELLDEVM-VGWQLKRLPRIDRDILRLAVVEILFL-NTPAAVAINEAVELAKRYSDEQG 188 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 99999999999999975899999999872-69987775788999999999998035-99951139999999998678861
Q ss_pred CCHHHHHHHHHHHHHH
Q ss_conf 3149999999995233
Q gi|254780345|r 143 PKFINAVLDKVSRKEE 158 (170)
Q Consensus 143 ~~fVNaVL~ki~k~~~ 158 (170)
++|||||||++.....
T Consensus 189 ~~FINGVL~r~~~~~~ 204 (206)
T PRK09634 189 RRFINGVLRRLQDALS 204 (206)
T ss_pred HHHHHHHHHHHHHHHC
T ss_conf 1449989888987651
No 8
>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.
Probab=99.92 E-value=2.8e-24 Score=165.94 Aligned_cols=124 Identities=23% Similarity=0.221 Sum_probs=111.1
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf 99999999999999569998999999998531001322112014434399999999999998999999999741035763
Q gi|254780345|r 18 IARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSF 97 (170)
Q Consensus 18 ~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w~~ 97 (170)
.+|..|+++|++.+..+.+.+.++..+.. ...+..|++|++++++|+++++..+|.+|.+++.++ +
T Consensus 2 naR~~A~~iL~~V~~~~~~~~~~l~~~~~------------~~l~~~Dra~~~~lv~g~lR~~~~ld~~l~~~l~~p--~ 67 (126)
T cd00620 2 NARSTAAEVLRDVLQRGASLNAVLSALQK------------KDKSDRDRGLATELVYGTLRWLALLDWIINPLLKKP--D 67 (126)
T ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHHH------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--C
T ss_conf 89999999999999679989999999886------------579988899999999999981999999999985777--1
Q ss_pred HHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 32353489999999999864355781033988999999833877231499999999952
Q gi|254780345|r 98 SRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK 156 (170)
Q Consensus 98 ~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~ 156 (170)
+++++..++|||+|+||++++ ++|++++|||+|++||.+++++.+||||||||++.|+
T Consensus 68 ~~~~~~~~~lLrlg~yql~~~-~~p~~A~VneaV~lak~~~~~~~~~lVNAVLR~~~Re 125 (126)
T cd00620 68 VGKDPDVRNLLRLGLYQLLYL-DVPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRFERE 125 (126)
T ss_pred CCCCHHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf 107999999999999998707-9996106999999999868997666138983087625
No 9
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=99.89 E-value=2.2e-22 Score=154.56 Aligned_cols=128 Identities=19% Similarity=0.223 Sum_probs=113.7
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 46999999999999995699989999999985310013221120144343999999999999989999999997410357
Q gi|254780345|r 16 RGIARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKW 95 (170)
Q Consensus 16 r~~aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w 95 (170)
..++|..|+++|++....+..++.++.... ..++..|++|+++||+|++|++..+|.+|+++++++
T Consensus 3 ~~n~R~~A~~~L~~v~~~g~~~~~~L~~~~-------------~~l~~~Dr~l~~elvyG~lR~~~~LD~il~~~~~~p- 68 (428)
T PRK10901 3 QYNLRSIAAQAVEQVVEQGQSLSNVLPPLQ-------------QKVSDKDKALLQELCFGVLRTLSQLEWLINKLMARP- 68 (428)
T ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHHH-------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-
T ss_conf 764999999999999986992999999987-------------059998899999999999976899999999983799-
Q ss_pred CHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 6332353489999999999864355781033988999999833877231499999999952333
Q gi|254780345|r 96 SFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEI 159 (170)
Q Consensus 96 ~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~ 159 (170)
++.+++..+.+||+|+||++|+ .+|++++|||+|++||........||||||||++.|+.+.
