Query 022911
Match_columns 290
No_of_seqs 187 out of 1431
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 07:03:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022911.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022911hhsearch_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 2E-29 4.3E-34 209.5 12.3 124 144-269 2-134 (134)
2 PRK00202 nusB transcription an 100.0 3.8E-28 8.3E-33 203.6 11.5 130 143-274 4-135 (137)
3 cd00619 Terminator_NusB Transc 100.0 3.3E-28 7.2E-33 201.7 10.9 126 143-270 2-129 (130)
4 TIGR01951 nusB transcription a 99.9 7.3E-28 1.6E-32 199.1 11.0 125 144-270 3-129 (129)
5 COG0781 NusB Transcription ter 99.9 1.2E-27 2.6E-32 206.0 11.1 131 143-275 11-149 (151)
6 cd00620 Methyltransferase_Sun 99.9 4.6E-27 1E-31 194.5 12.0 123 145-270 3-125 (126)
7 cd00447 NusB_Sun RNA binding d 99.9 1.5E-25 3.3E-30 184.8 11.7 124 145-270 2-128 (129)
8 PRK09634 nusB transcription an 99.9 4.3E-24 9.3E-29 192.3 11.4 93 177-271 110-202 (207)
9 PRK10901 16S rRNA methyltransf 99.9 2.8E-23 6.1E-28 203.5 12.3 125 144-272 3-127 (427)
10 PRK14904 16S rRNA methyltransf 99.9 2.6E-22 5.5E-27 197.6 11.3 126 144-272 3-130 (445)
11 PRK14901 16S rRNA methyltransf 99.9 4.7E-22 1E-26 195.2 11.5 124 145-272 3-128 (434)
12 PRK14902 16S rRNA methyltransf 99.9 1.2E-21 2.5E-26 192.7 10.5 124 144-271 4-129 (444)
13 TIGR00563 rsmB ribosomal RNA s 99.8 9.3E-21 2E-25 185.5 12.5 121 146-272 1-122 (426)
14 PRK14903 16S rRNA methyltransf 99.8 1.1E-20 2.4E-25 185.9 10.4 118 144-270 4-122 (431)
15 TIGR01446 DnaD_dom DnaD and ph 51.5 16 0.00035 26.9 2.8 32 238-270 32-63 (73)
16 PF09185 DUF1948: Domain of un 49.2 41 0.00089 28.2 5.0 55 212-267 85-139 (140)
17 PF12862 Apc5: Anaphase-promot 39.8 52 0.0011 25.5 4.2 50 219-268 41-91 (94)
18 PF07261 DnaB_2: Replication i 38.4 35 0.00076 25.0 2.9 35 235-270 29-63 (77)
19 PF02284 COX5A: Cytochrome c o 25.3 60 0.0013 27.0 2.3 48 219-266 25-74 (108)
20 PF10752 DUF2533: Protein of u 22.9 1.1E+02 0.0025 24.3 3.4 36 233-269 24-59 (84)
21 cd00923 Cyt_c_Oxidase_Va Cytoc 22.8 74 0.0016 26.3 2.4 49 219-267 22-72 (103)
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=99.96 E-value=2e-29 Score=209.46 Aligned_cols=124 Identities=27% Similarity=0.352 Sum_probs=105.5
Q ss_pred HHHHHHHHHHHhhh-------hcchhHHHHhc-CCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcC
Q 022911 144 ETVEEADELLRSDE-------EESAIEAEVLS-APPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAG 215 (290)
Q Consensus 144 ~aRe~AlqlL~~ve-------~~~~l~~~lL~-~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~ 215 (290)
++|+.|+|+|++++ ..+......+. ......+++.|++|+++|++|++++++.||++|++++ ++|+++|++
T Consensus 2 ~aR~~A~q~L~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~d~~~~~~lv~gv~~~~~~ld~~i~~~~-~~~~~~rl~ 80 (134)
