Query 022136
Match_columns 302
No_of_seqs 183 out of 1670
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 08:19:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022136.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022136hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01029 NusB: NusB family; I 100.0 9E-32 1.9E-36 223.0 13.9 93 187-281 41-134 (134)
2 COG0781 NusB Transcription ter 100.0 2.2E-31 4.7E-36 230.9 13.5 140 93-286 7-148 (151)
3 PRK00202 nusB transcription an 100.0 3.8E-31 8.3E-36 221.7 14.3 133 95-286 2-135 (137)
4 cd00619 Terminator_NusB Transc 100.0 9.1E-31 2E-35 216.7 13.4 128 96-282 1-129 (130)
5 TIGR01951 nusB transcription a 100.0 2E-30 4.4E-35 214.0 13.5 127 96-281 1-128 (129)
6 cd00620 Methyltransferase_Sun 100.0 6.8E-29 1.5E-33 205.5 14.4 123 99-282 3-125 (126)
7 cd00447 NusB_Sun RNA binding d 99.9 1.2E-26 2.5E-31 191.0 14.3 124 99-282 2-128 (129)
8 PRK09634 nusB transcription an 99.9 3.2E-26 7E-31 207.6 14.0 94 189-284 110-203 (207)
9 PRK10901 16S rRNA methyltransf 99.9 1.7E-25 3.6E-30 218.7 14.7 124 98-283 3-126 (427)
10 PRK14904 16S rRNA methyltransf 99.9 2.1E-24 4.6E-29 211.9 13.9 126 98-283 3-129 (445)
11 PRK14901 16S rRNA methyltransf 99.9 4.5E-24 9.8E-29 209.0 13.2 126 98-284 2-128 (434)
12 PRK14902 16S rRNA methyltransf 99.9 1E-23 2.2E-28 206.7 12.8 125 98-283 4-129 (444)
13 TIGR00563 rsmB ribosomal RNA s 99.9 4.6E-22 1E-26 194.3 12.6 92 189-284 30-122 (426)
14 PRK14903 16S rRNA methyltransf 99.9 1.4E-21 3E-26 192.3 12.7 118 98-282 4-122 (431)
15 PF09185 DUF1948: Domain of un 78.8 37 0.0008 29.1 10.5 85 189-279 55-139 (140)
16 TIGR01446 DnaD_dom DnaD and ph 38.2 33 0.00071 25.5 2.7 31 250-281 32-62 (73)
17 PF12862 Apc5: Anaphase-promot 33.3 74 0.0016 24.9 4.1 49 232-280 42-91 (94)
18 PF02284 COX5A: Cytochrome c o 28.6 45 0.00097 28.3 2.2 49 231-279 25-75 (108)
19 cd00923 Cyt_c_Oxidase_Va Cytoc 28.3 52 0.0011 27.8 2.5 49 231-279 22-72 (103)
20 PF07261 DnaB_2: Replication i 24.7 74 0.0016 23.4 2.6 33 249-282 31-63 (77)
21 PF11573 Med23: Mediator compl 22.6 1.2E+02 0.0027 35.5 4.9 68 191-262 1093-1162(1341)
22 PHA02674 ORF107 virion morphog 20.2 93 0.002 23.8 2.3 28 55-82 23-50 (60)
No 1
>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=99.98 E-value=9e-32 Score=223.02 Aligned_cols=93 Identities=28% Similarity=0.432 Sum_probs=88.2
Q ss_pred ccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhcc-CCChhhHHHHHHHHHHhhCC
Q 022136 187 YSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCD 265 (302)
Q Consensus 187 ~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~-diP~~VaINEAVELAKky~~ 265 (302)
.+..|++|+++|++|+++|+..||++|++++ ++|+++|++++ +++|||+|+|||+|+ ++|++++|||||++||+|++
T Consensus 41 ~~~~d~~~~~~lv~gv~~~~~~ld~~i~~~~-~~~~~~rl~~~-~~~iLrla~~El~~~~~~p~~v~InEaVelak~~~~ 118 (134)
T PF01029_consen 41 LSEEDRAFARELVYGVLRNKEELDALISKLL-KNWPLERLPPV-DRAILRLAIYELLFLDDIPPHVAINEAVELAKKYGD 118 (134)
T ss_dssp STHHHHHHHHHHHHHHHHTHHHHHHHHHHTS-TSSTGGGSGHH-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHS-