T Consensus 69 -~~~~~~~v~~lLrlg~yQll~~-~iP~~AaVne~Ve~ak~~~~~~~~glVNAVLR~~~r~~~~ 130 (428)
T PRK10901 69 -MTGKQRTVHYLIMVGLYQLLYT-RIPPHAALAETVEGAVAIKRPQLKGLINGVLRQFQRQQEE 130 (428)
T ss_pred -CCCCCHHHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHH
T ss_conf -8543479999999999999617-9995147989999998616630467889999998604321
No 10
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase B; InterPro: IPR004573 This family consists of bacterial sequences related to Escherichia coli rsmB, an rRNA SAM-dependent methyltransferase. All, are likely to be functionally equivalent and based on comparison of core motifs would appear to belong to a larger superfamily of S-adenosyl-methionine (AdoMet)-dependent RNA m5C methyltransferases . In E. coli, originally, the reading frame, encoding this protein, was interpreted as two reading frames, fmu and fmv. It has since been renamed, rsmB (Alternate Gene Symbols: rrmB, sun, fmu, fmv, yhdB). The recombinant protein, commonly referred to as Fmu, has been demonstrated to methylate only C967 of the 16S ribosomal RNA and to produce only m5C at that position. . The structure of the E. coli protein (Fmu) has been determined . Fmu contains three subdomains which share structural homology to DNA m5C methyltransferases and two RNA binding protein families. The N-terminal sequence of Fmu shares homology to another (noncatalytic) RNA binding protein, e.g. the ribosomal RNA antiterminator protein NusB (IPR011605 from INTERPRO). The catalytic lobe of Fmu, N1 domain, comprises the conserved core identified in all of the putative RNA m5C MTase sequences. Although the N1 domain is structurally homologous to known RNA binding proteins, there is no clear sequence motif that defines its role in RNA binding and recognition. At the functional centre of the catalytic lobe is the MTase domain of Fmu (residues 232-429), which adopts a fold typical of known AdoMet-dependent methyltransferases. In spite of the lack of a conserved RNA binding motif in the N1 domain, the close association of the N1 and MTase domains suggest that any RNA bound in the active site of the MTase domain is likely to interact with the N1 domain. ; GO: 0008649 rRNA methyltransferase activity, 0006364 rRNA processing.
Probab=99.81 E-value=1.2e-19 Score=138.03 Aligned_cols=128 Identities=20% Similarity=0.262 Sum_probs=107.0
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf 99999999999956999899999999853100132211201443439999999999999899999999974103576332
Q gi|254780345|r 20 RLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFSR 99 (170)
Q Consensus 20 R~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w~~~r 99 (170)
|.+|+++|-+..=.+.+..+++-+. .......++.|+.|+++||+||++++..+|.+|++...++ +..
T Consensus 1 R~~A~~~l~~V~~~~~sys~~~~~~----------~~~~~~ls~~dr~Ll~ELvyGv~r~~~~Ld~li~~L~~kP--~~~ 68 (487)
T TIGR00563 1 RDIAAEALIQVLEQGQSYSNLLPDL----------VLKQNELSDQDRRLLTELVYGVLRRLRALDYLIKKLIDKP--LKG 68 (487)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHH----------HHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCC
T ss_conf 9578999999973155145678998----------8630578830032311122232135045789999974178--888
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 353489999999999864355781033988999999833877231499999999952333
Q gi|254780345|r 100 LDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEI 159 (170)
Q Consensus 100 l~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~ 159 (170)
-.++.+-+|+++.|.+.|...||++++|+|+|++||..+.+.-.||||||||++.|+.+.
T Consensus 69 k~~~~~r~l~L~ly~~~yl~~vP~~AAv~e~V~~Ak~~g~~~l~~lVNGvLR~~qR~~~~ 128 (487)
T TIGR00563 69 KPRVVHRLLRLVLYQQLYLERVPAHAAVNEAVELAKALGLKGLKGLVNGVLRRFQREQVQ 128 (487)
T ss_pred CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 748999999999999999750782467889989999716752236788888888603576
No 11
>pfam09185 DUF1948 Domain of unknown function (DUF1948). Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined.
Probab=97.35 E-value=0.01 Score=35.88 Aligned_cols=133 Identities=19% Similarity=0.270 Sum_probs=86.5
Q ss_pred CHHHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHHHH----HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 346999999999999995-69998999999998531001----3221120144343999999999999989999999997
Q gi|254780345|r 15 RRGIARLAAVQALYQIDI-IGCSTTEIISEYETYRFCAD----TELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISS 89 (170)
Q Consensus 15 ~r~~aR~~aiq~Ly~~~~-~~~~~~~~~~~f~~~~~~~~----~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~ 89 (170)
.|+..|.+++..+|...| -....+.+-..|.++.-... -....-..++..-.+|...+-.--.+|..++..--+
T Consensus 2 trtqrriaivefifa~lfflpk~ad~iqa~fldyd~~er~lndwqk~ivk~fse~~~~f~~~ie~qq~knq~eiqskyn- 80 (140)
T pfam09185 2 TRTQRRIAIVEFIFALLFFLPKEADQIQAAFLDYDTKERPLNDWQKEIVKAFSENCFEFIEKIEEQQLKNQAEIQSKYN- 80 (140)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_conf 5224557799999999997745188999999636888787207899999999999999999999999865899998873-
Q ss_pred HHCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 4103576332353489999999999864355781033988999999833877231499999999
Q gi|254780345|r 90 CLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKV 153 (170)
Q Consensus 90 ~l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki 153 (170)
+.+-++++..-.+++.+|+.|.- ...+..+..|+|++-+-..|+...+.+-..|.||++
T Consensus 81 ----kisgkkidllt~avilcalseq~-a~~tdkplliseallimdhysq~~ekkqthalldkl 139 (140)
T pfam09185 81 ----KISGKKIDLLTKAVILCALSEQH-AHATDKPLLISEALLIMDHYSQGAEKKQTHALLDKL 139 (140)
T ss_pred ----CCCCCHHHHHHHHHHHHHHHHHH-HHCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_conf ----05540425999999999823877-503577535889999998773142577799999842
No 12
>pfam11573 Med23 Mediator complex subunit 23. Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice.
