Query 027155
Match_columns 227
No_of_seqs 181 out of 1587
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 05:47:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027155.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027155hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0781 NusB Transcription ter 100.0 4E-33 8.6E-38 231.3 13.3 142 17-212 6-149 (151)
2 PF01029 NusB: NusB family; I 100.0 1.1E-32 2.3E-37 220.6 14.5 92 113-206 42-134 (134)
3 PRK00202 nusB transcription an 100.0 3.7E-32 8.1E-37 219.5 14.4 133 20-211 2-135 (137)
4 cd00619 Terminator_NusB Transc 100.0 1.2E-31 2.6E-36 214.0 13.5 128 21-207 1-129 (130)
5 TIGR01951 nusB transcription a 100.0 2.8E-31 6.2E-36 211.4 13.6 127 21-206 1-128 (129)
6 cd00620 Methyltransferase_Sun 100.0 1.1E-29 2.5E-34 202.3 14.3 124 23-207 2-125 (126)
7 cd00447 NusB_Sun RNA binding d 99.9 4E-27 8.8E-32 186.9 14.3 124 24-207 2-128 (129)
8 PRK09634 nusB transcription an 99.9 1.1E-26 2.5E-31 201.3 15.5 93 114-208 110-202 (207)
9 PRK10901 16S rRNA methyltransf 99.9 6.9E-26 1.5E-30 213.3 14.5 124 23-208 3-126 (427)
10 PRK14904 16S rRNA methyltransf 99.9 4.4E-25 9.5E-30 208.8 13.8 126 23-208 3-129 (445)
11 PRK14901 16S rRNA methyltransf 99.9 8.3E-25 1.8E-29 206.3 13.1 126 23-209 2-128 (434)
12 PRK14902 16S rRNA methyltransf 99.9 1.3E-24 2.9E-29 205.1 12.7 125 23-208 4-129 (444)
13 TIGR00563 rsmB ribosomal RNA s 99.9 7.4E-23 1.6E-27 192.5 12.5 92 114-209 30-122 (426)
14 PRK14903 16S rRNA methyltransf 99.9 5E-22 1.1E-26 187.9 12.4 118 23-207 4-122 (431)
15 PF09185 DUF1948: Domain of un 82.9 23 0.0005 28.5 11.0 85 114-204 55-139 (140)
16 TIGR01446 DnaD_dom DnaD and ph 51.7 21 0.00045 25.2 3.3 32 175-207 32-63 (73)
17 PF07261 DnaB_2: Replication i 39.8 34 0.00075 24.0 2.9 33 174-207 31-63 (77)
18 PF12862 Apc5: Anaphase-promot 32.4 42 0.00092 24.9 2.5 49 157-205 42-91 (94)
19 PF11573 Med23: Mediator compl 28.5 1.3E+02 0.0027 33.7 6.1 67 116-187 1093-1162(1341)
20 PF10752 DUF2533: Protein of u 22.3 93 0.002 23.8 2.7 35 170-205 24-58 (84)
21 cd00923 Cyt_c_Oxidase_Va Cytoc 21.3 1.1E+02 0.0024 24.3 3.0 49 156-204 22-72 (103)
22 COG3935 DnaD Putative primosom 20.9 93 0.002 28.2 2.9 32 174-206 160-191 (246)
No 1
>COG0781 NusB Transcription termination factor [Transcription]
Probab=100.00 E-value=4e-33 Score=231.25 Aligned_cols=142 Identities=25% Similarity=0.363 Sum_probs=117.5
Q ss_pred CCCccHHHHHHHHHHHHHHHhcCC-ChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhH
Q 027155 17 RFCSPRAARELALLVVYAACLEGS-DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEE 95 (227)
Q Consensus 17 ~~~~R~~aRe~Avq~Lyq~~~~~~-~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~ 95 (227)
+..+|+++|++|+|+||||++++. ++.++++.... .|..+ +.
T Consensus 6 ~~~~R~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~~---------------~~~~~---d~------------------- 48 (151)
T COG0781 6 PKLTRRQARELAVQALYQWELSGSVSAEDILEDIEE---------------EFVEN---EL------------------- 48 (151)
T ss_pred ccchHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHH---------------HHhhc---cc-------------------
Confidence 567899999999999999999765 45555543322 00000 00
Q ss_pred HHHHHHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcC-Cch
Q 027155 96 ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRH 174 (227)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~-iP~ 174 (227)
+ ....+..|+..|+.||.+|+..||.+|.++++ +|+++||+.+ ||+|||+|+|||+|.+ +|.
