Query 024057
Match_columns 273
No_of_seqs 155 out of 280
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 08:37:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024057.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024057hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0781 NusB Transcription ter 99.9 1.4E-27 3E-32 202.7 10.9 119 92-264 6-126 (151)
2 PF01029 NusB: NusB family; I 99.9 2.4E-23 5.1E-28 166.7 13.3 74 189-264 43-117 (134)
3 PRK00202 nusB transcription an 99.9 2.5E-21 5.4E-26 157.2 11.8 111 95-264 2-113 (137)
4 cd00619 Terminator_NusB Transc 99.9 2.6E-21 5.6E-26 154.9 11.5 110 96-264 1-111 (130)
5 TIGR01951 nusB transcription a 99.8 2.9E-20 6.2E-25 148.4 11.5 110 96-264 1-111 (129)
6 cd00620 Methyltransferase_Sun 99.8 9.3E-19 2E-23 140.4 12.3 105 99-264 3-107 (126)
7 PRK09634 nusB transcription an 99.8 1.2E-18 2.6E-23 155.1 8.7 74 189-264 110-183 (207)
8 cd00447 NusB_Sun RNA binding d 99.8 8.3E-18 1.8E-22 133.6 11.9 72 191-264 37-110 (129)
9 PRK10901 16S rRNA methyltransf 99.7 6.2E-17 1.3E-21 153.3 12.6 105 98-264 3-107 (427)
10 PRK14901 16S rRNA methyltransf 99.7 1.6E-16 3.4E-21 150.8 11.9 105 99-264 3-108 (434)
11 PRK14904 16S rRNA methyltransf 99.7 1.5E-16 3.2E-21 151.4 11.7 107 98-264 3-110 (445)
12 PRK14902 16S rRNA methyltransf 99.7 3.7E-16 7.9E-21 148.2 11.9 106 98-264 4-110 (444)
13 TIGR00563 rsmB ribosomal RNA s 99.5 3.2E-14 7E-19 134.6 10.3 70 191-264 32-102 (426)
14 PRK14903 16S rRNA methyltransf 99.4 2E-12 4.2E-17 123.8 11.6 101 99-263 5-106 (431)
15 COG3413 Predicted DNA binding 73.9 3 6.5E-05 36.6 2.8 37 225-266 155-191 (215)
16 PF04967 HTH_10: HTH DNA bindi 71.5 4.6 9.9E-05 29.6 2.9 31 231-265 5-35 (53)
17 PF01029 NusB: NusB family; I 35.7 92 0.002 24.9 5.1 41 193-234 43-83 (134)
18 PF08257 Sulfakinin: Sulfakini 33.0 17 0.00037 18.6 0.3 8 141-148 2-9 (9)
19 cd00619 Terminator_NusB Transc 32.2 43 0.00092 26.9 2.6 74 156-233 3-76 (130)
20 PF06580 His_kinase: Histidine 29.5 8.4 0.00018 29.4 -1.8 6 16-21 11-16 (82)
21 COG0781 NusB Transcription ter 23.2 75 0.0016 27.6 2.7 37 195-232 54-90 (151)
No 1
>COG0781 NusB Transcription termination factor [Transcription]
Probab=99.95 E-value=1.4e-27 Score=202.73 Aligned_cols=119 Identities=26% Similarity=0.265 Sum_probs=94.8
Q ss_pred CCCChHHHHHHHHHHHHHHHhcCC-ChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhH
Q 024057 92 RFCSPRAARELALLVVYAACLEGS-DPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEE 170 (273)
Q Consensus 92 Rf~srR~ARElALQvLYa~dl~g~-dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~ 170 (273)
+-.+||+||++|+|+||+|+++|. ++..+++.... . |.+ - +++..