Probab=88.45 E-value=1.8 Score=22.26 Aligned_cols=84 Identities=15% Similarity=0.242 Sum_probs=59.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCCCHHHCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH-HHHHC
Q ss_conf 434399999999999998999999999--741035763323534899999999998643557810339889999-99833
Q gi|254780345|r 62 LHVDLEWFRVIIHGVMDRKQHIDLLIS--SCLTEKWSFSRLDMILCSILRAGVLELIECHSVPVEVIISEYVCI-AHDFF 138 (170)
Q Consensus 62 ~~~d~~~~~~lv~~v~~~~~~id~~I~--~~l~~~w~~~rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~l-ak~f~ 138 (170)
..+|..|..+++. |-.+.+|.+.. .+.+.+|++..++..--..|.+++.|++-.+ +++.++.|.-+++ .|.+.
T Consensus 1090 w~P~~~yy~~Li~---Rlv~ti~~~~~~~~F~~~DWRfnEfpNp~ahaLy~tCVELmAlP-~~p~~V~naLiDVv~k~~~ 1165 (1341)
T pfam11573 1090 NWPELSYYMELIG---RMVDTIDGINPPPPFVATDWRFNEFPNPPAHALYVTCIELMALP-VSPEKVANALIDVIVKGYP 1165 (1341)
T ss_pred CCCCHHHHHHHHH---HHHHHHCCCCCCCCCCCCCCCHHCCCCHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHCCCC
T ss_conf 6860889999999---99987246679998776675041189858788999999998289-9889999999999844888
Q ss_pred CCC---CCCHHHHH
Q ss_conf 877---23149999
Q gi|254780345|r 139 YGD---EPKFINAV 149 (170)
Q Consensus 139 ~~~---~~~fVNaV 149 (170)
--. -...+|+|
T Consensus 1166 ~iP~~~i~~wiNai 1179 (1341)
T pfam11573 1166 VIPFEDIHNWFNAI 1179 (1341)
T ss_pred CCCHHHHHHHHHHH
T ss_conf 78544567999999
No 13
>TIGR02746 TraC-F-type type-IV secretion system protein TraC; InterPro: IPR014117 The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases..
Probab=58.44 E-value=11 Score=17.66 Aligned_cols=140 Identities=15% Similarity=0.115 Sum_probs=76.0
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH--------HHHHH-------H
Q ss_conf 99999999999569998999999998531001322112014434399999999999998--------99999-------9
Q gi|254780345|r 21 LAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDR--------KQHID-------L 85 (170)
Q Consensus 21 ~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~--------~~~id-------~ 85 (170)
..||...|.-.-....++++.+.+........... .+ ...+.-+.+.+.|-..+..- ...+| -
T Consensus 621 ~~AI~~~W~~~g~~a~~tdV~~~L~~~~~e~~~~~-~D-Gir~r~~~l~~~L~~Yt~~G~YG~~Fn~~~~l~~~~~~vvL 698 (900)
T TIGR02746 621 EEAILAAWKEKGNEATITDVADALEQLRLEEEDSE-ND-GIRPRIKDLGKLLNPYTSNGVYGRYFNGPNNLDFSNRFVVL 698 (900)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCC-CC-CCHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCCEEEE
T ss_conf 99999999971224884899999985213313456-88-60168999998732642487120112877756789876885
Q ss_pred HHHHHHCCC-CCHHHCCCHHHHHHHHHHHHHHHC--CCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 999741035-763323534899999999998643--55781033988999999833877231499999999952333203
Q gi|254780345|r 86 LISSCLTEK-WSFSRLDMILCSILRAGVLELIEC--HSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRS 162 (170)
Q Consensus 86 ~I~~~l~~~-w~~~rl~~~~~~iLr~a~~El~~~--~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~~ 162 (170)
.+. .|..+ ..+. ..|+.++|..-.-|+... .++|+-.+|+|+=+|-..+++..+..|||.-=|++.| =+
T Consensus 699 EL~-eL~~~Dp~l~--~~Vl~~L~~~I~~~my~~g~R~~rK~~~iDEAW~Ll~~g~~~~~~~FIE~gyRr~RK-----~~ 770 (900)
T TIGR02746 699 ELE-ELEDRDPELQ--AVVLFSLMVRITGEMYLTGDRKRRKILIIDEAWSLLDDGANPQAANFIETGYRRARK-----YG 770 (900)
T ss_pred ECC-CCCCCCHHHH--HHHHHHHHHHHHHHHHHCCCCCCCEEEEEHHHHHHHHCCCCCHHHHHHHHHHHCCHH-----HC
T ss_conf 122-5757785677--999999999998776305889755167644248987427851358988876320111-----16
Q ss_pred CCCCCCCC
Q ss_conf 78763789
Q gi|254780345|r 163 GCVSAITQ 170 (170)
Q Consensus 163 ~~~~~~~~ 170 (170)
|+..-+||
T Consensus 771 Ga~~tiTQ 778 (900)
T TIGR02746 771 GAFITITQ 778 (900)
T ss_pred CCEEEEEC
T ss_conf 43689964
No 14
>pfam02284 COX5A Cytochrome c oxidase subunit Va. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit Va.