T Consensus 49 ------~---------~~~~~~~~~~~lv~gv~~~~~~iD~~I~~~L~-~w~~~rL~~v-erAILRla~yEl~~~~dvP~ 111 (151)
T COG0781 49 ------D---------IELADSEYFRSLVKGVLENQEELDELISPHLK-KWSLERLDLV-ERAILRLALYELLFRDDVPY 111 (151)
T ss_pred ------c---------hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHc-cCCHHHhhHH-HHHHHHHHHHHHHhcCCCCC
Confidence 0 01147899999999999999999999999994 6999999997 9999999999999975 999
Q ss_pred hhHHHHHHHHHHhhCCCCCCChhHHHHhHHHhhhhccc
Q 027155 175 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA 212 (227)
Q Consensus 175 ~vaInEaVeLAK~~g~~~s~~FVNaVLr~i~r~~~~~e 212 (227)
.|+|||||+|||.||.+++++||||||+++++..++.+
T Consensus 112 ~VvInEaielaK~f~~e~s~kFINgVLd~i~~~~~~~~ 149 (151)
T COG0781 112 KVVINEAIELAKKFSGEDSHKFVNGVLDKIAKKLRPKE 149 (151)
T ss_pred cchHHHHHHHHHHhCCCCchHHHHHHHHHHHHHhhhhc
Confidence 99999999999999999999999999999998876543
No 2
>PF01029 NusB: NusB family; InterPro: IPR006027 This domain is found in a number of functionally different proteins: NusB a prokaryotic transcription factor involved in antitermination TIM44, the mitochondrial inner membrane translocase subunit RsmB, the 16S rRNA m5C967 methyltransferase NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site. Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. An N-terminal arginine-rich sequence is the probable RNA binding site, exhibiting aromatic residues as potential stacking partners for the RNA bases. The RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. In certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes [, ]. The antitermination proteins of E. 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.; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1SQG_A 1SQF_A 3IMQ_A 3D3C_C 3D3B_A 1EY1_A 1EYV_A 1TZV_A 1TZT_B 1TZX_B ....
Probab=100.00 E-value=1.1e-32 Score=220.57 Aligned_cols=92 Identities=28% Similarity=0.437 Sum_probs=87.6
Q ss_pred cHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhc-CCchhhHHHHHHHHHHhhCCC
Q 027155 113 SKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDG 191 (227)
Q Consensus 113 ~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~-~iP~~vaInEaVeLAK~~g~~ 191 (227)
+..|++|+++|++||++|+..||++|++++ ++|+++|++++ +++|||+|+|||+|+ ++|++++|||||++||+||++
T Consensus 42 ~~~d~~~~~~lv~gv~~~~~~ld~~i~~~~-~~~~~~rl~~~-~~~iLrla~~El~~~~~~p~~v~InEaVelak~~~~~ 119 (134)
T PF01029_consen 42 SEEDRAFARELVYGVLRNKEELDALISKLL-KNWPLERLPPV-DRAILRLAIYELLFLDDIPPHVAINEAVELAKKYGDE 119 (134)
T ss_dssp THHHHHHHHHHHHHHHHTHHHHHHHHHHTS-TSSTGGGSGHH-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHS-T
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCccccCHH-HHHHHHHHHHHHHhcCCCCccchHHHHHHHHHHhCCC
Confidence 568999999999999999999999999987 68999999997 799999999999998 899999999999999999999
Q ss_pred CCCChhHHHHhHHHh
Q 027155 192 AAPRIINGCLRTFVR 206 (227)
Q Consensus 192 ~s~~FVNaVLr~i~r 206 (227)
+++||||||||+++|
T Consensus 120 ~~~~fVNaVL~~~~R 134 (134)
T PF01029_consen 120 KSAGFVNAVLRRIAR 134 (134)
T ss_dssp THHHHHHHHHHHHHH
T ss_pred CcchhHHHHHHHhhC
Confidence 999999999999986
No 3
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=100.00 E-value=3.7e-32 Score=219.46 Aligned_cols=133 Identities=29% Similarity=0.428 Sum_probs=119.4
Q ss_pred ccHHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHH
Q 027155 20 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI 99 (227)
Q Consensus 20 ~R~~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~ 99 (227)
+|+.+|+.|+++||+++..|.++.++++..+.. ..
T Consensus 2 ~r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~------------------~~--------------------------- 36 (137)
T PRK00202 2 ARRKAREAAVQALYQWELSGNDIAEIIEAQLLE------------------EQ--------------------------- 36 (137)
T ss_pred chHHHHHHHHHHHHHHHccCCCHHHHHHHHHHh------------------cc---------------------------
Confidence 589999999999999999999999988765431 00
Q ss_pred HHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhc-CCchhhHH
Q 027155 100 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVI 178 (227)
Q Consensus 100 ~~~~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~-~iP~~vaI 178 (227)
.+..|++|+++||+||++|+..||++|++++ ++|++++++++ +++|||+|+|||+|+ ++|++++|
T Consensus 37 ------------~~~~d~~~~~~lv~gvlr~~~~lD~ii~~~l-~~~~~~~l~~~-~~~iLr~a~~Ell~~~~~p~~~vi 102 (137)
T PRK00202 37 ------------YDKADPAYFRSLVRGVVENQAELDELISPYL-KDWTLERLDPV-ERAILRLALYELLFRDDVPYKVVI 102 (137)
T ss_pred ------------cchhhHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCHHHhhHH-HHHHHHHHHHHHHhCCCCCCcchH
Confidence 1345799999999999999999999999999 56999999997 799999999999998 89999999
Q ss_pred HHHHHHHHhhCCCCCCChhHHHHhHHHhhhhcc
Q 027155 179 NEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT 211 (227)
Q Consensus 179 nEaVeLAK~~g~~~s~~FVNaVLr~i~r~~~~~ 211 (227)
||||++||.|+.+++++|||||||++.|.....
T Consensus 103 nEaV~lak~~~~~~~~~fVNaVLr~i~r~~~~~ 135 (137)
T PRK00202 103 NEAIELAKKFGDEDSHKFVNGVLDKIAKELRPA 135 (137)
T ss_pred HHHHHHHHHHCCCCcchhHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999987654
No 4
>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=99.97 E-value=1.2e-31 Score=214.04 Aligned_cols=128 Identities=30% Similarity=0.399 Sum_probs=114.3
Q ss_pred cHHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHH
Q 027155 21 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 100 (227)
Q Consensus 21 R~~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~ 100 (227)
|+.+|+.|+|+||+++.+|.++.++++..+.. .