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCccccCHH-HHHHHHHHHHHHHhcCCCCccchHHHHHHHHHHhCC
Confidence 4578999999999999999999999999988 68999999999 799999999999999 89999999999999999999
Q ss_pred CCCCCchhHHHhHHHh
Q 022136 266 GAAPRIINGCLRTFVR 281 (302)
Q Consensus 266 ~~s~gFVNAVLrkI~R 281 (302)
++++||||||||+++|
T Consensus 119 ~~~~~fVNaVL~~~~R 134 (134)
T PF01029_consen 119 EKSAGFVNAVLRRIAR 134 (134)
T ss_dssp TTHHHHHHHHHHHHHH
T ss_pred CCcchhHHHHHHHhhC
Confidence 9999999999999986
No 2
>COG0781 NusB Transcription termination factor [Transcription]
Probab=99.97 E-value=2.2e-31 Score=230.89 Aligned_cols=140 Identities=26% Similarity=0.365 Sum_probs=116.6
Q ss_pred CCCcHHHHHHHHHHHHHHHhcCC-CHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHH
Q 022136 93 FCSPRAARELALLVVYAACLEGS-DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEE 171 (302)
Q Consensus 93 ~~~R~~ARe~Avq~LYq~e~~g~-~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~ 171 (302)
...|+++|++|+|+||||++++. .++++++.+.. .|..+.
T Consensus 7 ~~~R~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~~---------------~~~~~d------------------------ 47 (151)
T COG0781 7 KLTRRQARELAVQALYQWELSGSVSAEDILEDIEE---------------EFVENE------------------------ 47 (151)
T ss_pred cchHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHH---------------HHhhcc------------------------
Confidence 34789999999999999999665 55566554332 110000
Q ss_pred HHHHHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccC-CChh
Q 022136 172 SAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQ 250 (302)
Q Consensus 172 ~~~~~~~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~d-iP~~ 250 (302)
.+ ....+..|+..|+.||++|+..||.+|.+++ ++|+++||+.+ ||+|||+|+|||+|.+ +|..
T Consensus 48 ----------~~---~~~~~~~~~~~lv~gv~~~~~~iD~~I~~~L-~~w~~~rL~~v-erAILRla~yEl~~~~dvP~~ 112 (151)
T COG0781 48 ----------LD---IELADSEYFRSLVKGVLENQEELDELISPHL-KKWSLERLDLV-ERAILRLALYELLFRDDVPYK 112 (151)
T ss_pred ----------cc---hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH-ccCCHHHhhHH-HHHHHHHHHHHHHhcCCCCCc
Confidence 00 1125789999999999999999999999999 46999999999 9999999999999975 9999
Q ss_pred hHHHHHHHHHHhhCCCCCCCchhHHHhHHHhhhhcc
Q 022136 251 IVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT 286 (302)
Q Consensus 251 VaINEAVELAKky~~~~s~gFVNAVLrkI~R~l~~~ 286 (302)
|+|||||+|||.|+++++++||||||+++++..++.
T Consensus 113 VvInEaielaK~f~~e~s~kFINgVLd~i~~~~~~~ 148 (151)
T COG0781 113 VVINEAIELAKKFSGEDSHKFVNGVLDKIAKKLRPK 148 (151)
T ss_pred chHHHHHHHHHHhCCCCchHHHHHHHHHHHHHhhhh
Confidence 999999999999999999999999999999877653
No 3
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=99.97 E-value=3.8e-31 Score=221.69 Aligned_cols=133 Identities=29% Similarity=0.434 Sum_probs=119.6
Q ss_pred CcHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHH
Q 022136 95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI 174 (302)
Q Consensus 95 ~R~~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~ 174 (302)
+|+.+|+.|+++||+++..|.+++++++..+... .