Probab=46.15 E-value=21 Score=15.85 Aligned_cols=54 Identities=22% Similarity=0.190 Sum_probs=43.1
Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHH
Q ss_conf 34899999999998643557810339889999998338-7723149999999995
Q gi|254780345|r 102 MILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFY-GDEPKFINAVLDKVSR 155 (170)
Q Consensus 102 ~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~-~~~~~fVNaVL~ki~k 155 (170)
-+|..-+|-|+-.+.-..-+|.+.||..++.-++...+ .-+.+|.-||=+|...
T Consensus 23 ~iD~we~rr~mN~l~~~DlVPeP~Ii~AaL~AcRRvND~alAVR~lE~vK~K~~~ 77 (108)
T pfam02284 23 DIDAWELRKGMNTLVGYDLVPEPKIIEAALRACRRVNDFASAIRILEVVKDKAGP 77 (108)
T ss_pred CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 6429999999999850566898399999999998851079999999999999647
No 15
>TIGR01320 mal_quin_oxido malate:quinone-oxidoreductase; InterPro: IPR006231 The membrane-associated enzyme, malate:quinone-oxidoreductase, is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in E. coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase . ; GO: 0008924 malate dehydrogenase (acceptor) activity, 0006099 tricarboxylic acid cycle.
Probab=45.86 E-value=5.9 Score=19.22 Aligned_cols=41 Identities=29% Similarity=0.292 Sum_probs=25.4
Q ss_pred HHHHHHHHHCCCCC-CCCHHHHHHHHHHHH-------------CC-CCCCCHHHHH
Q ss_conf 99999986435578-103398899999983-------------38-7723149999
Q gi|254780345|r 109 RAGVLELIECHSVP-VEVIISEYVCIAHDF-------------FY-GDEPKFINAV 149 (170)
Q Consensus 109 r~a~~El~~~~~~p-~~vvInE~V~lak~f-------------~~-~~~~~fVNaV 149 (170)
+.|+|||=|.|..+ =.|=|.-||.|+..| +. .+-..|||.|
T Consensus 52 HSALCELNYtP~~~dG~idi~kAv~ine~F~VsrQFWa~lv~~G~L~dp~~FiNpV 107 (487)
T TIGR01320 52 HSALCELNYTPEVADGSIDIAKAVGINEQFQVSRQFWAHLVEEGVLEDPKSFINPV 107 (487)
T ss_pred HHHHHHHCCCCCCCCCCCCHHHHCCCCCCCEECHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 36876422478876782653556220114113188898998367246854022788
No 16
>PRK05590 hypothetical protein; Provisional
Probab=45.56 E-value=12 Score=17.39 Aligned_cols=58 Identities=14% Similarity=0.088 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCC--CCCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99999999864355781033988999999833877--2314999999999523332037876
Q gi|254780345|r 107 ILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGD--EPKFINAVLDKVSRKEEIKRSGCVS 166 (170)
Q Consensus 107 iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~--~~~fVNaVL~ki~k~~~~~~~~~~~ 166 (170)
-+--++||-+.. -|..++=-.--+||.+|..+. ..||+-||=+++--..++++...-|
T Consensus 29 ~~Ek~IY~~iL~--~~~~vv~Gtv~eLAeKy~~~~~~f~GFLDGINdSLk~~~~le~~eedt 88 (165)
T PRK05590 29 SVEKNIYTQILA--NHKEVIEGTVKELAEKFDTTVVFFMGFLDGINDSLKEPLDLEKLEEDT 88 (165)
T ss_pred HHHHHHHHHHHH--CCCCEEEEEHHHHHHHHCCCCEEEEEECCCCHHHHCCCCCHHHCCCCC
T ss_conf 999999999980--998433235999999849981586421026356518987533305676
No 17
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=45.39 E-value=22 Score=15.78 Aligned_cols=52 Identities=21% Similarity=0.181 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC-CCCCCHHHHHHHHHH
Q ss_conf 4899999999998643557810339889999998338-772314999999999
Q gi|254780345|r 103 ILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFY-GDEPKFINAVLDKVS 154 (170)
Q Consensus 103 ~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~-~~~~~fVNaVL~ki~ 154 (170)
+|..-+|-|+-.+.-..-+|.+.||..++.-++...+ .-+.+|.-||=+|..
