Query 021860
Match_columns 306
No_of_seqs 181 out of 1615
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 06:13:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021860.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021860hhsearch_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 3E-30 6.6E-35 224.1 12.4 141 92-290 6-148 (151)
2 PF01029 NusB: NusB family; I 100.0 1.1E-29 2.4E-34 211.1 14.3 93 187-285 41-134 (134)
3 PRK00202 nusB transcription an 100.0 3.6E-29 7.9E-34 210.2 13.8 132 95-289 2-134 (137)
4 cd00619 Terminator_NusB Transc 100.0 6.8E-29 1.5E-33 206.0 13.4 128 96-286 1-129 (130)
5 TIGR01951 nusB transcription a 100.0 1.1E-28 2.3E-33 204.3 13.1 127 96-285 1-128 (129)
6 cd00620 Methyltransferase_Sun 100.0 1E-27 2.3E-32 198.8 14.3 123 99-286 3-125 (126)
7 PRK09634 nusB transcription an 99.9 8.8E-25 1.9E-29 198.6 14.1 93 189-287 110-202 (207)
8 cd00447 NusB_Sun RNA binding d 99.9 1.5E-24 3.3E-29 178.9 14.2 124 99-286 2-128 (129)
9 PRK10901 16S rRNA methyltransf 99.9 4.9E-24 1.1E-28 208.9 14.6 124 98-287 3-126 (427)
10 PRK14904 16S rRNA methyltransf 99.9 5.2E-23 1.1E-27 202.7 14.0 126 98-287 3-129 (445)
11 PRK14902 16S rRNA methyltransf 99.9 7.7E-23 1.7E-27 201.0 12.6 125 98-287 4-129 (444)
12 PRK14901 16S rRNA methyltransf 99.9 1.4E-22 3.1E-27 199.1 13.6 125 99-288 3-128 (434)
13 TIGR00563 rsmB ribosomal RNA s 99.9 3.6E-21 7.9E-26 188.5 12.5 92 188-287 29-121 (426)
14 PRK14903 16S rRNA methyltransf 99.8 3E-20 6.5E-25 183.3 12.6 118 98-286 4-122 (431)
15 PF09185 DUF1948: Domain of un 65.2 90 0.002 26.9 9.8 85 189-283 55-139 (140)
16 TIGR01446 DnaD_dom DnaD and ph 40.4 29 0.00063 25.9 2.7 32 254-286 32-63 (73)
17 PF12862 Apc5: Anaphase-promot 30.1 41 0.00089 26.4 2.2 50 236-285 42-92 (94)
18 PF07261 DnaB_2: Replication i 27.7 60 0.0013 24.0 2.6 34 252-286 30-63 (77)
19 PF10752 DUF2533: Protein of u 26.3 80 0.0017 25.7 3.2 46 249-295 24-69 (84)
20 cd00923 Cyt_c_Oxidase_Va Cytoc 25.5 67 0.0015 27.1 2.7 50 234-283 21-72 (103)
No 1
>COG0781 NusB Transcription termination factor [Transcription]
Probab=99.97 E-value=3e-30 Score=224.13 Aligned_cols=141 Identities=26% Similarity=0.399 Sum_probs=113.7
Q ss_pred CCCCchHHHHHHHHHHHHHHhcCC-ChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhH
Q 021860 92 RFCSPRAARELALLVVYAACLEGS-DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEE 170 (306)
Q Consensus 92 ~~~~Rr~ARe~Avq~LYq~e~~g~-~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~ 170 (306)
.+..||++|++|||+||||++++. +++++++.... .|.+. +.
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 345789999999999999999765 45555553322 11000 00
Q ss_pred HHHHHHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-
Q 021860 171 ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV- 249 (306)
Q Consensus 171 ~~~~~~e~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~- 249 (306)
+ ....+..|+..|+.||.+|+.+||.+|.++|++ |+ +++++ .|||+|||+|+|||+|.
T Consensus 49 ------~---------~~~~~~~~~~~lv~gv~~~~~~iD~~I~~~L~~-w~---~~rL~--~verAILRla~yEl~~~~ 107 (151)
T COG0781 49 ------D---------IELADSEYFRSLVKGVLENQEELDELISPHLKK-WS---LERLD--LVERAILRLALYELLFRD 107 (151)
T ss_pred ------c---------hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHcc-CC---HHHhh--HHHHHHHHHHHHHHHhcC
Confidence 0 011478999999999999999999999999976 65 56665 69999999999999997
Q ss_pred CCChhhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhhhhcc
Q 021860 250 GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT 290 (306)
Q Consensus 250 diP~~VaINEAVELAKkyg~~~s~kFVNGVLrki~R~~~~~ 290 (306)
++|.+|+|||||+|||.|+++++++|||||||++++..+..