T Consensus 6 ~~~~R~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~~---~----~~~--------------------------~-d~~~~ 51 (151)
T COG0781 6 PKLTRRQARELAVQALYQWELSGSVSAEDILEDIEE---E----FVE--------------------------N-ELDIE 51 (151)
T ss_pred ccchHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHH---H----Hhh--------------------------c-ccchh
Confidence 346899999999999999999886 33344433211 0 100 0 00000
Q ss_pred HHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCc
Q 024057 171 ESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRH 249 (273)
Q Consensus 171 ~s~~ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~ 249 (273)
..+..|+.+|+.||.+|..++|+.|..++ .+|+++||+. |||+|||+|+|||+| .|||+
T Consensus 52 ------------------~~~~~~~~~lv~gv~~~~~~iD~~I~~~L-~~w~~~rL~~-verAILRla~yEl~~~~dvP~ 111 (151)
T COG0781 52 ------------------LADSEYFRSLVKGVLENQEELDELISPHL-KKWSLERLDL-VERAILRLALYELLFRDDVPY 111 (151)
T ss_pred ------------------hhhHHHHHHHHHHHHHHHHHHHHHHHHHH-ccCCHHHhhH-HHHHHHHHHHHHHHhcCCCCC
Confidence 13579999999999999999999999999 4699999998 799999999999999 56999
Q ss_pred cchHhHHHHHHHHHh
Q 024057 250 QIVINEARLTLHFLF 264 (273)
Q Consensus 250 kVaINEAVELAK~f~ 264 (273)
+|+|||||||||+|+
T Consensus 112 ~VvInEaielaK~f~ 126 (151)
T COG0781 112 KVVINEAIELAKKFS 126 (151)
T ss_pred cchHHHHHHHHHHhC
Confidence 999999999999996
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=99.90 E-value=2.4e-23 Score=166.71 Aligned_cols=74 Identities=22% Similarity=0.224 Sum_probs=69.7
Q ss_pred HHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc-CCCccchHhHHHHHHHHHh
Q 024057 189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEARLTLHFLF 264 (273)
Q Consensus 189 ~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~-DvP~kVaINEAVELAK~f~ 264 (273)
..+..|+++|+.|+..++..+|..|+++ .++|+++||+. ++++|||||+|||+|. ++|++|+|||||||||+|+
T Consensus 43 ~~d~~~~~~lv~gv~~~~~~ld~~i~~~-~~~~~~~rl~~-~~~~iLrla~~El~~~~~~p~~v~InEaVelak~~~ 117 (134)
T PF01029_consen 43 EEDRAFARELVYGVLRNKEELDALISKL-LKNWPLERLPP-VDRAILRLAIYELLFLDDIPPHVAINEAVELAKKYG 117 (134)
T ss_dssp HHHHHHHHHHHHHHHHTHHHHHHHHHHT-STSSTGGGSGH-HHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-hccCCccccCH-HHHHHHHHHHHHHHhcCCCCccchHHHHHHHHHHhC
Confidence 4578999999999999999999999996 48999999998 7999999999999996 9999999999999999994
No 3
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=99.86 E-value=2.5e-21 Score=157.19 Aligned_cols=111 Identities=27% Similarity=0.312 Sum_probs=97.0
Q ss_pred ChHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHH
Q 024057 95 SPRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAI 174 (273)
Q Consensus 95 srR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ 174 (273)
+||.+|++|+|+||++...|....+++++.+. .. +.
T Consensus 2 ~r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~---~~--~~--------------------------------------- 37 (137)
T PRK00202 2 ARRKAREAAVQALYQWELSGNDIAEIIEAQLL---EE--QY--------------------------------------- 37 (137)
T ss_pred chHHHHHHHHHHHHHHHccCCCHHHHHHHHHH---hc--cc---------------------------------------
Confidence 68999999999999999999998888887443 00 00
Q ss_pred HHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc-CCCccchH
Q 024057 175 EAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVI 253 (273)
Q Consensus 175 ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~-DvP~kVaI 253 (273)
+..+..|+++|+.|+..++..+|..|++.+ ++|+.++|+. ++++|||+|+|||+|. ++|+.++|
T Consensus 38 -------------~~~d~~~~~~lv~gvlr~~~~lD~ii~~~l-~~~~~~~l~~-~~~~iLr~a~~Ell~~~~~p~~~vi 102 (137)
T PRK00202 38 -------------DKADPAYFRSLVRGVVENQAELDELISPYL-KDWTLERLDP-VERAILRLALYELLFRDDVPYKVVI 102 (137)
T ss_pred -------------chhhHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCHHHhhH-HHHHHHHHHHHHHHhCCCCCCcchH
Confidence 123579999999999999999999999998 5699999998 7999999999999996 89999999
Q ss_pred hHHHHHHHHHh
Q 024057 254 NEARLTLHFLF 264 (273)
Q Consensus 254 NEAVELAK~f~ 264 (273)
||||||||+|+
T Consensus 103 nEaV~lak~~~ 113 (137)