T PF01029_consen 2 KARELALQALYQVEFNDEEDEEEGQFLDEALEEELEESELSEEDRAFARELVYGVLRNKEELDALISKLL-KNWPLERLP 80 (134)
T ss_dssp HHHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHHHHTHHHHHHHHHHTS-TSSTGGGSG
T ss_pred hHHHHHHHHHHHHHccCCchhhhhhhHHHHHhhcccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCccccC
Confidence 58999999999993 32222222222 0001137899999999999999999999999999987 689999999
Q ss_pred hHHHHHHHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHh
Q 022911 216 RILELSILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 269 (290)
Q Consensus 216 ~vLdraILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r 269 (290)
++ +++|||+|+|||+|+ ++|++++|||||++||+|+++++++|||||||+++|
T Consensus 81 ~~-~~~iLrla~~El~~~~~~p~~v~InEaVelak~~~~~~~~~fVNaVL~~~~R 134 (134)
T PF01029_consen 81 PV-DRAILRLAIYELLFLDDIPPHVAINEAVELAKKYGDEKSAGFVNAVLRRIAR 134 (134)
T ss_dssp HH-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHH
T ss_pred HH-HHHHHHHHHHHHHhcCCCCccchHHHHHHHHHHhCCCCcchhHHHHHHHhhC
Confidence 98 799999999999998 899999999999999999999999999999999986
No 2
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=99.95 E-value=3.8e-28 Score=203.64 Aligned_cols=130 Identities=27% Similarity=0.344 Sum_probs=111.3
Q ss_pred HHHHHHHHHHHHhhhhcchhHHHHhcCC-CCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHH
Q 022911 143 TETVEEADELLRSDEEESAIEAEVLSAP-PKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS 221 (290)
Q Consensus 143 ~~aRe~AlqlL~~ve~~~~l~~~lL~~~-~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdra 221 (290)
..+|+.|+++|++++.++.....++... ....+++.|++|+++|++||+++++.||++|++++ ++|++++++++ +++
T Consensus 4 ~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~~~~~~~d~~~~~~lv~gvlr~~~~lD~ii~~~l-~~~~~~~l~~~-~~~ 81 (137)
T PRK00202 4 RKAREAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYL-KDWTLERLDPV-ERA 81 (137)
T ss_pred HHHHHHHHHHHHHHHccCCCHHHHHHHHHHhcccchhhHHHHHHHHHHHHHhHHHHHHHHHHHh-cCCCHHHhhHH-HHH
Confidence 3589999999999987554332222221 11136788999999999999999999999999999 56999999998 699
Q ss_pred HHHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhcc
Q 022911 222 ILHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGT 274 (290)
Q Consensus 222 ILRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~ 274 (290)
|||+|+|||+|+ ++|++++|||||++||+|+++++++|||||||++.++....
T Consensus 82 iLr~a~~Ell~~~~~p~~~vinEaV~lak~~~~~~~~~fVNaVLr~i~r~~~~~ 135 (137)
T PRK00202 82 ILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPA 135 (137)
T ss_pred HHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCCcchhHHHHHHHHHHHhhcc
Confidence 999999999998 79999999999999999999999999999999999987543
No 3
>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.