T Consensus 108 dvP~~VvInEaielaK~f~~e~s~kFINgVLd~i~~~~~~~ 148 (151)
T COG0781 108 DVPYKVVINEAIELAKKFSGEDSHKFVNGVLDKIAKKLRPK 148 (151)
T ss_pred CCCCcchHHHHHHHHHHhCCCCchHHHHHHHHHHHHHhhhh
Confidence 59999999999999999999999999999999999876543
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=99.97 E-value=1.1e-29 Score=211.09 Aligned_cols=93 Identities=28% Similarity=0.461 Sum_probs=84.0
Q ss_pred ccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-CCChhhHHHHHHHHHH
Q 021860 187 YSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-GTRHQIVINEAVDLAK 265 (306)
Q Consensus 187 ~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-diP~~VaINEAVELAK 265 (306)
.+..|++|+++|++||++|+..||++|++++ ++| ++++++ +++++|||+|+|||+|+ ++|++++|||||+|||
T Consensus 41 ~~~~d~~~~~~lv~gv~~~~~~ld~~i~~~~-~~~---~~~rl~--~~~~~iLrla~~El~~~~~~p~~v~InEaVelak 114 (134)
T PF01029_consen 41 LSEEDRAFARELVYGVLRNKEELDALISKLL-KNW---PLERLP--PVDRAILRLAIYELLFLDDIPPHVAINEAVELAK 114 (134)
T ss_dssp STHHHHHHHHHHHHHHHHTHHHHHHHHHHTS-TSS---TGGGSG--HHHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccC---CccccC--HHHHHHHHHHHHHHHhcCCCCccchHHHHHHHHH
Confidence 4678999999999999999999999999965 455 456665 58899999999999998 9999999999999999
Q ss_pred hhCCCCCCCchhHHHhHHHh
Q 021860 266 RFCDGAAPRIINGCLRTFVR 285 (306)
Q Consensus 266 kyg~~~s~kFVNGVLrki~R 285 (306)
+|++++++||||||||+++|
T Consensus 115 ~~~~~~~~~fVNaVL~~~~R 134 (134)
T PF01029_consen 115 KYGDEKSAGFVNAVLRRIAR 134 (134)
T ss_dssp HHS-TTHHHHHHHHHHHHHH
T ss_pred HhCCCCcchhHHHHHHHhhC
Confidence 99999999999999999986
No 3
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=99.96 E-value=3.6e-29 Score=210.25 Aligned_cols=132 Identities=30% Similarity=0.456 Sum_probs=114.3
Q ss_pred CchHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHH
Q 021860 95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI 174 (306)
Q Consensus 95 ~Rr~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~ 174 (306)
.|+.+|+.|+++||+++..|.+++++++..+.. .
T Consensus 2 ~r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~------------------~---------------------------- 35 (137)
T PRK00202 2 ARRKAREAAVQALYQWELSGNDIAEIIEAQLLE------------------E---------------------------- 35 (137)
T ss_pred chHHHHHHHHHHHHHHHccCCCHHHHHHHHHHh------------------c----------------------------
Confidence 578999999999999999999999988765431 0
Q ss_pred HHhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-CCCh
Q 021860 175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-GTRH 253 (306)
Q Consensus 175 ~~e~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-diP~ 253 (306)
. .++.|++|+++|++||++|+..||++|++++++ |+ +++++ +++++|||+|+|||+|+ ++|+
T Consensus 36 --~---------~~~~d~~~~~~lv~gvlr~~~~lD~ii~~~l~~-~~---~~~l~--~~~~~iLr~a~~Ell~~~~~p~ 98 (137)
T PRK00202 36 --Q---------YDKADPAYFRSLVRGVVENQAELDELISPYLKD-WT---LERLD--PVERAILRLALYELLFRDDVPY 98 (137)
T ss_pred --c---------cchhhHHHHHHHHHHHHHhHHHHHHHHHHHhcC-CC---HHHhh--HHHHHHHHHHHHHHHhCCCCCC
Confidence 0 134589999999999999999999999999844 54 44554 47899999999999998 8999
Q ss_pred hhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhhhhc
Q 021860 254 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEG 289 (306)
Q Consensus 254 ~VaINEAVELAKkyg~~~s~kFVNGVLrki~R~~~~ 289 (306)
+++|||||++||.|+++++++|||||||++.++...
T Consensus 99 ~~vinEaV~lak~~~~~~~~~fVNaVLr~i~r~~~~ 134 (137)
T PRK00202 99 KVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRP 134 (137)
T ss_pred cchHHHHHHHHHHHCCCCcchhHHHHHHHHHHHhhc
Confidence 999999999999999999999999999999998754
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=99.96 E-value=6.8e-29 Score=206.01 Aligned_cols=128 Identities=33% Similarity=0.446 Sum_probs=109.8
Q ss_pred chHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHH
Q 021860 96 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 175 (306)
Q Consensus 96 Rr~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~ 175 (306)
|+.+|+.|+|+||+++..|.++.++++..+.. .