T PRK00202 103 NEAIELAKKFG 113 (137)
T ss_pred HHHHHHHHHHC
Confidence 99999999875
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=99.86 E-value=2.6e-21 Score=154.95 Aligned_cols=110 Identities=28% Similarity=0.255 Sum_probs=94.5
Q ss_pred hHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHH
Q 024057 96 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 175 (273)
Q Consensus 96 rR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~e 175 (273)
||.+|+.|+|+||++...|.+..+++++.+. . .+
T Consensus 1 r~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~---~----~~--------------------------------------- 34 (130)
T cd00619 1 RRRARELAVQALYAWELAPEILAEVVSLLEL---L----QY--------------------------------------- 34 (130)
T ss_pred ChHHHHHHHHHHHHHHhcCCCHHHHHHHHHH---h----cc---------------------------------------
Confidence 6789999999999999999888777765332 0 00
Q ss_pred HhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccC-CCccchHh
Q 024057 176 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVIN 254 (273)
Q Consensus 176 a~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~D-vP~kVaIN 254 (273)
. ++.+..|+.+|+.|+..++..+|..|++++ ++|+.++++. ++++|||+|+|||+|.+ +|+.|+||
T Consensus 35 -----~------~~~d~~~~~~lv~gvlr~~~~ld~ii~~~l-~~~~~~~l~~-~~~~iLria~~el~~~~~~p~~~vin 101 (130)
T cd00619 35 -----K------SKKVLPFALKLVRGVLENIEEIDELIEKHL-RNWSLDRLAI-VERAILRLAVYELLFLPDVPHPVVIN 101 (130)
T ss_pred -----c------chhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCCHHHhhH-HHHHHHHHHHHHHHhCCCCCCcchHH
Confidence 0 022579999999999999999999999998 6999889998 69999999999999965 99999999
Q ss_pred HHHHHHHHHh
Q 024057 255 EARLTLHFLF 264 (273)
Q Consensus 255 EAVELAK~f~ 264 (273)
|||||||+|+
T Consensus 102 EaV~lak~~~ 111 (130)
T cd00619 102 EAIELAKRFG 111 (130)
T ss_pred HHHHHHHHHC
Confidence 9999999985
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=99.83 E-value=2.9e-20 Score=148.42 Aligned_cols=110 Identities=25% Similarity=0.258 Sum_probs=95.1
Q ss_pred hHHHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHH
Q 024057 96 PRAARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIE 175 (273)
Q Consensus 96 rR~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~e 175 (273)
||.+|+.|+|+||++...|....+++++.+. . +
T Consensus 1 ~~~~R~~a~~~l~~~~~~~~~~~~~l~~~~~---~----~---------------------------------------- 33 (129)
T TIGR01951 1 RRKARELALQALYQWELSGNDVEEIIEEFLE---E----R---------------------------------------- 33 (129)
T ss_pred ChHHHHHHHHHHHHHHcCCCCHHHHHHHHHH---h----c----------------------------------------
Confidence 5789999999999999999988888876432 0 0
Q ss_pred HhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc-CCCccchHh
Q 024057 176 AEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVIN 254 (273)
Q Consensus 176 a~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~-DvP~kVaIN 254 (273)
..+ ..+..|+++|+.|+..++..+|..|+++++ +|+.++++. ++++|||+|+|||+|. ++|+.++||
T Consensus 34 ----~l~------~~d~~~~~~lv~~~lr~~~~ld~~i~~~~~-~~~~~~l~~-~~~~iLr~a~~el~~~~~~p~~avin 101 (129)
T TIGR01951 34 ----ELD------EEDREYFLELVRGVLENQEEIDELISPHLK-DWSLERLDP-VDRAILRLAAYELLYRPDVPYKVVIN 101 (129)
T ss_pred ----ccc------hhHHHHHHHHHHHHHHhHHHHHHHHHHHhc-CCCHHHhhH-HHHHHHHHHHHHHHhCCCCCCcchHH
Confidence 001 225799999999999999999999999985 899999998 6999999999999996 799999999
Q ss_pred HHHHHHHHHh
Q 024057 255 EARLTLHFLF 264 (273)
Q Consensus 255 EAVELAK~f~ 264 (273)
|||||||+++
T Consensus 102 eaV~lak~~~ 111 (129)
T TIGR01951 102 EAVELAKKFG 111 (129)
T ss_pred HHHHHHHHHC
Confidence 9999999975
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=99.79 E-value=9.3e-19 Score=140.42 Aligned_cols=105 Identities=10% Similarity=0.014 Sum_probs=89.0
Q ss_pred HHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHhh
Q 024057 99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV 178 (273)
Q Consensus 99 ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~v 178 (273)
+|+.|+|+||++...|....+++.+.+. . .