T Consensus 21 iD~we~rrgmN~l~~~DlVPeP~Ii~AALrAcRRvND~alAVR~lE~vK~K~~ 73 (103)
T cd00923 21 IDGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCG 73 (103)
T ss_pred CCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 41999999999985056689839999999999886107999999999999813
No 18
>PRK05257 malate:quinone oxidoreductase; Validated
Probab=42.53 E-value=8.3 Score=18.31 Aligned_cols=30 Identities=23% Similarity=0.224 Sum_probs=20.5
Q ss_pred HHHHHHHHHHCCC-------CCCCCHHHHHHHHHHHH
Q ss_conf 9999999864355-------78103398899999983
Q gi|254780345|r 108 LRAGVLELIECHS-------VPVEVIISEYVCIAHDF 137 (170)
Q Consensus 108 Lr~a~~El~~~~~-------~p~~vvInE~V~lak~f 137 (170)
-..|.||+=|.+. +.+.+.|||.-++++.|
T Consensus 60 GHaa~CELNYTp~~~dG~i~i~KA~~Ine~Fe~SrQf 96 (499)
T PRK05257 60 GHSALCELNYTPEQADGSIDISKAVKINEQFQISRQF 96 (499)
T ss_pred CHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 0213022148877679837089999999999999999
No 19
>KOG4077 consensus
Probab=42.44 E-value=24 Score=15.50 Aligned_cols=57 Identities=18% Similarity=0.214 Sum_probs=43.1
Q ss_pred CHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHH
Q ss_conf 34899999999998643557810339889999998338-7723149999999995233
Q gi|254780345|r 102 MILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFY-GDEPKFINAVLDKVSRKEE 158 (170)
Q Consensus 102 ~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~-~~~~~fVNaVL~ki~k~~~ 158 (170)
-+|..=+|-|+.++.-..-+|.+.||..++.-++...+ .-+.++.-||=+|.--+.+
T Consensus 62 ~iD~wEvrkglN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K~g~~k~ 119 (149)
T KOG4077 62 EIDGWEVRKGLNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDKCGAQKQ 119 (149)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHH
T ss_conf 1038999999976512466788689999999998740199999999999875164877
No 20
>pfam04271 consensus
Probab=41.16 E-value=25 Score=15.38 Aligned_cols=51 Identities=16% Similarity=0.049 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 353489999999999864355781033988999999833877231499999999952
Q gi|254780345|r 100 LDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK 156 (170)
Q Consensus 100 l~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~ 156 (170)
+++.+...|.--+-+. . .| .-+|.+|++.|-. .+....++|+|||.+=.++
T Consensus 13 lsp~e~e~i~~w~~~~--~--~~-~elI~~Al~~av~-~~~~~~~Yi~~IL~~W~~~ 63 (73)
T pfam04271 13 LSPFEIEDLNKWLDEF--G--FD-PELVKEALKEAVL-NNKANFRYIQAILKNWKNN 63 (73)
T ss_pred CCHHHHHHHHHHHHHH--C--CC-HHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHHC
T ss_conf 9999999999999881--9--99-9999999999999-5999879999999999995
No 21
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=39.43 E-value=27 Score=15.22 Aligned_cols=51 Identities=20% Similarity=0.052 Sum_probs=35.4
Q ss_pred HCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 235348999999999986435578103398899999983387723149999999995
Q gi|254780345|r 99 RLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSR 155 (170)
Q Consensus 99 rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k 155 (170)
-|+++..-=|..-+-| ...| .-+|.+|++.|.. .+....++|++||+.=-+
T Consensus 141 ~lsP~e~E~L~~wld~----d~~~-~elI~~ALkeAv~-~gK~n~~YI~~IL~nW~k 191 (246)
T COG3935 141 MLSPFEIEDLQKWLDE----DSHD-PELIKAALKEAVE-NGKLNFKYIDAILRNWKK 191 (246)
T ss_pred CCCCHHHHHHHHHHHH----CCCC-HHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHH
T ss_conf 4784519999999983----2898-9999999999998-587468999999999998
No 22
>KOG3583 consensus
Probab=32.11 E-value=33 Score=14.71 Aligned_cols=28 Identities=25% Similarity=0.310 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHHHHHHH-HHCCCCCCCCC
Q ss_conf 31499999999952333-20378763789
Q gi|254780345|r 143 PKFINAVLDKVSRKEEI-KRSGCVSAITQ 170 (170)
Q Consensus 143 ~~fVNaVL~ki~k~~~~-~~~~~~~~~~~ 170 (170)
.|.|-|+|+.+.+..++ -+++.-+|++|
T Consensus 143 NK~is~ll~~lsk~~re~tEs~~~~piqQ 171 (279)
T KOG3583 143 NKNISGLLNHLSKVDREHTESAIEKPIQQ 171 (279)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 98999999987888888777641376311
No 23
>pfam07261 DnaB_2 Replication initiation and membrane attachment protein (DnaB). This family consists of several bacterial replication initiation and membrane attachment (DnaB) proteins, as well as DnaD which is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication. DnaD has been merged into this family.