T Consensus 1 r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~---------------~-------------------------------- 33 (130)
T cd00619 1 RRRARELAVQALYAWELAPEILAEVVSLLELL---------------Q-------------------------------- 33 (130)
T ss_pred ChHHHHHHHHHHHHHHhcCCCHHHHHHHHHHh---------------c--------------------------------
Confidence 57889999999999999999988887754321 0
Q ss_pred HhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhccC-CChh
Q 021860 176 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVG-TRHQ 254 (306)
Q Consensus 176 ~e~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~d-iP~~ 254 (306)
..++.|++|+++|++||++|+..||++|+++++ +|+ +++++ +++++|||+|+|||+|++ +|++
T Consensus 34 ----------~~~~~d~~~~~~lv~gvlr~~~~ld~ii~~~l~-~~~---~~~l~--~~~~~iLria~~el~~~~~~p~~ 97 (130)
T cd00619 34 ----------YKSKKVLPFALKLVRGVLENIEEIDELIEKHLR-NWS---LDRLA--IVERAILRLAVYELLFLPDVPHP 97 (130)
T ss_pred ----------ccchhHHHHHHHHHHHHHHhHHHHHHHHHHHcc-CCC---HHHhh--HHHHHHHHHHHHHHHhCCCCCCc
Confidence 013458999999999999999999999999995 453 44444 478999999999999986 9999
Q ss_pred hHHHHHHHHHHhhCCCCCCCchhHHHhHHHhh
Q 021860 255 IVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 286 (306)
Q Consensus 255 VaINEAVELAKkyg~~~s~kFVNGVLrki~R~ 286 (306)
++|||||+|||+|+++++++||||||+++.++
T Consensus 98 ~vinEaV~lak~~~~~~~~~fVNaVLr~i~r~ 129 (130)
T cd00619 98 VVINEAIELAKRFGGDDSHKFVNGVLDKIAKD 129 (130)
T ss_pred chHHHHHHHHHHHCCCcchhHHHHHHHHHhhc
Confidence 99999999999999999999999999999875
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=99.96 E-value=1.1e-28 Score=204.27 Aligned_cols=127 Identities=29% Similarity=0.422 Sum_probs=109.9
Q ss_pred chHHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHH
Q 021860 96 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 175 (306)
Q Consensus 96 Rr~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~ 175 (306)
|+.+|+.|+++||+++..|.+++++++..+.. +
T Consensus 1 ~~~~R~~a~~~l~~~~~~~~~~~~~l~~~~~~---------------~-------------------------------- 33 (129)
T TIGR01951 1 RRKARELALQALYQWELSGNDVEEIIEEFLEE---------------R-------------------------------- 33 (129)
T ss_pred ChHHHHHHHHHHHHHHcCCCCHHHHHHHHHHh---------------c--------------------------------
Confidence 46789999999999999999999988765431 0
Q ss_pred HhhhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-CCChh
Q 021860 176 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-GTRHQ 254 (306)
Q Consensus 176 ~e~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-diP~~ 254 (306)
+ ++++|++|+++|++|+++|+..||++|+++++ +|+ +++++ +++++|||+|+|||+|+ ++|++
T Consensus 34 -~---------l~~~d~~~~~~lv~~~lr~~~~ld~~i~~~~~-~~~---~~~l~--~~~~~iLr~a~~el~~~~~~p~~ 97 (129)
T TIGR01951 34 -E---------LDEEDREYFLELVRGVLENQEEIDELISPHLK-DWS---LERLD--PVDRAILRLAAYELLYRPDVPYK 97 (129)
T ss_pred -c---------cchhHHHHHHHHHHHHHHhHHHHHHHHHHHhc-CCC---HHHhh--HHHHHHHHHHHHHHHhCCCCCCc
Confidence 0 23458999999999999999999999999985 554 44444 47799999999999998 79999
Q ss_pred hHHHHHHHHHHhhCCCCCCCchhHHHhHHHh
Q 021860 255 IVINEAVDLAKRFCDGAAPRIINGCLRTFVR 285 (306)
Q Consensus 255 VaINEAVELAKkyg~~~s~kFVNGVLrki~R 285 (306)
++|||+|++||+|+++++++|||||||++.+
T Consensus 98 avineaV~lak~~~~~~~~~fVNaVLr~i~r 128 (129)
T TIGR01951 98 VVINEAVELAKKFGDEDSHKFVNGVLDKIAK 128 (129)
T ss_pred chHHHHHHHHHHHCCCCchhhHHHHHHHHhh
Confidence 9999999999999999999999999999986
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=99.95 E-value=1e-27 Score=198.85 Aligned_cols=123 Identities=17% Similarity=0.123 Sum_probs=106.5
Q ss_pred HHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHhh
Q 021860 99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV 178 (306)
Q Consensus 99 ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~e~ 178 (306)
+|+.|+|+||+++.+|..+.+++...+.. .