T Consensus 2 ~r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~~------------------~--------------------------- 36 (137)
T PRK00202 2 ARRKAREAAVQALYQWELSGNDIAEIIEAQLLEE------------------Q--------------------------- 36 (137)
T ss_pred chHHHHHHHHHHHHHHHccCCCHHHHHHHHHHhc------------------c---------------------------
Confidence 5889999999999999999999999887655310 0
Q ss_pred HHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhcc-CCChhhHH
Q 022136 175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVI 253 (302)
Q Consensus 175 ~~~~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~-diP~~VaI 253 (302)
+++.|++|+++||+|+++|++.||++|++++ ++|++++++++ +++|||+|+|||+|+ ++|++++|
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 2346899999999999999999999999999 56999999999 699999999999998 79999999
Q ss_pred HHHHHHHHhhCCCCCCCchhHHHhHHHhhhhcc
Q 022136 254 NEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT 286 (302)
Q Consensus 254 NEAVELAKky~~~~s~gFVNAVLrkI~R~l~~~ 286 (302)
||||++||+|+.++++||||||||++.+..+..
T Consensus 103 nEaV~lak~~~~~~~~~fVNaVLr~i~r~~~~~ 135 (137)
T PRK00202 103 NEAIELAKKFGDEDSHKFVNGVLDKIAKELRPA 135 (137)
T ss_pred HHHHHHHHHHCCCCcchhHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999987653
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=9.1e-31 Score=216.71 Aligned_cols=128 Identities=30% Similarity=0.405 Sum_probs=114.6
Q ss_pred cHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHH
Q 022136 96 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 175 (302)
Q Consensus 96 R~~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~ 175 (302)
|+.+|+.|+|+||+++..|.+.+++++......
T Consensus 1 r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~~----------------------------------------------- 33 (130)
T cd00619 1 RRRARELAVQALYAWELAPEILAEVVSLLELLQ----------------------------------------------- 33 (130)
T ss_pred ChHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhc-----------------------------------------------
Confidence 578899999999999999999988877544310
Q ss_pred HhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccC-CChhhHHH
Q 022136 176 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVIN 254 (302)
Q Consensus 176 ~~~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~d-iP~~VaIN 254 (302)
..++.|++|+++|++|+++|+..||++|++++ ++|.+++++++ +++|||+|+|||+|++ +|++++||
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 01246899999999999999999999999999 58999999999 6999999999999987 99999999
Q ss_pred HHHHHHHhhCCCCCCCchhHHHhHHHhh
Q 022136 255 EAVDLAKRFCDGAAPRIINGCLRTFVRN 282 (302)
Q Consensus 255 EAVELAKky~~~~s~gFVNAVLrkI~R~ 282 (302)
|||++||+|++++++||||||||++.++
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=2e-30 Score=214.00 Aligned_cols=127 Identities=29% Similarity=0.415 Sum_probs=114.5
Q ss_pred cHHHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHH
Q 022136 96 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 175 (302)
Q Consensus 96 R~~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~ 175 (302)
|+.+|+.|+++||+++..|.+++++++..+... .
T Consensus 1 ~~~~R~~a~~~l~~~~~~~~~~~~~l~~~~~~~------------------~---------------------------- 34 (129)
T TIGR01951 1 RRKARELALQALYQWELSGNDVEEIIEEFLEER------------------E---------------------------- 34 (129)
T ss_pred ChHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhc------------------c----------------------------
Confidence 467899999999999999999999987665310 0
Q ss_pred HhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhcc-CCChhhHHH
Q 022136 176 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVIN 254 (302)
Q Consensus 176 ~~~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~-diP~~VaIN 254 (302)
+++.|++|+++|++|+++|++.||++|+++++ +|++++++++ +++|||+|+|||+|+ ++|++++||
T Consensus 35 -----------l~~~d~~~~~~lv~~~lr~~~~ld~~i~~~~~-~~~~~~l~~~-~~~iLr~a~~el~~~~~~p~~avin 101 (129)
T TIGR01951 35 -----------LDEEDREYFLELVRGVLENQEEIDELISPHLK-DWSLERLDPV-DRAILRLAAYELLYRPDVPYKVVIN 101 (129)
T ss_pred -----------cchhHHHHHHHHHHHHHHhHHHHHHHHHHHhc-CCCHHHhhHH-HHHHHHHHHHHHHhCCCCCCcchHH
Confidence 23468999999999999999999999999994 7999999999 699999999999999 799999999
Q ss_pred HHHHHHHhhCCCCCCCchhHHHhHHHh
Q 022136 255 EAVDLAKRFCDGAAPRIINGCLRTFVR 281 (302)
Q Consensus 255 EAVELAKky~~~~s~gFVNAVLrkI~R 281 (302)
|||++||+|+.+++++|||||||++.+
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=99.96 E-value=6.8e-29 Score=205.46 Aligned_cols=123 Identities=18% Similarity=0.164 Sum_probs=109.4
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHHHhh
Q 022136 99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV 178 (302)
Q Consensus 99 ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~~~~ 178 (302)
+|+.|+|+||+++..|.++++++.+.+...