Probab=99.95 E-value=3.3e-28 Score=201.67 Aligned_cols=126 Identities=31% Similarity=0.391 Sum_probs=109.1
Q ss_pred HHHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHH
Q 022911 143 TETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELS 221 (290)
Q Consensus 143 ~~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdra 221 (290)
..+|+.|+++|++++.++.....++.... ...+++.|++|+++|++|++++++.+|++|++++ ++|++++++++ +++
T Consensus 2 ~~~R~~a~~~L~~~~~~~~~~~~~l~~~~~~~~~~~~d~~~~~~lv~gvlr~~~~ld~ii~~~l-~~~~~~~l~~~-~~~ 79 (130)
T cd00619 2 RRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHL-RNWSLDRLAIV-ERA 79 (130)
T ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCCHHHhhHH-HHH
Confidence 35799999999999876544333432211 1125678999999999999999999999999999 58989999998 699
Q ss_pred HHHHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911 222 ILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 270 (290)
Q Consensus 222 ILRlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~ 270 (290)
|||+|+|||+|++ +|++++|||||++||+|+++++++|||||||++.++
T Consensus 80 iLria~~el~~~~~~p~~~vinEaV~lak~~~~~~~~~fVNaVLr~i~r~ 129 (130)
T cd00619 80 ILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKD 129 (130)
T ss_pred HHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCcchhHHHHHHHHHhhc
Confidence 9999999999987 999999999999999999999999999999999875
No 4
>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=99.95 E-value=7.3e-28 Score=199.12 Aligned_cols=125 Identities=22% Similarity=0.263 Sum_probs=107.8
Q ss_pred HHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHH
Q 022911 144 ETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSI 222 (290)
Q Consensus 144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraI 222 (290)
.+|+.|+++|++++.++.....++.... ...+++.|++|+++|++|++++++.||++|+++++ +|++++++++ +++|
T Consensus 3 ~~R~~a~~~l~~~~~~~~~~~~~l~~~~~~~~l~~~d~~~~~~lv~~~lr~~~~ld~~i~~~~~-~~~~~~l~~~-~~~i 80 (129)
T TIGR01951 3 KARELALQALYQWELSGNDVEEIIEEFLEERELDEEDREYFLELVRGVLENQEEIDELISPHLK-DWSLERLDPV-DRAI 80 (129)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhHHHHHHHHHHHhc-CCCHHHhhHH-HHHH
Confidence 4799999999999865543332332211 11367889999999999999999999999999994 8999999998 6999
Q ss_pred HHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911 223 LHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 270 (290)
Q Consensus 223 LRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~ 270 (290)
||+|+|||+|+ ++|++++|||||++||+|+++++++|||||||++++.
T Consensus 81 Lr~a~~el~~~~~~p~~avineaV~lak~~~~~~~~~fVNaVLr~i~r~ 129 (129)
T TIGR01951 81 LRLAAYELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAKE 129 (129)
T ss_pred HHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCCchhhHHHHHHHHhhC
Confidence 99999999998 7999999999999999999999999999999999863
No 5
>COG0781 NusB Transcription termination factor [Transcription]
Probab=99.95 E-value=1.2e-27 Score=206.03 Aligned_cols=131 Identities=23% Similarity=0.298 Sum_probs=109.4
Q ss_pred HHHHHHHHHHHHhhhhcch-----hHHHHhcCCC--CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcC
Q 022911 143 TETVEEADELLRSDEEESA-----IEAEVLSAPP--KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAG 215 (290)
Q Consensus 143 ~~aRe~AlqlL~~ve~~~~-----l~~~lL~~~~--~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~ 215 (290)
..+|+.|+|+||+++.++. ....+..... .......+..|+..|+.||.+|...||.+|.+++ ++|+++|++
T Consensus 11 ~~aR~~avq~Ly~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~lv~gv~~~~~~iD~~I~~~L-~~w~~~rL~ 89 (151)
T COG0781 11 RQARELAVQALYQWELSGSVSAEDILEDIEEEFVENELDIELADSEYFRSLVKGVLENQEELDELISPHL-KKWSLERLD 89 (151)
T ss_pred HHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHhhcccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH-ccCCHHHhh
Confidence 4699999999999998544 1111221110 0012227899999999999999999999999999 569999999
Q ss_pred hHHHHHHHHHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhhccc
Q 022911 216 RILELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLEGTA 275 (290)
Q Consensus 216 ~vLdraILRlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~~~~ 275 (290)
.+ ||+|||+|+|||+|.+ +|..|+|||||||||.|+++++++||||||+++++......