Probab=30.87 E-value=37 Score=14.38 Aligned_cols=51 Identities=24% Similarity=0.214 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 353489999999999864355781033988999999833877231499999999952
Q gi|254780345|r 100 LDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK 156 (170)
Q Consensus 100 l~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~ 156 (170)
+++.+...|.--+-+. ..| .-+|.++++.|.. .+..+.++|++||.+-.++
T Consensus 13 ls~~e~~~i~~~~~~~----~~~-~elI~~a~~~a~~-~~~~~~~Yi~~Il~~W~~~ 63 (77)
T pfam07261 13 LSPIEIEIIEEWIDED----KLS-PELINEALKYAVE-NNKRSLKYIEKILRNWKRK 63 (77)
T ss_pred CCHHHHHHHHHHHHHH----CCC-HHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHHC
T ss_conf 9999999999999882----999-9999999999999-4999799999999999986
No 24
>PRK11001 mtlR mannitol repressor protein; Provisional
Probab=29.46 E-value=39 Score=14.23 Aligned_cols=54 Identities=17% Similarity=0.185 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH----------HHHHCCCCCHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 439999999999999899999999----------9741035763323534899999999998643
Q gi|254780345|r 64 VDLEWFRVIIHGVMDRKQHIDLLI----------SSCLTEKWSFSRLDMILCSILRAGVLELIEC 118 (170)
Q Consensus 64 ~d~~~~~~lv~~v~~~~~~id~~I----------~~~l~~~w~~~rl~~~~~~iLr~a~~El~~~ 118 (170)
.+..|....+.+-+.+...++..- ...+ -.|...|...+.|+-|-+|+.|++..
T Consensus 100 ~e~~FtD~~I~~~i~~Lh~v~~~~~~~~~~~~~~d~~l-~qmq~~R~~q~VrS~LvLaiTei~~~ 163 (170)
T PRK11001 100 NEYRFTDDEILGPFGELHCVAAMGLPPPPQFEDADSSL-YQMQLQRYQQVVRSTLVLAITEIISE 163 (170)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 54786868999999870887616899988655533699-99999999849999999999999999
No 25
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=27.08 E-value=43 Score=13.98 Aligned_cols=52 Identities=23% Similarity=0.284 Sum_probs=35.6
Q ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999864355781033988999999833877231499999999952333203787
Q gi|254780345|r 108 LRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKEEIKRSGCV 165 (170)
Q Consensus 108 Lr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~~~~~~~~~ 165 (170)
+---+++++.. .+...+ -+..|||.++-.+ +=||-+|-++.|+.+..+.+.-
T Consensus 7 ~eqkil~~L~~--~g~~~~--tA~~lak~lg~~K--k~vN~~LY~L~k~g~v~~~~~~ 58 (68)
T smart00550 7 LEEKILEFLEN--SGDETS--TALQLAKNLGLPK--KEVNRVLYSLEKKGKVCKQGGT 58 (68)
T ss_pred HHHHHHHHHHH--CCCCCC--HHHHHHHHHCCCH--HHHHHHHHHHHHCCCEECCCCC
T ss_conf 99999999997--488640--3999999949989--9999999999974883106998
No 26
>TIGR01446 DnaD_dom DnaD and phage-associated domain; InterPro: IPR006343 These sequences contain a conserved domain. It is found in DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria ..