T Consensus 3 ~R~~A~~~L~~v~~~~~~~~~~l~~~~~~~-------------------------------------------------- 32 (126)
T cd00620 3 ARSTAAEVLRDVLQRGASLNAVLSALQKKD-------------------------------------------------- 32 (126)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHHhc--------------------------------------------------
Confidence 699999999999999999999887655310
Q ss_pred hcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccCCChhhHHHHHHH
Q 022136 179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVD 258 (302)
Q Consensus 179 ~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~diP~~VaINEAVE 258 (302)
.++.|++|+++|++|+++|+..||.+|+++++ |++.+++++ +++|||+|+|||+|+++|++++|||||+
T Consensus 33 --------~~~~d~~~~~~lv~g~~r~~~~ld~~i~~~l~--~~~~~~~~~-~~~iLr~a~~el~~~~~p~~avvneaVe 101 (126)
T cd00620 33 --------KSDRDRGLATELVYGTLRWLALLDWIINPLLK--KPDVGKDPD-VRNLLRLGLYQLLYLDVPPHAAVDETVE 101 (126)
T ss_pred --------CCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhC--CCccccCHH-HHHHHHHHHHHHHhcCCCchHHHHHHHH
Confidence 01357999999999999999999999999994 345689999 6999999999999999999999999999
Q ss_pred HHHhhCCCCCCCchhHHHhHHHhh
Q 022136 259 LAKRFCDGAAPRIINGCLRTFVRN 282 (302)
Q Consensus 259 LAKky~~~~s~gFVNAVLrkI~R~ 282 (302)
+||+|++++++||||||||++.|+
T Consensus 102 lak~~~~~~~~~fVNaVLr~i~r~ 125 (126)
T cd00620 102 IAKIRKDLGRAGLVNAVLRRFERE 125 (126)
T ss_pred HHHHhCCCchhhHHHHHHHHHhcc
Confidence 999999999999999999999873
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=99.94 E-value=1.2e-26 Score=190.97 Aligned_cols=124 Identities=26% Similarity=0.396 Sum_probs=109.5
Q ss_pred HHHHHHHHHHHHHhc-CCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHHHh
Q 022136 99 ARELALLVVYAACLE-GSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (302)
Q Consensus 99 ARe~Avq~LYq~e~~-g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~~~ 177 (302)
+|+.|+++||+++.. |.+...++...... .
T Consensus 2 ~R~~a~~~L~~~~~~~~~~~~~~~~~~~~~-------------------~------------------------------ 32 (129)
T cd00447 2 AREIAFQALYQVEIRNGISLEAVLSALEKL-------------------Q------------------------------ 32 (129)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHc-------------------c------------------------------
Confidence 699999999999988 88888876653320 0
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhcc--CCChhhHHHH
Q 022136 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV--GTRHQIVINE 255 (302)
Q Consensus 178 ~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~--diP~~VaINE 255 (302)
..+.|++|+++|++||++|+..||++|++++ ++|+++|++.+ ++.|||++.+|+.++ ++|++++|||
T Consensus 33 ---------~~~~d~~~~~~lv~gv~r~~~~ld~~i~~~~-~~~~~~r~~~~-~~~il~l~~~el~~~~~~~p~~~vine 101 (129)
T cd00447 33 ---------LAKKDRPFALELVYGVLRNLPELDDIISPLL-KKWLLDRLDKV-DRAILRLLLYELYQLLYDVPPPVAINE 101 (129)
T ss_pred ---------cchhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCChhhhhHH-HHHHHHHHHHHHHhCcCCCCchhHHHH
Confidence 1236899999999999999999999999999 68999999998 899999999998886 4999999999
Q ss_pred HHHHHHhhCCCCCCCchhHHHhHHHhh
Q 022136 256 AVDLAKRFCDGAAPRIINGCLRTFVRN 282 (302)
Q Consensus 256 AVELAKky~~~~s~gFVNAVLrkI~R~ 282 (302)
||++||+|+.+++++|||||||++.++
T Consensus 102 aVelak~~~~~~~~~fVNaVLr~~~r~ 128 (129)
T cd00447 102 AVELAKRFGDDDSAKFVNGVLRRIAKE 128 (129)
T ss_pred HHHHHHHHCCCCcchhHHHHHHHHhhc
Confidence 999999999999999999999999874
No 8
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=99.94 E-value=3.2e-26 Score=207.58 Aligned_cols=94 Identities=33% Similarity=0.485 Sum_probs=90.6