T Consensus 3 ~R~~A~~~L~~v~~~~~~~~~~l~~~~~~------------------~-------------------------------- 32 (126)
T cd00620 3 ARSTAAEVLRDVLQRGASLNAVLSALQKK------------------D-------------------------------- 32 (126)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHHh------------------c--------------------------------
Confidence 69999999999999999999888765431 0
Q ss_pred hcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhccCCChhhHHH
Q 021860 179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVIN 258 (306)
Q Consensus 179 ~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~diP~~VaIN 258 (306)
.++.|++|+++|++|+++|+..||++|++++++++ .+++ +++++|||+|+|||+|+++|++++||
T Consensus 33 --------~~~~d~~~~~~lv~g~~r~~~~ld~~i~~~l~~~~-----~~~~--~~~~~iLr~a~~el~~~~~p~~avvn 97 (126)
T cd00620 33 --------KSDRDRGLATELVYGTLRWLALLDWIINPLLKKPD-----VGKD--PDVRNLLRLGLYQLLYLDVPPHAAVD 97 (126)
T ss_pred --------CCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCCCc-----cccC--HHHHHHHHHHHHHHHhcCCCchHHHH
Confidence 02347999999999999999999999999996533 2333 47799999999999998899999999
Q ss_pred HHHHHHHhhCCCCCCCchhHHHhHHHhh
Q 021860 259 EAVDLAKRFCDGAAPRIINGCLRTFVRN 286 (306)
Q Consensus 259 EAVELAKkyg~~~s~kFVNGVLrki~R~ 286 (306)
|||++||+|+++++++|||||||++.|+
T Consensus 98 eaVelak~~~~~~~~~fVNaVLr~i~r~ 125 (126)
T cd00620 98 ETVEIAKIRKDLGRAGLVNAVLRRFERE 125 (126)
T ss_pred HHHHHHHHhCCCchhhHHHHHHHHHhcc
Confidence 9999999999999999999999999874
No 7
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=99.92 E-value=8.8e-25 Score=198.62 Aligned_cols=93 Identities=31% Similarity=0.492 Sum_probs=86.2
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHhhC
Q 021860 189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFC 268 (306)
Q Consensus 189 ~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~diP~~VaINEAVELAKkyg 268 (306)
+.+++|+++|++||++|+..||++|++++ ++| ++++++ .+|++|||+|+|||+|+++|++++|||||++||+|+
T Consensus 110 ~~~r~~a~~Lv~gvlr~~~~LD~iI~~~l-~~W---~l~rL~--~idr~ILRlavyELl~l~~P~~vaINEAVeLAK~~~ 183 (207)
T PRK09634 110 EEVREYALERIGAVIRNRKEIDQLLDTVM-VGW---QLKRLP--RIDRDILRLAVVEILFLNTPAAVAINEAVELAKRYS 183 (207)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHh-ccc---cccCCC--HHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHhC
Confidence 78999999999999999999999999998 455 455655 589999999999999999999999999999999999
Q ss_pred CCCCCCchhHHHhHHHhhh
Q 021860 269 DGAAPRIINGCLRTFVRNL 287 (306)
Q Consensus 269 ~~~s~kFVNGVLrki~R~~ 287 (306)
++++++|||||||++.|..
T Consensus 184 ~~~~~~FVNaVLrri~r~~ 202 (207)
T PRK09634 184 DEQGRRFINGVLRRLQDAL 202 (207)
T ss_pred CCcccchHHHHHHHHHHHh
Confidence 9999999999999999876
No 8
>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=99.92 E-value=1.5e-24 Score=178.89 Aligned_cols=124 Identities=27% Similarity=0.415 Sum_probs=104.0
Q ss_pred HHHHHHHHHHHHHhc-CCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 021860 99 ARELALLVVYAACLE-GSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (306)
Q Consensus 99 ARe~Avq~LYq~e~~-g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~e 177 (306)
+|+.|+++||+++.. |....+++...... .
T Consensus 2 ~R~~a~~~L~~~~~~~~~~~~~~~~~~~~~-------------------------------------------------~ 32 (129)
T cd00447 2 AREIAFQALYQVEIRNGISLEAVLSALEKL-------------------------------------------------Q 32 (129)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHc-------------------------------------------------c
Confidence 699999999999988 77787776643220 0
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc--CCChhh
Q 021860 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV--GTRHQI 255 (306)
Q Consensus 178 ~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~--diP~~V 255 (306)
.++.|++|+++|++||++|+..||++|+++++ .|. ++++. .+++.|||++.+||.+. ++|+++
T Consensus 33 ---------~~~~d~~~~~~lv~gv~r~~~~ld~~i~~~~~-~~~---~~r~~--~~~~~il~l~~~el~~~~~~~p~~~ 97 (129)
T cd00447 33 ---------LAKKDRPFALELVYGVLRNLPELDDIISPLLK-KWL---LDRLD--KVDRAILRLLLYELYQLLYDVPPPV 97 (129)
T ss_pred ---------cchhHHHHHHHHHHHHHHhHHHHHHHHHHHcc-CCC---hhhhh--HHHHHHHHHHHHHHHhCcCCCCchh
Confidence 12358999999999999999999999999984 443 45554 48899999999888876 599999
Q ss_pred HHHHHHHHHHhhCCCCCCCchhHHHhHHHhh
Q 021860 256 VINEAVDLAKRFCDGAAPRIINGCLRTFVRN 286 (306)
Q Consensus 256 aINEAVELAKkyg~~~s~kFVNGVLrki~R~ 286 (306)
+|||+|++||+|+++++++|||||||++.++
T Consensus 98 vineaVelak~~~~~~~~~fVNaVLr~~~r~ 128 (129)
T cd00447 98 AINEAVELAKRFGDDDSAKFVNGVLRRIAKE 128 (129)
T ss_pred HHHHHHHHHHHHCCCCcchhHHHHHHHHhhc
Confidence 9999999999999999999999999999875
No 9
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=99.91 E-value=4.9e-24 Score=208.94 Aligned_cols=124 Identities=15% Similarity=0.174 Sum_probs=108.2
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 021860 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (306)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~e 177 (306)
.+|+.|+|+||+++.+|..+.+++++.+..