T Consensus 3 ~R~~A~~~L~~v~~~~~~~~~~l~~~~~---~----~------------------------------------------- 32 (126)
T cd00620 3 ARSTAAEVLRDVLQRGASLNAVLSALQK---K----D------------------------------------------- 32 (126)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHH---h----c-------------------------------------------
Confidence 6999999999999999988888876332 0 0
Q ss_pred hcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccCCCccchHhHHHH
Q 024057 179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARL 258 (273)
Q Consensus 179 l~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEAVE 258 (273)
.+ ..+..|+.+|+.|+..++.++|..|++++ ..|. .+++. ++++|||+|+|||+|.++|+.++||||||
T Consensus 33 --~~------~~d~~~~~~lv~g~~r~~~~ld~~i~~~l-~~~~-~~~~~-~~~~iLr~a~~el~~~~~p~~avvneaVe 101 (126)
T cd00620 33 --KS------DRDRGLATELVYGTLRWLALLDWIINPLL-KKPD-VGKDP-DVRNLLRLGLYQLLYLDVPPHAAVDETVE 101 (126)
T ss_pred --CC------HHHHHHHHHHHHHHHHhHHHHHHHHHHHh-CCCc-cccCH-HHHHHHHHHHHHHHhcCCCchHHHHHHHH
Confidence 01 12579999999999999999999999998 3444 48888 69999999999999977999999999999
Q ss_pred HHHHHh
Q 024057 259 TLHFLF 264 (273)
Q Consensus 259 LAK~f~ 264 (273)
|||+++
T Consensus 102 lak~~~ 107 (126)
T cd00620 102 IAKIRK 107 (126)
T ss_pred HHHHhC
Confidence 999985
No 7
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=99.76 E-value=1.2e-18 Score=155.09 Aligned_cols=74 Identities=23% Similarity=0.276 Sum_probs=70.7
Q ss_pred HHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccCCCccchHhHHHHHHHHHh
Q 024057 189 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLF 264 (273)
Q Consensus 189 ~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEAVELAK~f~ 264 (273)
+.+..|+.+|+.||..++..+|..|++++ ++|++.|+++ +|++|||||+|||+|.++|+.|+|||||||||+|+
T Consensus 110 ~~~r~~a~~Lv~gvlr~~~~LD~iI~~~l-~~W~l~rL~~-idr~ILRlavyELl~l~~P~~vaINEAVeLAK~~~ 183 (207)
T PRK09634 110 EEVREYALERIGAVIRNRKEIDQLLDTVM-VGWQLKRLPR-IDRDILRLAVVEILFLNTPAAVAINEAVELAKRYS 183 (207)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHh-ccccccCCCH-HHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHhC
Confidence 55789999999999999999999999998 7999999999 69999999999999989999999999999999986
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=99.76 E-value=8.3e-18 Score=133.65 Aligned_cols=72 Identities=19% Similarity=0.212 Sum_probs=67.5
Q ss_pred HHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc--CCCccchHhHHHHHHHHHh
Q 024057 191 LLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV--GTRHQIVINEARLTLHFLF 264 (273)
Q Consensus 191 ~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~--DvP~kVaINEAVELAK~f~ 264 (273)
+..|+.+|+.|+.+++..+|..|++++ ++|..+||+. +|+.||||+++||.+. ++|+.++|||||||||+++
T Consensus 37 d~~~~~~lv~gv~r~~~~ld~~i~~~~-~~~~~~r~~~-~~~~il~l~~~el~~~~~~~p~~~vineaVelak~~~ 110 (129)
T cd00447 37 DRPFALELVYGVLRNLPELDDIISPLL-KKWLLDRLDK-VDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFG 110 (129)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCChhhhhH-HHHHHHHHHHHHHHhCcCCCCchhHHHHHHHHHHHHC
Confidence 579999999999999999999999998 7999999999 6999999999999974 6899999999999999985
No 9
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=99.71 E-value=6.2e-17 Score=153.27 Aligned_cols=105 Identities=11% Similarity=0.083 Sum_probs=91.4
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHh
Q 024057 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (273)
Q Consensus 98 ~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~ 177 (273)
.+|+.|+|+||++..+|.....++.+.++ . +
T Consensus 3 ~~R~~a~~~L~~~~~~~~~~~~~l~~~~~---~----l------------------------------------------ 33 (427)
T PRK10901 3 NLRALAAAAILQVVDQGQSLSAALPALQQ---K----V------------------------------------------ 33 (427)
T ss_pred hHHHHHHHHHHHHHHcCCcHHHHHHHHHh---h----C------------------------------------------
Confidence 47999999999999999988887766221 0 0
Q ss_pred hhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccCCCccchHhHHH
Q 024057 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAR 257 (273)
Q Consensus 178 vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEAV 257 (273)
.+.+..|+.+||.||+.++..+|.+|++++ +|+.++++. ++|+|||||+|||+|.++|+.++|||||
T Consensus 34 ----------~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~--~~~~~~l~~-~~r~iLrla~yell~~~iP~~a~vneaV 100 (427)