Probab=26.76 E-value=44 Score=13.94 Aligned_cols=53 Identities=17% Similarity=0.098 Sum_probs=38.2
Q ss_pred HCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 23534899999999998643557810339889999998338772314999999999523
Q gi|254780345|r 99 RLDMILCSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRKE 157 (170)
Q Consensus 99 rl~~~~~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~~ 157 (170)
.+++....-|..-+-+. . -+.-+|.+++.+|.. .+....++|++||..=.++.
T Consensus 13 ~l~p~~~e~l~~~~~~~----~-~~~el~~~al~~a~~-~~k~~~~y~~~iL~~W~~~g 65 (74)
T TIGR01446 13 MLSPFEIEDLKYWLDEF----G-FSPELVKEALKEAVE-NNKRNYKYIDAILKNWKKNG 65 (74)
T ss_pred CCCHHHHHHHHHHHHHC----C-CCHHHHHHHHHHHHH-CCCCCHHHHHHHHHHHHHCC
T ss_conf 13646599999999734----8-977999999999887-06655789999999898758
No 27
>pfam10752 DUF2533 Protein of unknown function (DUF2533). This family of proteins with unknown function appears to be restricted to Bacillus spp.
Probab=25.33 E-value=47 Score=13.78 Aligned_cols=30 Identities=20% Similarity=0.120 Sum_probs=15.6
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 8103398899999983387723149999999
Q gi|254780345|r 122 PVEVIISEYVCIAHDFFYGDEPKFINAVLDK 152 (170)
Q Consensus 122 p~~vvInE~V~lak~f~~~~~~~fVNaVL~k 152 (170)
..-.+|.|+|.+++. +.+-+..-||+|-..
T Consensus 27 ~RE~aIe~aV~~c~~-g~~Fs~d~IN~iTk~ 56 (84)
T pfam10752 27 KREAAIEEAVSLCRQ-GKPFTTDAINEITKQ 56 (84)
T ss_pred HHHHHHHHHHHHHHC-CCCCCHHHHHHHHHH
T ss_conf 999999999999877-998729999999999
No 28
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=23.72 E-value=50 Score=13.60 Aligned_cols=128 Identities=17% Similarity=0.123 Sum_probs=67.3
Q ss_pred HHHHHHHHHHHHHH------------H--CCC----CHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999------------5--699----98999999998531001322112014434399999999999998
Q gi|254780345|r 18 IARLAAVQALYQID------------I--IGC----STTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDR 79 (170)
Q Consensus 18 ~aR~~aiq~Ly~~~------------~--~~~----~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~ 79 (170)
+.-+.++.-||... + .+. ++.+++..|.+|+...........-....++. +++.|...-
T Consensus 316 ~d~~~vln~Lyk~T~Lq~sf~~N~~al~~dg~P~~l~Lk~iL~~~l~hR~~vi~rrt~~~L~Ka~~Rl---hIleGLliA 392 (745)
T PRK05561 316 VDPEALMNHLFATTDLESSYRVNMNVIGLDGRPRVKGLKEILSEWLDHRREVVTRRSQFRLDKVEKRL---HILEGLLIA 392 (745)
T ss_pred CCHHHHHHHHHHHCCCHHHCCCEEEEEECCCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHH
T ss_conf 79999999999857624213714899937997558279999999999999999999999999999999---999889999
Q ss_pred HHHHHHHH---HHH------HCCCCCHHHCCCHHHHHHHHHHHH-------------------------HHHCCCCCCCC
Q ss_conf 99999999---974------103576332353489999999999-------------------------86435578103
Q gi|254780345|r 80 KQHIDLLI---SSC------LTEKWSFSRLDMILCSILRAGVLE-------------------------LIECHSVPVEV 125 (170)
Q Consensus 80 ~~~id~~I---~~~------l~~~w~~~rl~~~~~~iLr~a~~E-------------------------l~~~~~~p~~v 125 (170)
...||++| ..+ |-+.+.+. ...-.+||-+=++. ++..++.=.++
T Consensus 393 ~~~iD~VI~iIR~S~dak~~L~~~f~ls--e~QA~AIL~mrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~~~~i 470 (745)
T PRK05561 393 FLNIDEVIEIIRESDEPKANLMARFGLT--EIQAEAILELRLRRLAKLEEIEIRKEQDELRKEIAELEAILASERKLWKL 470 (745)
T ss_pred HHCHHHHHHHHHCCCHHHHHHHHHHCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
T ss_conf 9676899999970632667775550879--99999999999999876679999999999999999999996389999999
Q ss_pred HHHHHHHHHHHHCCCCCCCHHHHHH
Q ss_conf 3988999999833877231499999
Q gi|254780345|r 126 IISEYVCIAHDFFYGDEPKFINAVL 150 (170)
Q Consensus 126 vInE~V~lak~f~~~~~~~fVNaVL 150 (170)
+++|-.++.+.|+++.-...++..-