T Consensus 3 ~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~-------------------------------------------------- 32 (427)
T PRK10901 3 NLRALAAAAILQVVDQGQSLSAALPALQQK-------------------------------------------------- 32 (427)
T ss_pred hHHHHHHHHHHHHHHcCCcHHHHHHHHHhh--------------------------------------------------
Confidence 479999999999999999998887764320
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhccCCChhhHH
Q 021860 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVI 257 (306)
Q Consensus 178 ~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~diP~~VaI 257 (306)
++..|++|+++|++||++|+..||++|+++++.+ +++++ +++|+|||||+|||+|+++|++++|
T Consensus 33 ---------l~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~~~~-----~~~l~--~~~r~iLrla~yell~~~iP~~a~v 96 (427)
T PRK10901 33 ---------VSDKDRALLQELCYGVLRRLPRLEWLIAQLLAKP-----LKGKQ--RIVHALLLVGLYQLLYTRIPAHAAV 96 (427)
T ss_pred ---------CCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCCC-----ccccC--HHHHHHHHHHHHHHhccCCCcchHH
Confidence 1335899999999999999999999999998643 33443 4789999999999999889999999
Q ss_pred HHHHHHHHhhCCCCCCCchhHHHhHHHhhh
Q 021860 258 NEAVDLAKRFCDGAAPRIINGCLRTFVRNL 287 (306)
Q Consensus 258 NEAVELAKkyg~~~s~kFVNGVLrki~R~~ 287 (306)
||+|+|||+|+++++++|||||||++.++.
T Consensus 97 neaVelak~~~~~~~~~fVNaVLr~i~~~~ 126 (427)
T PRK10901 97 DETVEAAKALKRPWAKGLVNAVLRRFQREQ 126 (427)
T ss_pred HHHHHHHHhcCCccchhhHHHHHHHhhhhh
Confidence 999999999999999999999999999863
No 10
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=99.89 E-value=5.2e-23 Score=202.71 Aligned_cols=126 Identities=21% Similarity=0.263 Sum_probs=109.2
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 021860 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (306)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~e 177 (306)
.+|++|+|+||+++.+|..+++++.+++... .
T Consensus 3 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~~------------------------------------------------~ 34 (445)
T PRK14904 3 TARELALQVLQELETGERKSDTLLHRMLERS------------------------------------------------S 34 (445)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHHHHhc------------------------------------------------C
Confidence 4799999999999999999999888765410 0
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-CCChhhH
Q 021860 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-GTRHQIV 256 (306)
Q Consensus 178 ~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-diP~~Va 256 (306)
++.+|++|+++||+||++|+..||++|+++++. + ++++. +++|+|||+|+|||+|+ ++|++++
T Consensus 35 ---------l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~~~--~---~~rl~--~~~r~iLrla~~ell~~~~~p~~a~ 98 (445)
T PRK14904 35 ---------LERNDRALATELVNGVLRYRLQLDFIISRFYHH--D---LEKAA--PVLKNILRLGVYQLLFLDRVPRWAA 98 (445)
T ss_pred ---------CChHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC--C---hhhCC--HHHHHHHHHHHHHHHhCCCCCCeee
Confidence 244689999999999999999999999999853 2 34444 47899999999999997 5999999
Q ss_pred HHHHHHHHHhhCCCCCCCchhHHHhHHHhhh
Q 021860 257 INEAVDLAKRFCDGAAPRIINGCLRTFVRNL 287 (306)
Q Consensus 257 INEAVELAKkyg~~~s~kFVNGVLrki~R~~ 287 (306)
|||+|+|||+|+++++++|||||||++.++.
T Consensus 99 vneaVelak~~~~~~~~~fVNgVLr~i~~~~ 129 (445)
T PRK14904 99 VNECVKLARKYKGEHMAKLVNGVLRNISPET 129 (445)
T ss_pred HHHHHHHHHHhCCCccccchHHHHHHHHHhh
Confidence 9999999999999999999999999999975
No 11
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=99.89 E-value=7.7e-23 Score=201.01 Aligned_cols=125 Identities=22% Similarity=0.249 Sum_probs=109.2
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 021860 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (306)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~e 177 (306)
.+|+.|+|+||+++.+|.+++++++.++.. . .