T PRK10901 34 ----------SDKDRALLQELCYGVLRRLPRLEWLIAQLL--AKPLKGKQR-IVHALLLVGLYQLLYTRIPAHAAVDETV 100 (427)
T ss_pred ----------CHHHHHHHHHHHHHHHHhHHHHHHHHHHHh--CCCccccCH-HHHHHHHHHHHHHhccCCCcchHHHHHH
Confidence 123579999999999999999999999987 678889998 7999999999999997799999999999
Q ss_pred HHHHHHh
Q 024057 258 LTLHFLF 264 (273)
Q Consensus 258 ELAK~f~ 264 (273)
||||+|+
T Consensus 101 elak~~~ 107 (427)
T PRK10901 101 EAAKALK 107 (427)
T ss_pred HHHHhcC
Confidence 9999985
No 10
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=99.69 E-value=1.6e-16 Score=150.84 Aligned_cols=105 Identities=15% Similarity=0.062 Sum_probs=87.9
Q ss_pred HHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHhh
Q 024057 99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV 178 (273)
Q Consensus 99 ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~v 178 (273)
+|+.|+|+||+++. |.+..+++++.+...+ +
T Consensus 3 ~R~~A~~~L~~i~~-~~~~~~~l~~~~~~~~-----l------------------------------------------- 33 (434)
T PRK14901 3 ARQLAWEILQAVAR-GAYADVALERVLRKYP-----L------------------------------------------- 33 (434)
T ss_pred HHHHHHHHHHHHHc-CCchHHHHHHHHHhcC-----C-------------------------------------------
Confidence 79999999999988 7777777776443000 1
Q ss_pred hcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhccc-CCCccchHhHHH
Q 024057 179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVV-GTRHQIVINEAR 257 (273)
Q Consensus 179 l~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~-DvP~kVaINEAV 257 (273)
+..+..|+.+||.||+.++..+|..|++++ +|...+|+. ++|+|||||+|||+|. ++|+.++|||||
T Consensus 34 ---------~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~--~~~~~~l~~-~~r~iLrla~yel~~~~~~p~~aavneaV 101 (434)
T PRK14901 34 ---------SGADRALVTELVYGCIRRRRTLDAWIDQLG--KKPAHKQPP-DLRWLLHLGLYQLRYMDRIPASAAVNTTV 101 (434)
T ss_pred ---------ChhHHHHHHHHHHHHHHhHHHHHHHHHHhc--CCChhhcCH-HHHHHHHHHHHHHHhCccCCcHHHHHHHH
Confidence 122579999999999999999999999985 566678998 7999999999999994 689999999999
Q ss_pred HHHHHHh
Q 024057 258 LTLHFLF 264 (273)
Q Consensus 258 ELAK~f~ 264 (273)
||||+|+
T Consensus 102 elak~~~ 108 (434)
T PRK14901 102 ELAKQNG 108 (434)
T ss_pred HHHHHcC
Confidence 9999985
No 11
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=99.69 E-value=1.5e-16 Score=151.43 Aligned_cols=107 Identities=18% Similarity=0.091 Sum_probs=91.6
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHh
Q 024057 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (273)
Q Consensus 98 ~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~ 177 (273)
.+|++|+|+||+++..|.....++.+.+. . +
T Consensus 3 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~---~----~------------------------------------------ 33 (445)
T PRK14904 3 TARELALQVLQELETGERKSDTLLHRMLE---R----S------------------------------------------ 33 (445)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHHHH---h----c------------------------------------------
Confidence 58999999999999999888888876442 0 0
Q ss_pred hhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchHhHH
Q 024057 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEA 256 (273)
Q Consensus 178 vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaINEA 256 (273)
. +++.+..|+.+||.||+.++..+|..|++++ +|+..+|+. ++|+|||+|+|||+| .++|+.|+||||
T Consensus 34 ---~-----l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~--~~~~~rl~~-~~r~iLrla~~ell~~~~~p~~a~vnea 102 (445)
T PRK14904 34 ---S-----LERNDRALATELVNGVLRYRLQLDFIISRFY--HHDLEKAAP-VLKNILRLGVYQLLFLDRVPRWAAVNEC 102 (445)
T ss_pred ---C-----CChHHHHHHHHHHHHHHHHHHHHHHHHHHHc--CCChhhCCH-HHHHHHHHHHHHHHhCCCCCCeeeHHHH
Confidence 0 0123579999999999999999999999997 588889998 799999999999999 568999999999
Q ss_pred HHHHHHHh
Q 024057 257 RLTLHFLF 264 (273)
Q Consensus 257 VELAK~f~ 264 (273)
|||||+|+
T Consensus 103 Velak~~~ 110 (445)
T PRK14904 103 VKLARKYK 110 (445)
T ss_pred HHHHHHhC
Confidence 99999984
No 12
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=99.67 E-value=3.7e-16 Score=148.24 Aligned_cols=106 Identities=15% Similarity=0.065 Sum_probs=91.0
Q ss_pred HHHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHh
Q 024057 98 AARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAE 177 (273)
Q Consensus 98 ~ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~ 177 (273)
.|||.|+|+||+++..|.++.+++++.+. . .