T Consensus 1 r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~------------------~----------------------------- 33 (130)
T cd00619 1 RRRARELAVQALYAWELAPEILAEVVSLLELL------------------Q----------------------------- 33 (130)
T ss_pred ChHHHHHHHHHHHHHHhcCCCHHHHHHHHHHh------------------c-----------------------------
Confidence 57899999999999999999988887754430 0
Q ss_pred HhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcC-CchhhHHH
Q 027155 101 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVIN 179 (227)
Q Consensus 101 ~~~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~-iP~~vaIn 179 (227)
..++.|++|+++||+|+++|+..||++|++++ ++|++++++++ +++|||+|+|||+|++ +|++++||
T Consensus 34 ----------~~~~~d~~~~~~lv~gvlr~~~~ld~ii~~~l-~~~~~~~l~~~-~~~iLria~~el~~~~~~p~~~vin 101 (130)
T cd00619 34 ----------YKSKKVLPFALKLVRGVLENIEEIDELIEKHL-RNWSLDRLAIV-ERAILRLAVYELLFLPDVPHPVVIN 101 (130)
T ss_pred ----------ccchhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCCHHHhhHH-HHHHHHHHHHHHHhCCCCCCcchHH
Confidence 01245899999999999999999999999999 58999999997 7999999999999986 99999999
Q ss_pred HHHHHHHhhCCCCCCChhHHHHhHHHhh
Q 027155 180 EAVDLAKRFCDGAAPRIINGCLRTFVRN 207 (227)
Q Consensus 180 EaVeLAK~~g~~~s~~FVNaVLr~i~r~ 207 (227)
|||++||+|+++++++|||||||++.|+
T Consensus 102 EaV~lak~~~~~~~~~fVNaVLr~i~r~ 129 (130)
T cd00619 102 EAIELAKRFGGDDSHKFVNGVLDKIAKD 129 (130)
T ss_pred HHHHHHHHHCCCcchhHHHHHHHHHhhc
Confidence 9999999999999999999999999875
No 5
>TIGR01951 nusB transcription antitermination factor NusB. A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10.
Probab=99.97 E-value=2.8e-31 Score=211.35 Aligned_cols=127 Identities=29% Similarity=0.407 Sum_probs=114.3
Q ss_pred cHHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHH
Q 027155 21 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 100 (227)
Q Consensus 21 R~~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~ 100 (227)
|+.+|+.|+++||+++..|.+++++++..+.. .
T Consensus 1 ~~~~R~~a~~~l~~~~~~~~~~~~~l~~~~~~------------------~----------------------------- 33 (129)
T TIGR01951 1 RRKARELALQALYQWELSGNDVEEIIEEFLEE------------------R----------------------------- 33 (129)
T ss_pred ChHHHHHHHHHHHHHHcCCCCHHHHHHHHHHh------------------c-----------------------------
Confidence 56789999999999999999999988765541 0
Q ss_pred HhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhc-CCchhhHHH
Q 027155 101 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVIN 179 (227)
Q Consensus 101 ~~~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~-~iP~~vaIn 179 (227)
+ .++.|++|+++||+|+++|+..||++|+++++ +|++++++++ +++|||+|+|||+|+ ++|++++||
T Consensus 34 -~---------l~~~d~~~~~~lv~~~lr~~~~ld~~i~~~~~-~~~~~~l~~~-~~~iLr~a~~el~~~~~~p~~avin 101 (129)
T TIGR01951 34 -E---------LDEEDREYFLELVRGVLENQEEIDELISPHLK-DWSLERLDPV-DRAILRLAAYELLYRPDVPYKVVIN 101 (129)
T ss_pred -c---------cchhHHHHHHHHHHHHHHhHHHHHHHHHHHhc-CCCHHHhhHH-HHHHHHHHHHHHHhCCCCCCcchHH
Confidence 0 13457999999999999999999999999994 7999999997 699999999999998 799999999
Q ss_pred HHHHHHHhhCCCCCCChhHHHHhHHHh
Q 027155 180 EAVDLAKRFCDGAAPRIINGCLRTFVR 206 (227)
Q Consensus 180 EaVeLAK~~g~~~s~~FVNaVLr~i~r 206 (227)
|+|++||.|+.+++++|||||||++.|
T Consensus 102 eaV~lak~~~~~~~~~fVNaVLr~i~r 128 (129)
T TIGR01951 102 EAVELAKKFGDEDSHKFVNGVLDKIAK 128 (129)
T ss_pred HHHHHHHHHCCCCchhhHHHHHHHHhh
Confidence 999999999999999999999999986
No 6
>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=99.97 E-value=1.1e-29 Score=202.33 Aligned_cols=124 Identities=18% Similarity=0.154 Sum_probs=109.5
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 027155 23 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 102 (227)
Q Consensus 23 ~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 102 (227)
.+|+.|+|+||++..+|.++.+++...+.. .