T Consensus 4 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~------------------~------------------------------~ 35 (444)
T PRK14902 4 NARELALEVLIKVENNGAYSNIALNKVLKK------------------S------------------------------E 35 (444)
T ss_pred cHHHHHHHHHHHHHhcCCCHHHHHHHHHHh------------------c------------------------------C
Confidence 579999999999999999999998876541 0 0
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-CCChhhH
Q 021860 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-GTRHQIV 256 (306)
Q Consensus 178 ~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-diP~~Va 256 (306)
++.+|++|+++||+|+++|+..||++|++++++ + .+++ +++|+|||+|+|||+|. ++|++++
T Consensus 36 ---------l~~~d~~~~~~lv~g~lr~~~~ld~~i~~~~~~-~--~~l~-----~~~r~iLrla~~el~~~~~~p~~~~ 98 (444)
T PRK14902 36 ---------LSDKDKALLTELVYGTIQRKLTLDYYLAPFIKK-R--KKLD-----PWVRNLLRMSLYQLLYLDKVPDHAA 98 (444)
T ss_pred ---------CChHHHHHHHHHHHHHHHhHHHHHHHHHHHhhh-h--hhCC-----HHHHHHHHHHHHHHHhccCCCCcee
Confidence 234589999999999999999999999999865 2 3444 48899999999999997 5999999
Q ss_pred HHHHHHHHHhhCCCCCCCchhHHHhHHHhhh
Q 021860 257 INEAVDLAKRFCDGAAPRIINGCLRTFVRNL 287 (306)
Q Consensus 257 INEAVELAKkyg~~~s~kFVNGVLrki~R~~ 287 (306)
|||||+|||.|+++++++|||||||++.++.
T Consensus 99 ineav~lak~~~~~~~~~fVNaVL~~i~~~~ 129 (444)
T PRK14902 99 VNEAVEIAKKRGHKGIAKFVNGVLRNILREG 129 (444)
T ss_pred HHHHHHHHHHhCCCchhHHHHHHHHHHhhcc
Confidence 9999999999999999999999999999864
No 12
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=99.88 E-value=1.4e-22 Score=199.06 Aligned_cols=125 Identities=22% Similarity=0.248 Sum_probs=105.5
Q ss_pred HHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHhh
Q 021860 99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV 178 (306)
Q Consensus 99 ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~e~ 178 (306)
+|+.|+++||+++. |..+++++++.+.. +.
T Consensus 3 ~R~~A~~~L~~i~~-~~~~~~~l~~~~~~------------------~~------------------------------- 32 (434)
T PRK14901 3 ARQLAWEILQAVAR-GAYADVALERVLRK------------------YP------------------------------- 32 (434)
T ss_pred HHHHHHHHHHHHHc-CCchHHHHHHHHHh------------------cC-------------------------------
Confidence 79999999999997 67888888765541 00
Q ss_pred hcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhcc-CCChhhHH
Q 021860 179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVV-GTRHQIVI 257 (306)
Q Consensus 179 ~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~-diP~~VaI 257 (306)
++.+|++|+++||+||++|+..||++|+++++. ...+++ +++|+|||+|+|||+|+ ++|++++|
T Consensus 33 --------l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~~~--~~~~l~-----~~~r~iLrla~yel~~~~~~p~~aav 97 (434)
T PRK14901 33 --------LSGADRALVTELVYGCIRRRRTLDAWIDQLGKK--PAHKQP-----PDLRWLLHLGLYQLRYMDRIPASAAV 97 (434)
T ss_pred --------CChhHHHHHHHHHHHHHHhHHHHHHHHHHhcCC--ChhhcC-----HHHHHHHHHHHHHHHhCccCCcHHHH
Confidence 234589999999999999999999999999742 223333 47799999999999997 58999999
Q ss_pred HHHHHHHHhhCCCCCCCchhHHHhHHHhhhh
Q 021860 258 NEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 288 (306)
Q Consensus 258 NEAVELAKkyg~~~s~kFVNGVLrki~R~~~ 288 (306)
||+|+|||+|+.+++++|||||||++.++..
T Consensus 98 neaVelak~~~~~~~~~fVNgVLr~~~r~~~ 128 (434)
T PRK14901 98 NTTVELAKQNGLGGLAGVVNGILRQYLRARE 128 (434)
T ss_pred HHHHHHHHHcCchhhhhhcCHHHHHHHHhhh
Confidence 9999999999999999999999999999643
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=99.85 E-value=3.6e-21 Score=188.51 Aligned_cols=92 Identities=18% Similarity=0.130 Sum_probs=79.3
Q ss_pred cHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhc-cCCChhhHHHHHHHHHHh
Q 021860 188 SKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITV-VGTRHQIVINEAVDLAKR 266 (306)
Q Consensus 188 ~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf-~diP~~VaINEAVELAKk 266 (306)
+..|++|+++||+||++|+..||++|+++++.++ +++. ++++ +||+++||++| +++|++++|||||+|||+
T Consensus 29 ~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~~~~~-----~~l~--~~~~-~L~~~~~e~l~~~~~p~~aainEaVelaK~ 100 (426)
T TIGR00563 29 SDQDRALLQELCFGVLRTLSQLDWLIKKLMDRPM-----KGKP--RTVH-YLILVGLYQLLYTRIPAHAAVAETVEGAKA 100 (426)
T ss_pred CHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCCCc-----cccC--HHHH-HHHHHHHHHHhcCCCCCEehHHHHHHHHHh
Confidence 3458999999999999999999999999986433 2333 3545 88888888876 689999999999999999
Q ss_pred hCCCCCCCchhHHHhHHHhhh
Q 021860 267 FCDGAAPRIINGCLRTFVRNL 287 (306)
Q Consensus 267 yg~~~s~kFVNGVLrki~R~~ 287 (306)
|+++++++|||||||++.++.