T Consensus 4 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~---~----~------------------------------------------ 34 (444)
T PRK14902 4 NARELALEVLIKVENNGAYSNIALNKVLK---K----S------------------------------------------ 34 (444)
T ss_pred cHHHHHHHHHHHHHhcCCCHHHHHHHHHH---h----c------------------------------------------
Confidence 68999999999999999999888887543 1 0
Q ss_pred hhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchHhHH
Q 024057 178 VLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEA 256 (273)
Q Consensus 178 vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaINEA 256 (273)
. .+..+..|+.+||.|++.++..+|.+|++++. + .+||+. ++|+|||||+|||+| +++|+.|+||||
T Consensus 35 ---~-----l~~~d~~~~~~lv~g~lr~~~~ld~~i~~~~~-~--~~~l~~-~~r~iLrla~~el~~~~~~p~~~~inea 102 (444)
T PRK14902 35 ---E-----LSDKDKALLTELVYGTIQRKLTLDYYLAPFIK-K--RKKLDP-WVRNLLRMSLYQLLYLDKVPDHAAVNEA 102 (444)
T ss_pred ---C-----CChHHHHHHHHHHHHHHHhHHHHHHHHHHHhh-h--hhhCCH-HHHHHHHHHHHHHHhccCCCCceeHHHH
Confidence 0 01235799999999999999999999999983 3 778998 799999999999998 569999999999
Q ss_pred HHHHHHHh
Q 024057 257 RLTLHFLF 264 (273)
Q Consensus 257 VELAK~f~ 264 (273)
|||||+|+
T Consensus 103 v~lak~~~ 110 (444)
T PRK14902 103 VEIAKKRG 110 (444)
T ss_pred HHHHHHhC
Confidence 99999984
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=99.53 E-value=3.2e-14 Score=134.64 Aligned_cols=70 Identities=11% Similarity=-0.038 Sum_probs=62.7
Q ss_pred HHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcc-cCCCccchHhHHHHHHHHHh
Q 024057 191 LLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITV-VGTRHQIVINEARLTLHFLF 264 (273)
Q Consensus 191 ~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~-~DvP~kVaINEAVELAK~f~ 264 (273)
+.+|+++||.||++++.++|..|++++ +|+..+++. +.+ |||+++||+++ .++|+.|+|||||||||+|+
T Consensus 32 d~~~~~~lv~gv~r~~~~lD~~i~~~~--~~~~~~l~~-~~~-~L~~~~~e~l~~~~~p~~aainEaVelaK~~~ 102 (426)
T TIGR00563 32 DRALLQELCFGVLRTLSQLDWLIKKLM--DRPMKGKPR-TVH-YLILVGLYQLLYTRIPAHAAVAETVEGAKAIK 102 (426)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHh--CCCccccCH-HHH-HHHHHHHHHHhcCCCCCEehHHHHHHHHHhcC
Confidence 579999999999999999999999986 577777886 455 99999999986 68999999999999999985
No 14
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=99.40 E-value=2e-12 Score=123.85 Aligned_cols=101 Identities=14% Similarity=0.002 Sum_probs=84.1
Q ss_pred HHHHHHHHHHHHHhcCCChHHHHHHHhhcccCCCCcccchhhhhhcccCCCCCCcccccHHHHHHhhhhhhHHHHHHHhh
Q 024057 99 ARELALLVVYAACLEGSDPIRLFEKRLNSRREPGYEFDKSSLLEYNHMSFGGPPVTTETVEEADELLRSDEEESAIEAEV 178 (273)
Q Consensus 99 ARElALQvLYa~dl~g~dp~~~~e~r~~~rre~~~~fd~~~l~~y~h~~~~g~p~~~~~~E~a~~L~~q~d~~s~~ea~v 178 (273)
+|++|+.+|+++.-.|.....++++.+. .