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHhhCCCCC
Q 022136 189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAA 268 (302)
Q Consensus 189 ~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~diP~~VaINEAVELAKky~~~~s 268 (302)
+.+++|+++||+||++|+..||++|+.++ +||+++|++.+ ||+|||+|+|||+|+++|++++|||||++||+|+++++
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 68999999999999999999999999999 69999999998 89999999999999999999999999999999999999
Q ss_pred CCchhHHHhHHHhhhh
Q 022136 269 PRIINGCLRTFVRNLE 284 (302)
Q Consensus 269 ~gFVNAVLrkI~R~l~ 284 (302)
+||||||||++.+...
T Consensus 188 ~~FVNaVLrri~r~~~ 203 (207)
T PRK09634 188 RRFINGVLRRLQDALS 203 (207)
T ss_pred cchHHHHHHHHHHHhh
Confidence 9999999999998763
No 9
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=99.93 E-value=1.7e-25 Score=218.70 Aligned_cols=124 Identities=17% Similarity=0.172 Sum_probs=112.9
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHHHh
Q 022136 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (302)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~~~ 177 (302)
.+|++|+|+||+++.+|.++++++++.+..
T Consensus 3 ~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~-------------------------------------------------- 32 (427)
T PRK10901 3 NLRALAAAAILQVVDQGQSLSAALPALQQK-------------------------------------------------- 32 (427)
T ss_pred hHHHHHHHHHHHHHHcCCcHHHHHHHHHhh--------------------------------------------------
Confidence 579999999999999999999988765430
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccCCChhhHHHHHH
Q 022136 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAV 257 (302)
Q Consensus 178 ~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~diP~~VaINEAV 257 (302)
++..|++|+++||+||++|+..||++|++++ +|++++++++ +|+|||||+|||+|+++|++++|||+|
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 1246899999999999999999999999998 3789999999 699999999999999999999999999
Q ss_pred HHHHhhCCCCCCCchhHHHhHHHhhh
Q 022136 258 DLAKRFCDGAAPRIINGCLRTFVRNL 283 (302)
Q Consensus 258 ELAKky~~~~s~gFVNAVLrkI~R~l 283 (302)
++||+|+++++++|||||||++.+..
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=99.91 E-value=2.1e-24 Score=211.95 Aligned_cols=126 Identities=21% Similarity=0.251 Sum_probs=113.8
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHHHh
Q 022136 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (302)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~~~ 177 (302)
.+|++|+|+||+++.+|.+++.++.+++... .
T Consensus 3 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~~------------------~------------------------------ 34 (445)
T PRK14904 3 TARELALQVLQELETGERKSDTLLHRMLERS------------------S------------------------------ 34 (445)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHHHHhc------------------C------------------------------
Confidence 4799999999999999999999988766410 0
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccC-CChhhHHHHH
Q 022136 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEA 256 (302)
Q Consensus 178 ~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~d-iP~~VaINEA 256 (302)
++..|++|+++||+||++++..||++|++++ +|+++|++++ +|+|||+|+|||+|++ +|++++||||
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 2346899999999999999999999999999 3899999999 7999999999999985 9999999999
Q ss_pred HHHHHhhCCCCCCCchhHHHhHHHhhh
Q 022136 257 VDLAKRFCDGAAPRIINGCLRTFVRNL 283 (302)
Q Consensus 257 VELAKky~~~~s~gFVNAVLrkI~R~l 283 (302)
|+|||+|+++.+++|||||||++.+..