T Consensus 2 ~~R~~A~~~L~~v~~~~~~~~~~l~~~~~~------------------~------------------------------- 32 (126)
T cd00620 2 NARSTAAEVLRDVLQRGASLNAVLSALQKK------------------D------------------------------- 32 (126)
T ss_pred CHHHHHHHHHHHHHHcCCcHHHHHHHHHHh------------------c-------------------------------
Confidence 369999999999999999999988765431 0
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcCCchhhHHHHHH
Q 027155 103 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAV 182 (227)
Q Consensus 103 ~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~iP~~vaInEaV 182 (227)
.++.|++|+++|++|+++|+..||++|+++++ |++.+++++ +++|||+|+|||+|+++|++++|||||
T Consensus 33 ---------~~~~d~~~~~~lv~g~~r~~~~ld~~i~~~l~--~~~~~~~~~-~~~iLr~a~~el~~~~~p~~avvneaV 100 (126)
T cd00620 33 ---------KSDRDRGLATELVYGTLRWLALLDWIINPLLK--KPDVGKDPD-VRNLLRLGLYQLLYLDVPPHAAVDETV 100 (126)
T ss_pred ---------CCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhC--CCccccCHH-HHHHHHHHHHHHHhcCCCchHHHHHHH
Confidence 01357999999999999999999999999994 445689997 699999999999999899999999999
Q ss_pred HHHHhhCCCCCCChhHHHHhHHHhh
Q 027155 183 DLAKRFCDGAAPRIINGCLRTFVRN 207 (227)
Q Consensus 183 eLAK~~g~~~s~~FVNaVLr~i~r~ 207 (227)
++||.|+++++++|||||||++.|+
T Consensus 101 elak~~~~~~~~~fVNaVLr~i~r~ 125 (126)
T cd00620 101 EIAKIRKDLGRAGLVNAVLRRFERE 125 (126)
T ss_pred HHHHHhCCCchhhHHHHHHHHHhcc
Confidence 9999999999999999999999874
No 7
>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=99.95 E-value=4e-27 Score=186.94 Aligned_cols=124 Identities=26% Similarity=0.400 Sum_probs=109.0
Q ss_pred HHHHHHHHHHHHHhc-CCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 027155 24 ARELALLVVYAACLE-GSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 102 (227)
Q Consensus 24 aRe~Avq~Lyq~~~~-~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 102 (227)
+|+.|+++||+++.+ |.++..++......
T Consensus 2 ~R~~a~~~L~~~~~~~~~~~~~~~~~~~~~-------------------------------------------------- 31 (129)
T cd00447 2 AREIAFQALYQVEIRNGISLEAVLSALEKL-------------------------------------------------- 31 (129)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHc--------------------------------------------------
Confidence 699999999999988 78887776543320
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhc--CCchhhHHHH
Q 027155 103 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV--GTRHQIVINE 180 (227)
Q Consensus 103 ~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~--~iP~~vaInE 180 (227)
. ..+.|++|+++||+||++|+..||++|++++ ++|+++|++.+ ++.||+++.+|+.++ ++|++++|||
T Consensus 32 ------~--~~~~d~~~~~~lv~gv~r~~~~ld~~i~~~~-~~~~~~r~~~~-~~~il~l~~~el~~~~~~~p~~~vine 101 (129)
T cd00447 32 ------Q--LAKKDRPFALELVYGVLRNLPELDDIISPLL-KKWLLDRLDKV-DRAILRLLLYELYQLLYDVPPPVAINE 101 (129)
T ss_pred ------c--cchhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCChhhhhHH-HHHHHHHHHHHHHhCcCCCCchhHHHH
Confidence 0 1235799999999999999999999999999 68999999996 899999999998886 4899999999
Q ss_pred HHHHHHhhCCCCCCChhHHHHhHHHhh
Q 027155 181 AVDLAKRFCDGAAPRIINGCLRTFVRN 207 (227)
Q Consensus 181 aVeLAK~~g~~~s~~FVNaVLr~i~r~ 207 (227)
+|++||+|+.+++++|||||||++.++
T Consensus 102 aVelak~~~~~~~~~fVNaVLr~~~r~ 128 (129)
T cd00447 102 AVELAKRFGDDDSAKFVNGVLRRIAKE 128 (129)
T ss_pred HHHHHHHHCCCCcchhHHHHHHHHhhc
Confidence 999999999999999999999999875
No 8
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=99.95 E-value=1.1e-26 Score=201.31 Aligned_cols=93 Identities=33% Similarity=0.489 Sum_probs=90.0
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcCCchhhHHHHHHHHHHhhCCCCC
Q 027155 114 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAA 193 (227)
Q Consensus 114 ~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~iP~~vaInEaVeLAK~~g~~~s 193 (227)
..+++|+++||+||++|+..||++|+.++ ++|+++|++.+ +|+|||+|+|||+|+++|++++|||||++||+|+.+++
T Consensus 110 ~~~r~~a~~Lv~gvlr~~~~LD~iI~~~l-~~W~l~rL~~i-dr~ILRlavyELl~l~~P~~vaINEAVeLAK~~~~~~~ 187 (207)
T PRK09634 110 EEVREYALERIGAVIRNRKEIDQLLDTVM-VGWQLKRLPRI-DRDILRLAVVEILFLNTPAAVAINEAVELAKRYSDEQG 187 (207)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHh-ccccccCCCHH-HHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHhCCCcc
Confidence 67899999999999999999999999999 69999999996 89999999999999999999999999999999999999
Q ss_pred CChhHHHHhHHHhhh
Q 027155 194 PRIINGCLRTFVRNL 208 (227)
Q Consensus 194 ~~FVNaVLr~i~r~~ 208 (227)
++|||||||++.|..