T Consensus 5 ~R~~A~~~L~~v~~~~~~~~~~l~~~~~---~------------------------------------------------ 33 (431)
T PRK14903 5 VRLLAYRLLRKYEKEKFIFREDVDSVLS---F------------------------------------------------ 33 (431)
T ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHHH---h------------------------------------------------
Confidence 6999999999998888766666654221 0
Q ss_pred hcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHHHHHHHhhhcccC-CCccchHhHHH
Q 024057 179 LSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVG-TRHQIVINEAR 257 (273)
Q Consensus 179 l~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ILRLAvYEml~~D-vP~kVaINEAV 257 (273)
++..+..|+.+||.||.+++..+|..|++++ .+| +|+. ++|+|||+|+|||+|.+ +|+.++|||||
T Consensus 34 --------l~~~d~~~~~~lv~gvlr~~~~lD~~i~~~~-~~~---~l~~-~~r~iLr~~~yel~~~~~~p~~aavneaV 100 (431)
T PRK14903 34 --------LDDKDRRFFKELVWGVVRKEELLDWYINQLL-KKK---DIPP-AVRVALRMGAYQLLFMNSVPDYAAVSETV 100 (431)
T ss_pred --------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCC---CCCH-HHHHHHHHHHHHHHhccCCCcceeHHHHH
Confidence 1134679999999999999999999999987 677 5887 69999999999999965 69999999999
Q ss_pred HHHHHH
Q 024057 258 LTLHFL 263 (273)
Q Consensus 258 ELAK~f 263 (273)
||||+.
T Consensus 101 ~lak~~ 106 (431)
T PRK14903 101 KLVKNE 106 (431)
T ss_pred HHHhcc
Confidence 999975
No 15
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=73.90 E-value=3 Score=36.62 Aligned_cols=37 Identities=16% Similarity=0.104 Sum_probs=31.0
Q ss_pred CcchhhhHHHHHHHHhhhcccCCCccchHhHHHHHHHHHhHH
Q 024057 225 PAGRILELSILHLAMSEITVVGTRHQIVINEARLTLHFLFIV 266 (273)
Q Consensus 225 Rm~rIVDr~ILRLAvYEml~~DvP~kVaINEAVELAK~f~~~ 266 (273)
.|.. -++.|||+| |+|=|-|.|-+|-+. ||||.|||-
T Consensus 155 ~LTd-rQ~~vL~~A-~~~GYFd~PR~~~l~---dLA~~lGIS 191 (215)
T COG3413 155 DLTD-RQLEVLRLA-YKMGYFDYPRRVSLK---DLAKELGIS 191 (215)
T ss_pred cCCH-HHHHHHHHH-HHcCCCCCCccCCHH---HHHHHhCCC
Confidence 3444 388999997 999999999999876 699999983
No 16
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=71.51 E-value=4.6 Score=29.58 Aligned_cols=31 Identities=23% Similarity=0.162 Sum_probs=27.4
Q ss_pred hHHHHHHHHhhhcccCCCccchHhHHHHHHHHHhH
Q 024057 231 ELSILHLAMSEITVVGTRHQIVINEARLTLHFLFI 265 (273)
Q Consensus 231 Dr~ILRLAvYEml~~DvP~kVaINEAVELAK~f~~ 265 (273)
++.||+.| ||+=|-|+|-.+.+. |||+.+||
T Consensus 5 Q~e~L~~A-~~~GYfd~PR~~tl~---elA~~lgi 35 (53)
T PF04967_consen 5 QREILKAA-YELGYFDVPRRITLE---ELAEELGI 35 (53)
T ss_pred HHHHHHHH-HHcCCCCCCCcCCHH---HHHHHhCC
Confidence 68899987 899999999999987 58999987
No 17
>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=35.75 E-value=92 Score=24.91 Aligned_cols=41 Identities=17% Similarity=0.118 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHHH
Q 024057 193 RFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSI 234 (273)
Q Consensus 193 ~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~I 234 (273)
.--+.++...+.+..++...||.+|.+.-+.|++.+ ++.-+
T Consensus 43 ~~d~~~~~~lv~gv~~~~~~ld~~i~~~~~~~~~~r-l~~~~ 83 (134)
T PF01029_consen 43 EEDRAFARELVYGVLRNKEELDALISKLLKNWPLER-LPPVD 83 (134)
T ss_dssp HHHHHHHHHHHHHHHHTHHHHHHHHHHTSTSSTGGG-SGHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCccc-cCHHH
Confidence 566788899999999999999999988667999999 88743
No 18
>PF08257 Sulfakinin: Sulfakinin family; InterPro: IPR013259 The sulfakinin (SK) family of neuropeptides have only been identified in crustaceans and insects. For most species there is the potential for producing two sulfakinin peptides, one has a short sulfakinin sequence. The function of the sulfakinins is difficult to assess. For the Periplaneta americana (American cockroach), various forms of the endogenous sulfakinins have been shown to be active on the hindgut, and also on the heart. In Calliphora vomitoria (Blue blowfly) the peptides act as neurotransmitters or neuromodulators, linking the brain with all thoracic and abdominal ganglia. In adults of Penaeus monodon (Penoeid shrimp) they appear to be restricted to a few neurones in the brain with a neural pathway extending along to the ventral thoracic and abdominal ganglia [].