T Consensus 103 Velak~~~~~~~~~fVNgVLr~i~~~~ 129 (445)
T PRK14904 103 VKLARKYKGEHMAKLVNGVLRNISPET 129 (445)
T ss_pred HHHHHHhCCCccccchHHHHHHHHHhh
Confidence 999999999999999999999999965
No 11
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=99.91 E-value=4.5e-24 Score=209.05 Aligned_cols=126 Identities=21% Similarity=0.232 Sum_probs=111.0
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHHHh
Q 022136 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (302)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~~~ 177 (302)
.+|++|+++||+++. |.++++++++.+... .
T Consensus 2 ~~R~~A~~~L~~i~~-~~~~~~~l~~~~~~~------------------~------------------------------ 32 (434)
T PRK14901 2 NARQLAWEILQAVAR-GAYADVALERVLRKY------------------P------------------------------ 32 (434)
T ss_pred CHHHHHHHHHHHHHc-CCchHHHHHHHHHhc------------------C------------------------------
Confidence 379999999999998 688888887765410 0
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccC-CChhhHHHHH
Q 022136 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEA 256 (302)
Q Consensus 178 ~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~d-iP~~VaINEA 256 (302)
++..|++|+++||+||+|++..||++|++++ +|++.+|+++ +|+|||+|+|||+|++ +|++++||||
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 2346899999999999999999999999997 3677889999 6999999999999985 8999999999
Q ss_pred HHHHHhhCCCCCCCchhHHHhHHHhhhh
Q 022136 257 VDLAKRFCDGAAPRIINGCLRTFVRNLE 284 (302)
Q Consensus 257 VELAKky~~~~s~gFVNAVLrkI~R~l~ 284 (302)
|++||+|+.+++++|||||||++.+...
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=99.90 E-value=1e-23 Score=206.70 Aligned_cols=125 Identities=19% Similarity=0.228 Sum_probs=112.2
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHHHh
Q 022136 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (302)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~~~ 177 (302)
.+|++|+++||+++.+|.+++++++.++... .
T Consensus 4 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~~------------------~------------------------------ 35 (444)
T PRK14902 4 NARELALEVLIKVENNGAYSNIALNKVLKKS------------------E------------------------------ 35 (444)
T ss_pred cHHHHHHHHHHHHHhcCCCHHHHHHHHHHhc------------------C------------------------------
Confidence 5899999999999999999999988766410 0
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccC-CChhhHHHHH
Q 022136 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEA 256 (302)
Q Consensus 178 ~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~d-iP~~VaINEA 256 (302)
++..|++|+++||+|+++++..||++|++++ ++ ++|++++ +|+|||+|+|||+|++ +|++++||||
T Consensus 36 ---------l~~~d~~~~~~lv~g~lr~~~~ld~~i~~~~-~~--~~~l~~~-~r~iLrla~~el~~~~~~p~~~~inea 102 (444)
T PRK14902 36 ---------LSDKDKALLTELVYGTIQRKLTLDYYLAPFI-KK--RKKLDPW-VRNLLRMSLYQLLYLDKVPDHAAVNEA 102 (444)
T ss_pred ---------CChHHHHHHHHHHHHHHHhHHHHHHHHHHHh-hh--hhhCCHH-HHHHHHHHHHHHHhccCCCCceeHHHH
Confidence 2346899999999999999999999999999 33 8999999 6999999999999975 9999999999
Q ss_pred HHHHHhhCCCCCCCchhHHHhHHHhhh
Q 022136 257 VDLAKRFCDGAAPRIINGCLRTFVRNL 283 (302)
Q Consensus 257 VELAKky~~~~s~gFVNAVLrkI~R~l 283 (302)
|++||+|+++++++|||||||++.+..
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=99.87 E-value=4.6e-22 Score=194.30 Aligned_cols=92 Identities=20% Similarity=0.145 Sum_probs=83.0
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhc-cCCChhhHHHHHHHHHHhhCCCC
Q 022136 189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGA 267 (302)
Q Consensus 189 ~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~-~diP~~VaINEAVELAKky~~~~ 267 (302)
+.|++|+++||+||++|+..||++|++++ +|++++++++ .+ +||+++||++| +++|++++|||||+|||+|++++
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 46899999999999999999999999998 3788999998 47 88888888766 58999999999999999999999
Q ss_pred CCCchhHHHhHHHhhhh
Q 022136 268 APRIINGCLRTFVRNLE 284 (302)
Q Consensus 268 s~gFVNAVLrkI~R~l~ 284 (302)
+++|||||||++.+...