T Consensus 188 ~~FVNaVLrri~r~~ 202 (207)
T PRK09634 188 RRFINGVLRRLQDAL 202 (207)
T ss_pred cchHHHHHHHHHHHh
Confidence 999999999999876
No 9
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=99.93 E-value=6.9e-26 Score=213.25 Aligned_cols=124 Identities=17% Similarity=0.172 Sum_probs=112.4
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 027155 23 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 102 (227)
Q Consensus 23 ~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 102 (227)
.+|+.|+|+||+++.+|.++.+++++.+..
T Consensus 3 ~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~-------------------------------------------------- 32 (427)
T PRK10901 3 NLRALAAAAILQVVDQGQSLSAALPALQQK-------------------------------------------------- 32 (427)
T ss_pred hHHHHHHHHHHHHHHcCCcHHHHHHHHHhh--------------------------------------------------
Confidence 589999999999999999998888764420
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcCCchhhHHHHHH
Q 027155 103 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAV 182 (227)
Q Consensus 103 ~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~iP~~vaInEaV 182 (227)
.+..|++|+++||+||++|+..||++|++++ +|++++++++ +|+|||+|+|||+|+++|++++|||+|
T Consensus 33 ---------l~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~--~~~~~~l~~~-~r~iLrla~yell~~~iP~~a~vneaV 100 (427)
T PRK10901 33 ---------VSDKDRALLQELCYGVLRRLPRLEWLIAQLL--AKPLKGKQRI-VHALLLVGLYQLLYTRIPAHAAVDETV 100 (427)
T ss_pred ---------CCHHHHHHHHHHHHHHHHhHHHHHHHHHHHh--CCCccccCHH-HHHHHHHHHHHHhccCCCcchHHHHHH
Confidence 1235799999999999999999999999998 3799999997 699999999999999999999999999
Q ss_pred HHHHhhCCCCCCChhHHHHhHHHhhh
Q 027155 183 DLAKRFCDGAAPRIINGCLRTFVRNL 208 (227)
Q Consensus 183 eLAK~~g~~~s~~FVNaVLr~i~r~~ 208 (227)
++||+|+++++++|||||||++.+..
T Consensus 101 elak~~~~~~~~~fVNaVLr~i~~~~ 126 (427)
T PRK10901 101 EAAKALKRPWAKGLVNAVLRRFQREQ 126 (427)
T ss_pred HHHHhcCCccchhhHHHHHHHhhhhh
Confidence 99999999999999999999999863
No 10
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=99.92 E-value=4.4e-25 Score=208.79 Aligned_cols=126 Identities=21% Similarity=0.245 Sum_probs=113.5
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 027155 23 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 102 (227)
Q Consensus 23 ~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 102 (227)
.+|++|+|+||+++.++.+++.++.+++.. ..
T Consensus 3 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~------------------~~------------------------------ 34 (445)
T PRK14904 3 TARELALQVLQELETGERKSDTLLHRMLER------------------SS------------------------------ 34 (445)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHHHHh------------------cC------------------------------
Confidence 589999999999999999998888876641 00
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhc-CCchhhHHHHH
Q 027155 103 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEA 181 (227)
Q Consensus 103 ~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~-~iP~~vaInEa 181 (227)
.+..|++|+++||+||++|+..||++|++++ +|++.|++++ +|+|||+|+|||+|+ ++|++++|||+
T Consensus 35 ---------l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~--~~~~~rl~~~-~r~iLrla~~ell~~~~~p~~a~vnea 102 (445)
T PRK14904 35 ---------LERNDRALATELVNGVLRYRLQLDFIISRFY--HHDLEKAAPV-LKNILRLGVYQLLFLDRVPRWAAVNEC 102 (445)
T ss_pred ---------CChHHHHHHHHHHHHHHHHHHHHHHHHHHHc--CCChhhCCHH-HHHHHHHHHHHHHhCCCCCCeeeHHHH
Confidence 1346899999999999999999999999998 3899999997 799999999999997 58999999999
Q ss_pred HHHHHhhCCCCCCChhHHHHhHHHhhh
Q 027155 182 VDLAKRFCDGAAPRIINGCLRTFVRNL 208 (227)
Q Consensus 182 VeLAK~~g~~~s~~FVNaVLr~i~r~~ 208 (227)
|++||+|+++++++|||||||+++++.
T Consensus 103 Velak~~~~~~~~~fVNgVLr~i~~~~ 129 (445)
T PRK14904 103 VKLARKYKGEHMAKLVNGVLRNISPET 129 (445)
T ss_pred HHHHHHhCCCccccchHHHHHHHHHhh
Confidence 999999999999999999999999975
No 11
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=99.92 E-value=8.3e-25 Score=206.34 Aligned_cols=126 Identities=21% Similarity=0.236 Sum_probs=110.3
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 027155 23 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 102 (227)
Q Consensus 23 ~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 102 (227)
.+|+.|+++||+++. |.++.+++++.+.. +.