T Consensus 90 ~v-erAILRla~yEl~~~~dvP~~VvInEaielaK~f~~e~s~kFINgVLd~i~~~~~~~~ 149 (151)
T COG0781 90 LV-ERAILRLALYELLFRDDVPYKVVINEAIELAKKFSGEDSHKFVNGVLDKIAKKLRPKE 149 (151)
T ss_pred HH-HHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHhCCCCchHHHHHHHHHHHHHhhhhc
Confidence 98 9999999999999965 99999999999999999999999999999999998776543
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=99.94 E-value=4.6e-27 Score=194.53 Aligned_cols=123 Identities=22% Similarity=0.182 Sum_probs=103.1
Q ss_pred HHHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHHH
Q 022911 145 TVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILH 224 (290)
Q Consensus 145 aRe~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraILR 224 (290)
+|+.|+++|+++..++.....++........++.|++|+++|++|++++++.||++|+++++ +| ..+++++ +++|||
T Consensus 3 ~R~~A~~~L~~v~~~~~~~~~~l~~~~~~~~~~~d~~~~~~lv~g~~r~~~~ld~~i~~~l~-~~-~~~~~~~-~~~iLr 79 (126)
T cd00620 3 ARSTAAEVLRDVLQRGASLNAVLSALQKKDKSDRDRGLATELVYGTLRWLALLDWIINPLLK-KP-DVGKDPD-VRNLLR 79 (126)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhC-CC-ccccCHH-HHHHHH
Confidence 69999999999977554333333221100125789999999999999999999999999994 34 4589998 699999
Q ss_pred HHHHHhhccCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911 225 LAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 270 (290)
Q Consensus 225 lAiyELlf~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~ 270 (290)
+|+|||+|+++|++++|||||++||+|+++++++|||||||++.|+
T Consensus 80 ~a~~el~~~~~p~~avvneaVelak~~~~~~~~~fVNaVLr~i~r~ 125 (126)
T cd00620 80 LGLYQLLYLDVPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRFERE 125 (126)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHhCCCchhhHHHHHHHHHhcc
Confidence 9999999988999999999999999999999999999999999874
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=99.93 E-value=1.5e-25 Score=184.80 Aligned_cols=124 Identities=29% Similarity=0.357 Sum_probs=105.4
Q ss_pred HHHHHHHHHHhhhhc-chhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911 145 TVEEADELLRSDEEE-SAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL 223 (290)
Q Consensus 145 aRe~AlqlL~~ve~~-~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL 223 (290)
+|+.|+++|++++.. +.....++.......+++.|++|+++|++||+++++.||++|++++ ++|+++|++.+ ++.||
T Consensus 2 ~R~~a~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~gv~r~~~~ld~~i~~~~-~~~~~~r~~~~-~~~il 79 (129)
T cd00447 2 AREIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLL-KKWLLDRLDKV-DRAIL 79 (129)
T ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHcccchhHHHHHHHHHHHHHHhHHHHHHHHHHHc-cCCChhhhhHH-HHHHH
Confidence 699999999999765 4333323222111136678999999999999999999999999999 68999999998 89999
Q ss_pred HHHHHHhhcc--CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911 224 HLAMSEITVV--GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 270 (290)
Q Consensus 224 RlAiyELlf~--diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~ 270 (290)
+++.+|+.+. ++|++++|||||++||+|+++++++|||||||++.++
T Consensus 80 ~l~~~el~~~~~~~p~~~vineaVelak~~~~~~~~~fVNaVLr~~~r~ 128 (129)
T cd00447 80 RLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKE 128 (129)
T ss_pred HHHHHHHHhCcCCCCchhHHHHHHHHHHHHCCCCcchhHHHHHHHHhhc
Confidence 9999998876 5999999999999999999999999999999999875
No 8
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=99.91 E-value=4.3e-24 Score=192.34 Aligned_cols=93 Identities=33% Similarity=0.489 Sum_probs=90.3
Q ss_pred HHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHHHHHHHHhhccCCChhhHHHHHHHHHHhhCCCCC
Q 022911 177 KLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAA 256 (290)
Q Consensus 177 ~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraILRlAiyELlf~diP~~vaINEAVeLAK~y~~~~s 256 (290)
+++++|+++|++||+++++.||++|++++ ++|+++|++.+ |++|||+|+|||+|+++|++++|||||++||+|+++++
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 78999999999999999999999999999 79999999998 89999999999999999999999999999999999999
Q ss_pred CCchHHHHhhHHhhh
Q 022911 257 PRIINGCLRTFVRNL 271 (290)
Q Consensus 257 ~~FVNaVLr~i~r~~ 271 (290)
++|||||||++.+..