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=99.86 E-value=1.4e-21 Score=192.29 Aligned_cols=118 Identities=17% Similarity=0.096 Sum_probs=104.5
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHhccCCCCCccchhhhhhhhcccCCCCCCcccchhhHHHhhhhhhHHHHHHHh
Q 022136 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (302)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~l~~~l~~~~~~~~e~d~~~l~e~~~~~~g~~~~~~~~~ee~~~l~~~~~~~~~~~~~ 177 (302)
++|++|+.+|+++...|...+.+|++.+..
T Consensus 4 ~~R~~A~~~L~~v~~~~~~~~~~l~~~~~~-------------------------------------------------- 33 (431)
T PRK14903 4 NVRLLAYRLLRKYEKEKFIFREDVDSVLSF-------------------------------------------------- 33 (431)
T ss_pred CHHHHHHHHHHHHHhCCCchHHHHHHHHHh--------------------------------------------------
Confidence 479999999999999998888887654420
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccC-CChhhHHHHH
Q 022136 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEA 256 (302)
Q Consensus 178 ~~~~~~~l~~~~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~d-iP~~VaINEA 256 (302)
++.+|++|+++||+||++++..||++|++++ ++| +++++ +|+|||+|+|||+|++ +|++++||||
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 556 58998 5999999999999987 7999999999
Q ss_pred HHHHHhhCCCCCCCchhHHHhHHHhh
Q 022136 257 VDLAKRFCDGAAPRIINGCLRTFVRN 282 (302)
Q Consensus 257 VELAKky~~~~s~gFVNAVLrkI~R~ 282 (302)
|++||++ ..++|||||||++.|+
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=78.84 E-value=37 Score=29.14 Aligned_cols=85 Identities=13% Similarity=0.161 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcchhHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHhhCCCCC
Q 022136 189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAA 268 (302)
Q Consensus 189 ~~Drafa~eLV~GVlr~~~~LD~iI~~~L~k~W~leRL~~vLDRaILRlAlyELl~~diP~~VaINEAVELAKky~~~~s 268 (302)
.+--.|...+-..-++|..++..-.++.+. .+++.. ..++...|+.|-.-..+.....|+||+-+-..|+....
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 344556666666666777776666666652 345555 57778888888766678888999999999999987777
Q ss_pred CCchhHHHhHH
Q 022136 269 PRIINGCLRTF 279 (302)
Q Consensus 269 ~gFVNAVLrkI 279 (302)
.+=.+|+|+++
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=38.20 E-value=33 Score=25.52 Aligned_cols=31 Identities=23% Similarity=0.188 Sum_probs=24.5
Q ss_pred hhHHHHHHHHHHhhCCCCCCCchhHHHhHHHh
Q 022136 250 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 281 (302)
Q Consensus 250 ~VaINEAVELAKky~~~~s~gFVNAVLrkI~R 281 (302)
.-+|++|++.|...+ ....++|++||.+-.+
T Consensus 32 ~evI~~ai~~a~~~~-~~~~~Yi~~Il~~W~~ 62 (73)
T TIGR01446 32 PELIKEALKEAVSNN-KANYKYIDAILNNWKN 62 (73)
T ss_pred HHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHH
Confidence 668899999987743 3457999999998765
No 17
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=33.33 E-value=74 Score=24.90 Aligned_cols=49 Identities=18% Similarity=0.144 Sum_probs=36.4
Q ss_pred HHHHHHHHHhhhccC-CChhhHHHHHHHHHHhhCCCCCCCchhHHHhHHH
Q 022136 232 LSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFV 280 (302)
Q Consensus 232 RaILRlAlyELl~~d-iP~~VaINEAVELAKky~~~~s~gFVNAVLrkI~ 280 (302)
.++|.+|.....+.+ -....++.|||.+|++-++...-.++...|-.+.