T Consensus 2 ~~R~~A~~~L~~i~~-~~~~~~~l~~~~~~------------------~~------------------------------ 32 (434)
T PRK14901 2 NARQLAWEILQAVAR-GAYADVALERVLRK------------------YP------------------------------ 32 (434)
T ss_pred CHHHHHHHHHHHHHc-CCchHHHHHHHHHh------------------cC------------------------------
Confidence 379999999999997 67888888776541 00
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcC-CchhhHHHHH
Q 027155 103 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEA 181 (227)
Q Consensus 103 ~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~-iP~~vaInEa 181 (227)
.+..|++|+++||+||+||+..||++|++++ +|++.+++++ +|+|||+|+|||+|++ +|++++|||+
T Consensus 33 ---------l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~--~~~~~~l~~~-~r~iLrla~yel~~~~~~p~~aavnea 100 (434)
T PRK14901 33 ---------LSGADRALVTELVYGCIRRRRTLDAWIDQLG--KKPAHKQPPD-LRWLLHLGLYQLRYMDRIPASAAVNTT 100 (434)
T ss_pred ---------CChhHHHHHHHHHHHHHHhHHHHHHHHHHhc--CCChhhcCHH-HHHHHHHHHHHHHhCccCCcHHHHHHH
Confidence 1346899999999999999999999999997 3777889997 6999999999999984 8999999999
Q ss_pred HHHHHhhCCCCCCChhHHHHhHHHhhhh
Q 027155 182 VDLAKRFCDGAAPRIINGCLRTFVRNLE 209 (227)
Q Consensus 182 VeLAK~~g~~~s~~FVNaVLr~i~r~~~ 209 (227)
|++||+|+++++++|||||||++.|...
T Consensus 101 Velak~~~~~~~~~fVNgVLr~~~r~~~ 128 (434)
T PRK14901 101 VELAKQNGLGGLAGVVNGILRQYLRARE 128 (434)
T ss_pred HHHHHHcCchhhhhhcCHHHHHHHHhhh
Confidence 9999999999999999999999999643
No 12
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=99.92 E-value=1.3e-24 Score=205.11 Aligned_cols=125 Identities=19% Similarity=0.218 Sum_probs=112.1
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 027155 23 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 102 (227)
Q Consensus 23 ~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 102 (227)
.+|+.|+++||+++.+|.+++++++.++.. +.
T Consensus 4 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~------------------~~------------------------------ 35 (444)
T PRK14902 4 NARELALEVLIKVENNGAYSNIALNKVLKK------------------SE------------------------------ 35 (444)
T ss_pred cHHHHHHHHHHHHHhcCCCHHHHHHHHHHh------------------cC------------------------------
Confidence 689999999999999999999998876541 00
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhc-CCchhhHHHHH
Q 027155 103 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEA 181 (227)
Q Consensus 103 ~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~-~iP~~vaInEa 181 (227)
++..|++|+++||+|+++|+..||++|+++++ + ++|++++ +|+|||+|+|||+|+ ++|++++||||
T Consensus 36 ---------l~~~d~~~~~~lv~g~lr~~~~ld~~i~~~~~--~-~~~l~~~-~r~iLrla~~el~~~~~~p~~~~inea 102 (444)
T PRK14902 36 ---------LSDKDKALLTELVYGTIQRKLTLDYYLAPFIK--K-RKKLDPW-VRNLLRMSLYQLLYLDKVPDHAAVNEA 102 (444)
T ss_pred ---------CChHHHHHHHHHHHHHHHhHHHHHHHHHHHhh--h-hhhCCHH-HHHHHHHHHHHHHhccCCCCceeHHHH
Confidence 13468999999999999999999999999993 3 8999997 799999999999997 59999999999
Q ss_pred HHHHHhhCCCCCCChhHHHHhHHHhhh
Q 027155 182 VDLAKRFCDGAAPRIINGCLRTFVRNL 208 (227)
Q Consensus 182 VeLAK~~g~~~s~~FVNaVLr~i~r~~ 208 (227)
|++||.|+++++++|||||||++.+..
T Consensus 103 v~lak~~~~~~~~~fVNaVL~~i~~~~ 129 (444)
T PRK14902 103 VEIAKKRGHKGIAKFVNGVLRNILREG 129 (444)
T ss_pred HHHHHHhCCCchhHHHHHHHHHHhhcc
Confidence 999999999999999999999999864
No 13
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.
Probab=99.89 E-value=7.4e-23 Score=192.53 Aligned_cols=92 Identities=20% Similarity=0.145 Sum_probs=83.1
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhh-cCCchhhHHHHHHHHHHhhCCCC
Q 027155 114 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGA 192 (227)
Q Consensus 114 ~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~-~~iP~~vaInEaVeLAK~~g~~~ 192 (227)
..|++|+++||+||++|+..||++|++++ +|++++++++ .+ +||+++||++| +++|++++|||||++||+|++++
T Consensus 30 ~~d~~~~~~lv~gv~r~~~~lD~~i~~~~--~~~~~~l~~~-~~-~L~~~~~e~l~~~~~p~~aainEaVelaK~~~~~~ 105 (426)
T TIGR00563 30 DQDRALLQELCFGVLRTLSQLDWLIKKLM--DRPMKGKPRT-VH-YLILVGLYQLLYTRIPAHAAVAETVEGAKAIKRKG 105 (426)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHh--CCCccccCHH-HH-HHHHHHHHHHhcCCCCCEehHHHHHHHHHhcCCcc
Confidence 46799999999999999999999999998 3788999986 46 88888888766 68999999999999999999999
Q ss_pred CCChhHHHHhHHHhhhh
Q 027155 193 APRIINGCLRTFVRNLE 209 (227)
Q Consensus 193 s~~FVNaVLr~i~r~~~ 209 (227)
+++|||||||++.|+..
T Consensus 106 ~~~fVNgVLr~i~r~~~ 122 (426)
T TIGR00563 106 LKGLVNGVLRRFQREQE 122 (426)
T ss_pred chhhHHHHHHHHhhcch
Confidence 99999999999999643
No 14
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=99.87 E-value=5e-22 Score=187.91 Aligned_cols=118 Identities=17% Similarity=0.096 Sum_probs=103.9
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 027155 23 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 102 (227)
Q Consensus 23 ~aRe~Avq~Lyq~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 102 (227)
++|+.|+.+|+++...|.....++++.+..