T Consensus 471 I~~EL~eik~kfgd~RRT~I~~~~~ 495 (745)
T PRK05561 471 IKKELKADAKKFGDPRRTPIEEREE 495 (745)
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf 9999999998638998630226742
No 29
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=21.88 E-value=55 Score=13.37 Aligned_cols=54 Identities=11% Similarity=0.012 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899999999853100132211201443439999999999999899999999974
Q gi|254780345|r 37 TTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSC 90 (170)
Q Consensus 37 ~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~ 90 (170)
+.+++..|++|+...-...+.-.-.++.++.++-+=+.-++.|.+++-.+|..+
T Consensus 342 Lk~~l~~f~~HR~~Vi~RRT~feLrKA~eRaHiL~GL~~AL~niDevI~lIr~S 395 (864)
T TIGR01063 342 LKELLEAFVEHRKDVITRRTIFELRKAEERAHILEGLLIALDNIDEVIALIRAS 395 (864)
T ss_pred HHHHHHHHHHCCEEEEEEEHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 889999998423133552100010226557899999999997212899997427
No 30
>PRK13339 malate:quinone oxidoreductase; Reviewed
Probab=20.98 E-value=57 Score=13.26 Aligned_cols=30 Identities=23% Similarity=0.107 Sum_probs=16.8
Q ss_pred HHHHHHHHHHCCCCC-------CCCHHHHHHHHHHHH
Q ss_conf 999999986435578-------103398899999983
Q gi|254780345|r 108 LRAGVLELIECHSVP-------VEVIISEYVCIAHDF 137 (170)
Q Consensus 108 Lr~a~~El~~~~~~p-------~~vvInE~V~lak~f 137 (170)
...|.||+=|.+.-+ +.+.|||.-++++.|
T Consensus 57 GHaa~CElNYTp~~~dg~i~i~KA~~IneqFe~S~Qf 93 (497)
T PRK13339 57 GHAALCELNYTVQQADGSIDIKKAKEINEQFEISKQF 93 (497)
T ss_pred CCHHHHHHCCCCCCCCCCEEHHHHHHHHHHHHHHHHH
T ss_conf 1001022048876569824179999999999999999
No 31
>pfam06039 Mqo Malate:quinone oxidoreductase (Mqo). This family consists of several bacterial Malate:quinone oxidoreductase (Mqo) proteins (EC:1.1.99.16). Mqo takes part in the citric acid cycle. It oxidizes L-malate to oxaloacetate and donates electrons to ubiquinone-1 and other artificial acceptors or, via the electron transfer chain, to oxygen. NAD is not an acceptor and the natural direct acceptor for the enzyme is most likely a quinone. The enzyme is therefore called malate:quinone oxidoreductase, abbreviated to Mqo. Mqo is a peripheral membrane protein and can be released from the membrane by addition of chelators.
Probab=20.76 E-value=58 Score=13.23 Aligned_cols=29 Identities=24% Similarity=0.208 Sum_probs=11.3
Q ss_pred HHHHHHHHHCCCCC-------CCCHHHHHHHHHHHH
Q ss_conf 99999986435578-------103398899999983
Q gi|254780345|r 109 RAGVLELIECHSVP-------VEVIISEYVCIAHDF 137 (170)
Q Consensus 109 r~a~~El~~~~~~p-------~~vvInE~V~lak~f 137 (170)
+.|.||+=|.+.-+ +.+.|||.-++++.|
T Consensus 56 Haa~cElNYTpe~~dg~i~i~KA~~IneqFe~Srqf 91 (489)
T pfam06039 56 HSALCELNYTPEGADGSIDISKAVKINEQFQISRQF 91 (489)
T ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 002134148876568844279999999999999999
No 32
>KOG1586 consensus
Probab=20.57 E-value=57 Score=13.27 Aligned_cols=52 Identities=23% Similarity=0.379 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 9999999999864355781033988999999833877231499999999952
Q gi|254780345|r 105 CSILRAGVLELIECHSVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK 156 (170)
Q Consensus 105 ~~iLr~a~~El~~~~~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~ 156 (170)
--.|+.|+|-+.....+...-++-.|-++--.|.+..+.+|+--.++.|-.+
T Consensus 196 dyflkAgLChl~~~D~v~a~~ALeky~~~dP~F~dsREckflk~L~~aieE~ 247 (288)
T KOG1586 196 DYFLKAGLCHLCKADEVNAQRALEKYQELDPAFTDSRECKFLKDLLDAIEEQ 247 (288)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 8999999886730207789999998875398646408879999999988554
Done!