T Consensus 101 ~~~~~~~~fVNgVLr~i~r~~ 121 (426)
T TIGR00563 101 IKRKGLKGLVNGVLRRFQREQ 121 (426)
T ss_pred cCCccchhhHHHHHHHHhhcc
Confidence 999999999999999999964
No 14
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=99.83 E-value=3e-20 Score=183.32 Aligned_cols=118 Identities=17% Similarity=0.116 Sum_probs=101.5
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhcccCCCCCccchhhhhhhhcccCCCCCCcccchhHHHHhhhhhhHHHHHHHh
Q 021860 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (306)
Q Consensus 98 ~ARe~Avq~LYq~e~~g~~~~e~le~~l~~~~~~~~~~~~~~~~e~~~~~~g~~~~~~~~~~e~~~~~~~~~~~~~~~~e 177 (306)
.+|++|+.+|+++...|.....+++..+..
T Consensus 4 ~~R~~A~~~L~~v~~~~~~~~~~l~~~~~~-------------------------------------------------- 33 (431)
T PRK14903 4 NVRLLAYRLLRKYEKEKFIFREDVDSVLSF-------------------------------------------------- 33 (431)
T ss_pred CHHHHHHHHHHHHHhCCCchHHHHHHHHHh--------------------------------------------------
Confidence 479999999999999998888877653320
Q ss_pred hhcCCCcccccHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhccC-CChhhH
Q 021860 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVG-TRHQIV 256 (306)
Q Consensus 178 ~~~~~p~~~~~~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~d-iP~~Va 256 (306)
++.+|++|+++||+||++++..||++|++++++ | ++++ ++|+|||+|+|||+|++ +|++++
T Consensus 34 ---------l~~~d~~~~~~lv~gvlr~~~~lD~~i~~~~~~-~---~l~~-----~~r~iLr~~~yel~~~~~~p~~aa 95 (431)
T PRK14903 34 ---------LDDKDRRFFKELVWGVVRKEELLDWYINQLLKK-K---DIPP-----AVRVALRMGAYQLLFMNSVPDYAA 95 (431)
T ss_pred ---------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-C---CCCH-----HHHHHHHHHHHHHHhccCCCccee
Confidence 245689999999999999999999999999854 3 3553 67999999999999986 699999
Q ss_pred HHHHHHHHHhhCCCCCCCchhHHHhHHHhh
Q 021860 257 INEAVDLAKRFCDGAAPRIINGCLRTFVRN 286 (306)
Q Consensus 257 INEAVELAKkyg~~~s~kFVNGVLrki~R~ 286 (306)
|||+|+|||.+ +.++|||||||++.|+
T Consensus 96 vneaV~lak~~---~~~~fVNaVLr~~~r~ 122 (431)
T PRK14903 96 VSETVKLVKNE---NFKKLVNAVLRRLRTV 122 (431)
T ss_pred HHHHHHHHhcc---chHHHHHHHHHHHHHh
Confidence 99999999986 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=65.17 E-value=90 Score=26.86 Aligned_cols=85 Identities=16% Similarity=0.192 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCcCCCCCCCcccHHHHHHHHHHHHhhhccCCChhhHHHHHHHHHHhhC
Q 021860 189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKVWKMDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFC 268 (306)
Q Consensus 189 ~~Dr~fa~eLV~GVlr~~~~LD~lId~lL~k~~k~~rldrl~~~~VdraILRlAlYELlf~diP~~VaINEAVELAKkyg 268 (306)
++--.|...+-..-.+|+.++..--.+. .+++++- +-.+++..|+.|-.-..+..+..|.||+-+.-.|+
T Consensus 55 e~~~~f~~~ie~qq~~nq~eiq~kynki-----sgkkidl-----lt~avilcalseq~a~~tdkplliseallimdhys 124 (140)
T PF09185_consen 55 ENCFSFQKKIENQQQRNQAEIQSKYNKI-----SGKKIDL-----LTKAVILCALSEQHAQNTDKPLLISEALLIMDHYS 124 (140)
T ss_dssp HHHHHHHHHHHHHHHH---S-------------------H-----HHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccc-----ccchhhH-----HHHHHHHHHhhHHHhhcCCCchhHHHHHHHHHHHh
Confidence 3444555555555566665544333332 2234442 33677777787776667889999999999999998
Q ss_pred CCCCCCchhHHHhHH
Q 021860 269 DGAAPRIINGCLRTF 283 (306)
Q Consensus 269 ~~~s~kFVNGVLrki 283 (306)
.....+=-+|.||++
T Consensus 125 q~~ekkqthalldkl 139 (140)
T PF09185_consen 125 QVPEKKQTHALLDKL 139 (140)
T ss_dssp ---TTS-S-TTTS--
T ss_pred hchhHHHHHHHHHhh
Confidence 777777788888876
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=40.42 E-value=29 Score=25.86 Aligned_cols=32 Identities=25% Similarity=0.222 Sum_probs=25.5
Q ss_pred hhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhh
Q 021860 254 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 286 (306)
Q Consensus 254 ~VaINEAVELAKkyg~~~s~kFVNGVLrki~R~ 286 (306)
.-+|++|++.|...+ ....++|++||.+-.+.