Probab=33.04 E-value=17 Score=18.64 Aligned_cols=8 Identities=50% Similarity=0.999 Sum_probs=6.3
Q ss_pred hhhcccCC
Q 024057 141 LEYNHMSF 148 (273)
Q Consensus 141 ~~y~h~~~ 148 (273)
++|-||-|
T Consensus 2 ~dyghmrf 9 (9)
T PF08257_consen 2 DDYGHMRF 9 (9)
T ss_pred CccccccC
Confidence 46999976
No 19
>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=32.22 E-value=43 Score=26.85 Aligned_cols=74 Identities=19% Similarity=0.109 Sum_probs=46.8
Q ss_pred ccHHHHHHhhhhhhHHHHHHHhhhcCCChhhhhHHHHHHHHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhHH
Q 024057 156 ETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS 233 (273)
Q Consensus 156 ~~~E~a~~L~~q~d~~s~~ea~vl~apPklvyn~~~~~yareLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr~ 233 (273)
+.|+.|.+++++.+.+.....+++..... ......--+.++...+.+..++...||.+|....+.|++++ ++.-
T Consensus 3 ~~R~~a~~~L~~~~~~~~~~~~~l~~~~~---~~~~~~~d~~~~~~lv~gvlr~~~~ld~ii~~~l~~~~~~~-l~~~ 76 (130)
T cd00619 3 RARELAVQALYAWELAPEILAEVVSLLEL---LQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDR-LAIV 76 (130)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHH---hcccchhHHHHHHHHHHHHHHhHHHHHHHHHHHccCCCHHH-hhHH
Confidence 35788888888776632111111111000 00001335679999999999999999999988888877887 6643
No 20
>PF06580 His_kinase: Histidine kinase; InterPro: IPR010559 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain IPR003594 from INTERPRO and/or IPR003660 from INTERPRO.; GO: 0000155 two-component sensor activity, 0000160 two-component signal transduction system (phosphorelay), 0016021 integral to membrane
Probab=29.47 E-value=8.4 Score=29.42 Aligned_cols=6 Identities=83% Similarity=1.547 Sum_probs=2.7
Q ss_pred ceeEEe
Q 024057 16 THFLFN 21 (273)
Q Consensus 16 ~~~~~~ 21 (273)
|||+||
T Consensus 11 PHFl~N 16 (82)
T PF06580_consen 11 PHFLFN 16 (82)
T ss_pred hHHHHH
Confidence 444444
No 21
>COG0781 NusB Transcription termination factor [Transcription]
Probab=23.19 E-value=75 Score=27.58 Aligned_cols=37 Identities=19% Similarity=0.281 Sum_probs=31.4
Q ss_pred HHHHHHHHHhcHHHHHHHHhhhcCCCCCCCCcchhhhH
Q 024057 195 TRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILEL 232 (273)
Q Consensus 195 areLV~GV~~~~de~d~~IDe~I~~~Wkl~Rm~rIVDr 232 (273)
......-.+.+..++.+.||..|.++.+.|.+.+ +|.
T Consensus 54 ~~~~~~~lv~gv~~~~~~iD~~I~~~L~~w~~~r-L~~ 90 (151)
T COG0781 54 DSEYFRSLVKGVLENQEELDELISPHLKKWSLER-LDL 90 (151)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHccCCHHH-hhH
Confidence 3456677889999999999999999999999998 543
Done!