T Consensus 188 ~~FVNaVLrri~r~~ 202 (207)
T PRK09634 188 RRFINGVLRRLQDAL 202 (207)
T ss_pred cchHHHHHHHHHHHh
Confidence 999999999999876
No 9
>PRK10901 16S rRNA methyltransferase B; Provisional
Probab=99.89 E-value=2.8e-23 Score=203.45 Aligned_cols=125 Identities=17% Similarity=0.152 Sum_probs=108.9
Q ss_pred HHHHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911 144 ETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL 223 (290)
Q Consensus 144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL 223 (290)
.+|+.|+++|++++.++.....++..... .+++.|++|+++|++||++++..||++|++++ +|++++++++ +++||
T Consensus 3 ~~R~~a~~~L~~~~~~~~~~~~~l~~~~~-~l~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~--~~~~~~l~~~-~r~iL 78 (427)
T PRK10901 3 NLRALAAAAILQVVDQGQSLSAALPALQQ-KVSDKDRALLQELCYGVLRRLPRLEWLIAQLL--AKPLKGKQRI-VHALL 78 (427)
T ss_pred hHHHHHHHHHHHHHHcCCcHHHHHHHHHh-hCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHh--CCCccccCHH-HHHHH
Confidence 47999999999998766544334332111 36788999999999999999999999999998 3688999998 69999
Q ss_pred HHHHHHhhccCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911 224 HLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 272 (290)
Q Consensus 224 RlAiyELlf~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~ 272 (290)
|||+|||+|+++|++++|||||++||+|+++++++|||||||++.++.+
T Consensus 79 rla~yell~~~iP~~a~vneaVelak~~~~~~~~~fVNaVLr~i~~~~~ 127 (427)
T PRK10901 79 LVGLYQLLYTRIPAHAAVDETVEAAKALKRPWAKGLVNAVLRRFQREQE 127 (427)
T ss_pred HHHHHHHhccCCCcchHHHHHHHHHHhcCCccchhhHHHHHHHhhhhhh
Confidence 9999999998899999999999999999999999999999999998643
No 10
>PRK14904 16S rRNA methyltransferase B; Provisional
Probab=99.87 E-value=2.6e-22 Score=197.62 Aligned_cols=126 Identities=17% Similarity=0.180 Sum_probs=108.7
Q ss_pred HHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHH
Q 022911 144 ETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSI 222 (290)
Q Consensus 144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraI 222 (290)
.+|+.|+++|++++.++.....++.... ...+++.|++|+++||+||++++..||++|++++ +|++++++++ +++|
T Consensus 3 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~~~l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~--~~~~~rl~~~-~r~i 79 (445)
T PRK14904 3 TARELALQVLQELETGERKSDTLLHRMLERSSLERNDRALATELVNGVLRYRLQLDFIISRFY--HHDLEKAAPV-LKNI 79 (445)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHc--CCChhhCCHH-HHHH
Confidence 5799999999999876554333332211 1137788999999999999999999999999998 3799999998 7999
Q ss_pred HHHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911 223 LHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 272 (290)
Q Consensus 223 LRlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~ 272 (290)
||+|+|||+|++ +|++++|||||++||+|+++++++|||||||+++++..