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 567888887777754 4567899999999999988766556655555544
No 18
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=28.62 E-value=45 Score=28.34 Aligned_cols=49 Identities=18% Similarity=0.203 Sum_probs=32.8
Q ss_pred HHHHHHHHHHhhhccC-CChhhHHHHHHHHHHhhCC-CCCCCchhHHHhHH
Q 022136 231 ELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCD-GAAPRIINGCLRTF 279 (302)
Q Consensus 231 DRaILRlAlyELl~~d-iP~~VaINEAVELAKky~~-~~s~gFVNAVLrkI 279 (302)
|..-||-|+-.|.-+| ||...||..|+..|++..+ .-+.+|.-||=.+.
T Consensus 25 D~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~ 75 (108)
T PF02284_consen 25 DGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKC 75 (108)
T ss_dssp -HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT
T ss_pred cHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc
Confidence 5566899998888787 8999999999999998754 22445555555443
No 19
>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=28.32 E-value=52 Score=27.76 Aligned_cols=49 Identities=18% Similarity=0.164 Sum_probs=38.8
Q ss_pred HHHHHHHHHHhhhccC-CChhhHHHHHHHHHHhhCC-CCCCCchhHHHhHH
Q 022136 231 ELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCD-GAAPRIINGCLRTF 279 (302)
Q Consensus 231 DRaILRlAlyELl~~d-iP~~VaINEAVELAKky~~-~~s~gFVNAVLrkI 279 (302)
|..-||-|+-.|.-+| ||..-||+-|+..|++..+ .-+.+|+-||=.+.
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 5667899999998888 9999999999999998754 33556666666554
No 20
>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=24.74 E-value=74 Score=23.43 Aligned_cols=33 Identities=21% Similarity=0.261 Sum_probs=24.8
Q ss_pred hhhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhh
Q 022136 249 HQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 282 (302)
Q Consensus 249 ~~VaINEAVELAKky~~~~s~gFVNAVLrkI~R~ 282 (302)
+.-+|++|++.|... +....++|.+||++-.+.
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 556788999999954 444589999999997653
No 21
>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=22.58 E-value=1.2e+02 Score=35.47 Aligned_cols=68 Identities=18% Similarity=0.162 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHHHcHHHHHHHH--HhhCCCCCCCCCcchhHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHh
Q 022136 191 LLRFTRKLLVAVVDKWDAHVHII--DKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKR 262 (302)
Q Consensus 191 Drafa~eLV~GVlr~~~~LD~iI--~~~L~k~W~leRL~~vLDRaILRlAlyELl~~diP~~VaINEAVELAKk 262 (302)
|..|+.+|+.+..+.. |..- ..+...+|++...+... -..|.+++.||+-+.+++..++|--+++.-+
T Consensus 1093 ~~~Y~~~Li~rL~~~~---~~~~~~~~f~~~dwrf~Ef~np~-a~aL~~~ciElmalP~~p~~v~~aLidvv~~ 1162 (1341)
T PF11573_consen 1093 DLDYYMELIDRLVDTI---DGINPPPPFVATDWRFNEFPNPA-AHALYVTCIELMALPVSPEDVANALIDVVVK 1162 (1341)
T ss_pred cHHHHHHHHHHHHHhc---cccCCCCCCCCCCcchhcCCCHH-HHHHHHHHHHHHcCCCCHHHHHHHHHHHHhc
Confidence 5688988887776653 3333 15566789999994433 5778999999999999999999999998865
No 22
>PHA02674 ORF107 virion morphogenesis; Provisional
Probab=20.17 E-value=93 Score=23.83 Aligned_cols=28 Identities=25% Similarity=0.272 Sum_probs=23.8
Q ss_pred ccchhhHHHHHHHHHHHHHHHhhccccc
Q 022136 55 VSCSAAAFAVQETLEKTRESVMASSAKE 82 (302)
Q Consensus 55 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~ 82 (302)
-.|+|++.||.|-+..+++.||+=+++.
T Consensus 23 ~d~aAtlaaIkelis~IN~kvlalNKKs 50 (60)
T PHA02674 23 GDAAAAAAAIKMLMDLVNERIMILNKKA 50 (60)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhHHh
Confidence 3578888999999999999999987544
Done!