T Consensus 32 ~evI~~ai~~a~~~~-~~~~~Yi~~Il~~W~~~ 63 (73)
T TIGR01446 32 PELIKEALKEAVSNN-KANYKYIDAILNNWKNN 63 (73)
T ss_pred HHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHc
Confidence 669999999988744 44578999999987654
No 17
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=30.12 E-value=41 Score=26.41 Aligned_cols=50 Identities=18% Similarity=0.159 Sum_probs=37.6
Q ss_pred HHHHHHHHHhhhccC-CChhhHHHHHHHHHHhhCCCCCCCchhHHHhHHHh
Q 021860 236 LSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 285 (306)
Q Consensus 236 raILRlAlYELlf~d-iP~~VaINEAVELAKkyg~~~s~kFVNGVLrki~R 285 (306)
.++|.+|.....+.+ -....+++|+|.+|++.++...-.++...|-.+.+
T Consensus 42 ~all~lA~~~~~~G~~~~A~~~l~eAi~~Are~~D~~~l~~al~~~~~l~~ 92 (94)
T PF12862_consen 42 YALLNLAELHRRFGHYEEALQALEEAIRLARENGDRRCLAYALSWLANLLK 92 (94)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHhh
Confidence 667788887777754 45677899999999999887666666666665543
No 18
>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=27.73 E-value=60 Score=24.01 Aligned_cols=34 Identities=21% Similarity=0.222 Sum_probs=25.7
Q ss_pred ChhhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhh
Q 021860 252 RHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 286 (306)
Q Consensus 252 P~~VaINEAVELAKkyg~~~s~kFVNGVLrki~R~ 286 (306)
=+.-+|++|++.|... +....++|.+||++-.+.
T Consensus 30 ~~~~~v~~ai~~~~~~-~~~~~~Yi~~Il~~W~~~ 63 (77)
T PF07261_consen 30 FSPEVVNEAIEYALEN-NKRSFNYIEKILNNWKQK 63 (77)
T ss_dssp HHHHHHHHHHHHHHHC-T--SHHHHHHHHHHHHHC
T ss_pred CCHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHc
Confidence 3556899999999954 444589999999998764
No 19
>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=26.34 E-value=80 Score=25.74 Aligned_cols=46 Identities=17% Similarity=0.150 Sum_probs=31.3
Q ss_pred cCCChhhHHHHHHHHHHhhCCCCCCCchhHHHhHHHhhhhccccccc
Q 021860 249 VGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTANIEA 295 (306)
Q Consensus 249 ~diP~~VaINEAVELAKkyg~~~s~kFVNGVLrki~R~~~~~e~~~~ 295 (306)
++---..+|+|||.+|++ |.+=+..-||+|-.++-.--..+-.|.+
T Consensus 24 Le~~RE~aIeeav~~c~~-g~pFs~d~IN~vT~~mN~LAk~givP~R 69 (84)
T PF10752_consen 24 LEQQREAAIEEAVSLCKQ-GEPFSTDKINEVTKEMNELAKQGIVPTR 69 (84)
T ss_pred HHHHHHHHHHHHHHHHHC-CCCCcHHHHHHHHHHHHHHHHcCCCCcc
Confidence 344567899999999998 5566677799987776443333444433
No 20
>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=25.46 E-value=67 Score=27.12 Aligned_cols=50 Identities=18% Similarity=0.179 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHhhhccC-CChhhHHHHHHHHHHhhCC-CCCCCchhHHHhHH
Q 021860 234 LELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCD-GAAPRIINGCLRTF 283 (306)
Q Consensus 234 VdraILRlAlYELlf~d-iP~~VaINEAVELAKkyg~-~~s~kFVNGVLrki 283 (306)
+|..-+|-|+-.|.-.+ ||.+.||+-|+..|++..+ .-+.+|+-||=+|.
T Consensus 21 iD~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~ 72 (103)
T cd00923 21 IDGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKC 72 (103)
T ss_pred ccHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc
Confidence 56778899998888654 9999999999999998754 34667777776665
Done!