T Consensus 80 Lrla~~ell~~~~~p~~a~vneaVelak~~~~~~~~~fVNgVLr~i~~~~~ 130 (445)
T PRK14904 80 LRLGVYQLLFLDRVPRWAAVNECVKLARKYKGEHMAKLVNGVLRNISPETI 130 (445)
T ss_pred HHHHHHHHHhCCCCCCeeeHHHHHHHHHHhCCCccccchHHHHHHHHHhhc
Confidence 999999999974 99999999999999999999999999999999999753
No 11
>PRK14901 16S rRNA methyltransferase B; Provisional
Probab=99.87 E-value=4.7e-22 Score=195.21 Aligned_cols=124 Identities=20% Similarity=0.191 Sum_probs=105.0
Q ss_pred HHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911 145 TVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL 223 (290)
Q Consensus 145 aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL 223 (290)
+|+.|+++|++++.+ .....++.... ...+++.|++|+++||+||+++++.||++|++++ + |+..+++++ +|+||
T Consensus 3 ~R~~A~~~L~~i~~~-~~~~~~l~~~~~~~~l~~~dr~~~~~lv~gvlr~~~~lD~~i~~~~-~-~~~~~l~~~-~r~iL 78 (434)
T PRK14901 3 ARQLAWEILQAVARG-AYADVALERVLRKYPLSGADRALVTELVYGCIRRRRTLDAWIDQLG-K-KPAHKQPPD-LRWLL 78 (434)
T ss_pred HHHHHHHHHHHHHcC-CchHHHHHHHHHhcCCChhHHHHHHHHHHHHHHhHHHHHHHHHHhc-C-CChhhcCHH-HHHHH
Confidence 799999999999875 32222222210 1136788999999999999999999999999997 3 666779998 69999
Q ss_pred HHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911 224 HLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 272 (290)
Q Consensus 224 RlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~ 272 (290)
|+|+|||+|++ +|++++|||||++||+|+++++++|||||||++.++..
T Consensus 79 rla~yel~~~~~~p~~aavneaVelak~~~~~~~~~fVNgVLr~~~r~~~ 128 (434)
T PRK14901 79 HLGLYQLRYMDRIPASAAVNTTVELAKQNGLGGLAGVVNGILRQYLRARE 128 (434)
T ss_pred HHHHHHHHhCccCCcHHHHHHHHHHHHHcCchhhhhhcCHHHHHHHHhhh
Confidence 99999999975 99999999999999999999999999999999999744
No 12
>PRK14902 16S rRNA methyltransferase B; Provisional
Probab=99.86 E-value=1.2e-21 Score=192.65 Aligned_cols=124 Identities=18% Similarity=0.179 Sum_probs=106.2
Q ss_pred HHHHHHHHHHHhhhhcchhHHHHhcCCC-CCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHH
Q 022911 144 ETVEEADELLRSDEEESAIEAEVLSAPP-KLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSI 222 (290)
Q Consensus 144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~-~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraI 222 (290)
.+|+.|+++|++++.++.....++.... ...+++.|++|+++||+|++++++.||++|+++++ + +++++++ +|+|
T Consensus 4 ~~R~~A~~~L~~~~~~~~~~~~~l~~~~~~~~l~~~d~~~~~~lv~g~lr~~~~ld~~i~~~~~-~--~~~l~~~-~r~i 79 (444)
T PRK14902 4 NARELALEVLIKVENNGAYSNIALNKVLKKSELSDKDKALLTELVYGTIQRKLTLDYYLAPFIK-K--RKKLDPW-VRNL 79 (444)
T ss_pred cHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHhHHHHHHHHHHHhh-h--hhhCCHH-HHHH
Confidence 5899999999999876543322322210 11378889999999999999999999999999994 3 7899998 6999
Q ss_pred HHHHHHHhhcc-CCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhh
Q 022911 223 LHLAMSEITVV-GTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNL 271 (290)
Q Consensus 223 LRlAiyELlf~-diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~ 271 (290)
||+|+|||+|. ++|++++|||||++||+|+++++++|||||||++.++.