T Consensus 4 ~~R~~A~~~L~~v~~~~~~~~~~l~~~~~~-------------------------------------------------- 33 (431)
T PRK14903 4 NVRLLAYRLLRKYEKEKFIFREDVDSVLSF-------------------------------------------------- 33 (431)
T ss_pred CHHHHHHHHHHHHHhCCCchHHHHHHHHHh--------------------------------------------------
Confidence 479999999999999998888887654320
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcC-CchhhHHHHH
Q 027155 103 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEA 181 (227)
Q Consensus 103 ~~~~~~~~~~~~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~-iP~~vaInEa 181 (227)
++..|++|+++||+||++++..||++|++++ ++| +++++ +|+|||+|+|||+|++ +|++++|||+
T Consensus 34 ---------l~~~d~~~~~~lv~gvlr~~~~lD~~i~~~~-~~~---~l~~~-~r~iLr~~~yel~~~~~~p~~aavnea 99 (431)
T PRK14903 34 ---------LDDKDRRFFKELVWGVVRKEELLDWYINQLL-KKK---DIPPA-VRVALRMGAYQLLFMNSVPDYAAVSET 99 (431)
T ss_pred ---------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCC---CCCHH-HHHHHHHHHHHHHhccCCCcceeHHHH
Confidence 2357899999999999999999999999999 457 58898 6999999999999987 6999999999
Q ss_pred HHHHHhhCCCCCCChhHHHHhHHHhh
Q 027155 182 VDLAKRFCDGAAPRIINGCLRTFVRN 207 (227)
Q Consensus 182 VeLAK~~g~~~s~~FVNaVLr~i~r~ 207 (227)
|++||.+ .+++|||||||++.|+
T Consensus 100 V~lak~~---~~~~fVNaVLr~~~r~ 122 (431)
T PRK14903 100 VKLVKNE---NFKKLVNAVLRRLRTV 122 (431)
T ss_pred HHHHhcc---chHHHHHHHHHHHHHh
Confidence 9999986 5679999999999986
No 15
>PF09185 DUF1948: Domain of unknown function (DUF1948); InterPro: IPR015268 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 []. ; PDB: 1Q8C_A.
Probab=82.86 E-value=23 Score=28.50 Aligned_cols=85 Identities=13% Similarity=0.161 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchHHHHHHHHHHHHhhhhcCCchhhHHHHHHHHHHhhCCCCC
Q 027155 114 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAA 193 (227)
Q Consensus 114 ~~Dr~~~~~Lv~gvlr~~~~lD~iI~~~l~k~w~l~Rl~~vldraILRlalyELl~~~iP~~vaInEaVeLAK~~g~~~s 193 (227)
.+-..|...+-..-.+|+.++..-.++... ++++-. -.++...|+.|-.-..+.....|+||+-+...|+....
T Consensus 55 e~~~~f~~~ie~qq~~nq~eiq~kynkisg-----kkidll-t~avilcalseq~a~~tdkplliseallimdhysq~~e 128 (140)
T PF09185_consen 55 ENCFSFQKKIENQQQRNQAEIQSKYNKISG-----KKIDLL-TKAVILCALSEQHAQNTDKPLLISEALLIMDHYSQVPE 128 (140)
T ss_dssp HHHHHHHHHHHHHHHH---S-------------------HH-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHTT---T
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccccc-----chhhHH-HHHHHHHHhhHHHhhcCCCchhHHHHHHHHHHHhhchh
Confidence 344566666666667777777666666642 344554 57888888888776678889999999999999998777
Q ss_pred CChhHHHHhHH
Q 027155 194 PRIINGCLRTF 204 (227)
Q Consensus 194 ~~FVNaVLr~i 204 (227)
.+=.+|.||++
T Consensus 129 kkqthalldkl 139 (140)
T PF09185_consen 129 KKQTHALLDKL 139 (140)
T ss_dssp TS-S-TTTS--
T ss_pred HHHHHHHHHhh
Confidence 78888888875
No 16
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of 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=51.70 E-value=21 Score=25.21 Aligned_cols=32 Identities=25% Similarity=0.222 Sum_probs=25.4
Q ss_pred hhHHHHHHHHHHhhCCCCCCChhHHHHhHHHhh
Q 027155 175 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 207 (227)
Q Consensus 175 ~vaInEaVeLAK~~g~~~s~~FVNaVLr~i~r~ 207 (227)
.-+|++|++.|...+ ..+.++|++||.+-.+.
T Consensus 32 ~evI~~ai~~a~~~~-~~~~~Yi~~Il~~W~~~ 63 (73)
T TIGR01446 32 PELIKEALKEAVSNN-KANYKYIDAILNNWKNN 63 (73)
T ss_pred HHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHc
Confidence 568899999988754 34579999999998764
No 17
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. 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 []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=39.82 E-value=34 Score=23.97 Aligned_cols=33 Identities=21% Similarity=0.261 Sum_probs=25.1
Q ss_pred hhhHHHHHHHHHHhhCCCCCCChhHHHHhHHHhh
Q 027155 174 HQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 207 (227)
Q Consensus 174 ~~vaInEaVeLAK~~g~~~s~~FVNaVLr~i~r~ 207 (227)
..-+|+++++.|... +..+.++|.+||++..+.