T Consensus 80 Lrla~~el~~~~~~p~~~~ineav~lak~~~~~~~~~fVNaVL~~i~~~~ 129 (444)
T PRK14902 80 LRMSLYQLLYLDKVPDHAAVNEAVEIAKKRGHKGIAKFVNGVLRNILREG 129 (444)
T ss_pred HHHHHHHHHhccCCCCceeHHHHHHHHHHhCCCchhHHHHHHHHHHhhcc
Confidence 99999999996 59999999999999999999999999999999999864
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=99.84 E-value=9.3e-21 Score=185.54 Aligned_cols=121 Identities=18% Similarity=0.126 Sum_probs=102.9
Q ss_pred HHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHHHH
Q 022911 146 VEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSILHL 225 (290)
Q Consensus 146 Re~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraILRl 225 (290)
|+.|+++|++++.++.....++.. ...+++.|++|+++||+||++++..||++|+++++ |++++++++ .+ +||+
T Consensus 1 R~~A~~~L~~~~~~~~~~~~~~~~--~~~l~~~d~~~~~~lv~gv~r~~~~lD~~i~~~~~--~~~~~l~~~-~~-~L~~ 74 (426)
T TIGR00563 1 RSIAAQALEQLEQGQSLSNLLPPL--QQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMD--RPMKGKPRT-VH-YLIL 74 (426)
T ss_pred CHHHHHHHHHHHcCCchHHHHHhh--hcCCCHHHHHHHHHHHHHHHHhHHHHHHHHHHHhC--CCccccCHH-HH-HHHH
Confidence 689999999998776654444332 22478899999999999999999999999999983 677888887 46 8888
Q ss_pred HHHHhhc-cCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhhhh
Q 022911 226 AMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRNLE 272 (290)
Q Consensus 226 AiyELlf-~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~~~ 272 (290)
++||++| +++|++++|||||++||+|+++++++|||||||++.++.+
T Consensus 75 ~~~e~l~~~~~p~~aainEaVelaK~~~~~~~~~fVNgVLr~i~r~~~ 122 (426)
T TIGR00563 75 VGLYQLLYTRIPAHAAVAETVEGAKAIKRKGLKGLVNGVLRRFQREQE 122 (426)
T ss_pred HHHHHHhcCCCCCEehHHHHHHHHHhcCCccchhhHHHHHHHHhhcch
Confidence 8888765 6899999999999999999999999999999999999643
No 14
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=99.83 E-value=1.1e-20 Score=185.91 Aligned_cols=118 Identities=19% Similarity=0.153 Sum_probs=100.5
Q ss_pred HHHHHHHHHHHhhhhcchhHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHcHHHHHHHHHhhCCCCCCCCCcChHHHHHHH
Q 022911 144 ETVEEADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPPIWKDQPAGRILELSIL 223 (290)
Q Consensus 144 ~aRe~AlqlL~~ve~~~~l~~~lL~~~~~~~l~~~Dr~fa~~Lv~Gvlr~~~~lD~iI~~~l~k~w~lerl~~vLdraIL 223 (290)
.+|+.|+++|.++..++......+..... .+++.|++|+++||+||+++++.||++|++++ ++| +++++ +|+||
T Consensus 4 ~~R~~A~~~L~~v~~~~~~~~~~l~~~~~-~l~~~d~~~~~~lv~gvlr~~~~lD~~i~~~~-~~~---~l~~~-~r~iL 77 (431)
T PRK14903 4 NVRLLAYRLLRKYEKEKFIFREDVDSVLS-FLDDKDRRFFKELVWGVVRKEELLDWYINQLL-KKK---DIPPA-VRVAL 77 (431)
T ss_pred CHHHHHHHHHHHHHhCCCchHHHHHHHHH-hCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCC---CCCHH-HHHHH
Confidence 57999999999998766433333332111 37899999999999999999999999999999 567 58888 59999
Q ss_pred HHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911 224 HLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 270 (290)
Q Consensus 224 RlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~ 270 (290)
|+|+|||+|++ +|++++|||||++||++ ++++|||||||++.++
T Consensus 78 r~~~yel~~~~~~p~~aavneaV~lak~~---~~~~fVNaVLr~~~r~ 122 (431)
T PRK14903 78 RMGAYQLLFMNSVPDYAAVSETVKLVKNE---NFKKLVNAVLRRLRTV 122 (431)
T ss_pred HHHHHHHHhccCCCcceeHHHHHHHHhcc---chHHHHHHHHHHHHHh
Confidence 99999999987 79999999999999986 5679999999999986
No 15
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=51.49 E-value=16 Score=26.88 Aligned_cols=32 Identities=25% Similarity=0.263 Sum_probs=25.3
Q ss_pred hhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911 238 QIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 270 (290)
Q Consensus 238 ~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~ 270 (290)
.-+|++|++.|... +..+.++|++||.+-.+.