T Consensus 31 ~~~~v~~ai~~~~~~-~~~~~~Yi~~Il~~W~~~ 63 (77)
T PF07261_consen 31 SPEVVNEAIEYALEN-NKRSFNYIEKILNNWKQK 63 (77)
T ss_dssp HHHHHHHHHHHHHHC-T--SHHHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHc
Confidence 456788999999954 444599999999998764
No 18
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=32.40 E-value=42 Score=24.90 Aligned_cols=49 Identities=18% Similarity=0.144 Sum_probs=36.6
Q ss_pred HHHHHHHHHhhhhcC-CchhhHHHHHHHHHHhhCCCCCCChhHHHHhHHH
Q 027155 157 LSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFV 205 (227)
Q Consensus 157 raILRlalyELl~~~-iP~~vaInEaVeLAK~~g~~~s~~FVNaVLr~i~ 205 (227)
.++|.+|.....+.. -....+++|+|.+|+.-++...-.+....|-.+.
T Consensus 42 ~all~lA~~~~~~G~~~~A~~~l~eAi~~Are~~D~~~l~~al~~~~~l~ 91 (94)
T PF12862_consen 42 YALLNLAELHRRFGHYEEALQALEEAIRLARENGDRRCLAYALSWLANLL 91 (94)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHh
Confidence 577888887877764 4677899999999999987666556555555443
No 19
>PF11573 Med23: Mediator complex subunit 23; InterPro: IPR021629 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=28.46 E-value=1.3e+02 Score=33.66 Aligned_cols=67 Identities=18% Similarity=0.181 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHHcHHHHHHHH--HhhCCCCCCCCCc-chHHHHHHHHHHHHhhhhcCCchhhHHHHHHHHHHh
Q 027155 116 LLRFTRKLLVAVVDKWDAHVHII--DKVVPPIWKDQPA-GRILELSILHLAMSEITVVGTRHQIVINEAVDLAKR 187 (227)
Q Consensus 116 Dr~~~~~Lv~gvlr~~~~lD~iI--~~~l~k~w~l~Rl-~~vldraILRlalyELl~~~iP~~vaInEaVeLAK~ 187 (227)
|..|+..|+.+.... +|..- ..+...+|.+... ++. -..|.+++.||+-..+++..++|--+++.-+
T Consensus 1093 ~~~Y~~~Li~rL~~~---~~~~~~~~~f~~~dwrf~Ef~np~--a~aL~~~ciElmalP~~p~~v~~aLidvv~~ 1162 (1341)
T PF11573_consen 1093 DLDYYMELIDRLVDT---IDGINPPPPFVATDWRFNEFPNPA--AHALYVTCIELMALPVSPEDVANALIDVVVK 1162 (1341)
T ss_pred cHHHHHHHHHHHHHh---ccccCCCCCCCCCCcchhcCCCHH--HHHHHHHHHHHHcCCCCHHHHHHHHHHHHhc
Confidence 568999998877664 33332 1555679999999 553 5666999999999999999999999998866
No 20
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=22.31 E-value=93 Score=23.77 Aligned_cols=35 Identities=23% Similarity=0.301 Sum_probs=26.5
Q ss_pred cCCchhhHHHHHHHHHHhhCCCCCCChhHHHHhHHH
Q 027155 170 VGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFV 205 (227)
Q Consensus 170 ~~iP~~vaInEaVeLAK~~g~~~s~~FVNaVLr~i~ 205 (227)
++---..+|+|||.+|+. |.+-+..-||+|-..+-
T Consensus 24 Le~~RE~aIeeav~~c~~-g~pFs~d~IN~vT~~mN 58 (84)
T PF10752_consen 24 LEQQREAAIEEAVSLCKQ-GEPFSTDKINEVTKEMN 58 (84)
T ss_pred HHHHHHHHHHHHHHHHHC-CCCCcHHHHHHHHHHHH
Confidence 345567899999999998 45667778898876653
No 21
>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=21.27 E-value=1.1e+02 Score=24.26 Aligned_cols=49 Identities=18% Similarity=0.164 Sum_probs=37.7
Q ss_pred HHHHHHHHHHhhhhcC-CchhhHHHHHHHHHHhhCC-CCCCChhHHHHhHH
Q 027155 156 ELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCD-GAAPRIINGCLRTF 204 (227)
Q Consensus 156 draILRlalyELl~~~-iP~~vaInEaVeLAK~~g~-~~s~~FVNaVLr~i 204 (227)
|.--+|=|+-.++-+| ||...||+.|+..|++... .-+.+|.-||=.+.
T Consensus 22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~ 72 (103)
T cd00923 22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKC 72 (103)
T ss_pred cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc
Confidence 5667888998888665 8999999999999998754 33566766666554
No 22
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=20.87 E-value=93 Score=28.17 Aligned_cols=32 Identities=19% Similarity=0.162 Sum_probs=27.2
Q ss_pred hhhHHHHHHHHHHhhCCCCCCChhHHHHhHHHh
Q 027155 174 HQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 206 (227)
Q Consensus 174 ~~vaInEaVeLAK~~g~~~s~~FVNaVLr~i~r 206 (227)
+.-+|.+|++.|..-|.. ..++|++||++..+
T Consensus 160 ~~elI~~ALkeAv~~gK~-n~~YI~~IL~nW~k 191 (246)
T COG3935 160 DPELIKAALKEAVENGKL-NFKYIDAILRNWKK 191 (246)
T ss_pred CHHHHHHHHHHHHHcCCc-cHHHHHHHHHHHHH
Confidence 377899999999988765 78999999998754
Done!