T Consensus 32 ~evI~~ai~~a~~~-~~~~~~Yi~~Il~~W~~~ 63 (73)
T TIGR01446 32 PELIKEALKEAVSN-NKANYKYIDAILNNWKNN 63 (73)
T ss_pred HHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHc
Confidence 67999999998874 445678999999887653
No 16
>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=49.25 E-value=41 Score=28.18 Aligned_cols=55 Identities=15% Similarity=0.231 Sum_probs=35.5
Q ss_pred CCcChHHHHHHHHHHHHHhhccCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhH
Q 022911 212 QPAGRILELSILHLAMSEITVVGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTF 267 (290)
Q Consensus 212 erl~~vLdraILRlAiyELlf~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i 267 (290)
++++.. -.++..+|+.|-.-..+.....|.||.-+-..|+.....+=-+|+||++
T Consensus 85 kkidll-t~avilcalseq~a~~tdkplliseallimdhysq~~ekkqthalldkl 139 (140)
T PF09185_consen 85 KKIDLL-TKAVILCALSEQHAQNTDKPLLISEALLIMDHYSQVPEKKQTHALLDKL 139 (140)
T ss_dssp ----HH-HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHTT---TTS-S-TTTS--
T ss_pred chhhHH-HHHHHHHHhhHHHhhcCCCchhHHHHHHHHHHHhhchhHHHHHHHHHhh
Confidence 345555 5888889999887777888999999999999999777777788888875
No 17
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=39.75 E-value=52 Score=25.46 Aligned_cols=50 Identities=18% Similarity=0.141 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHhhccC-CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHH
Q 022911 219 ELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFV 268 (290)
Q Consensus 219 draILRlAiyELlf~d-iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~ 268 (290)
-.++|.+|.....|.. -....++.|||.+|++-++...-.++...|-.+.
T Consensus 41 ~~all~lA~~~~~~G~~~~A~~~l~eAi~~Are~~D~~~l~~al~~~~~l~ 91 (94)
T PF12862_consen 41 AYALLNLAELHRRFGHYEEALQALEEAIRLARENGDRRCLAYALSWLANLL 91 (94)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHh
Confidence 3678888888888865 4567789999999999987755555555555444
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=38.45 E-value=35 Score=25.00 Aligned_cols=35 Identities=20% Similarity=0.206 Sum_probs=26.1
Q ss_pred CChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHhh
Q 022911 235 TRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVRN 270 (290)
Q Consensus 235 iP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r~ 270 (290)
-=+.-+|++|++.|... +..+.++|.+||++-.+.
T Consensus 29 ~~~~~~v~~ai~~~~~~-~~~~~~Yi~~Il~~W~~~ 63 (77)
T PF07261_consen 29 GFSPEVVNEAIEYALEN-NKRSFNYIEKILNNWKQK 63 (77)
T ss_dssp HHHHHHHHHHHHHHHHC-T--SHHHHHHHHHHHHHC
T ss_pred CCCHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHc
Confidence 34567899999999954 555689999999888654
No 19
>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=25.27 E-value=60 Score=27.03 Aligned_cols=48 Identities=19% Similarity=0.213 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHhhccC-CChhhHHHHHHHHHHhhCC-CCCCCchHHHHhh
Q 022911 219 ELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCD-GAAPRIINGCLRT 266 (290)
Q Consensus 219 draILRlAiyELlf~d-iP~~vaINEAVeLAK~y~~-~~s~~FVNaVLr~ 266 (290)
|..-+|-|+-.+.-.| +|...||..|+..|++..+ .-+.+|.-||=.+
T Consensus 25 D~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K 74 (108)
T PF02284_consen 25 DGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK 74 (108)
T ss_dssp -HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 7778899999988666 9999999999999998754 2344555555443
No 20
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=22.91 E-value=1.1e+02 Score=24.29 Aligned_cols=36 Identities=22% Similarity=0.296 Sum_probs=27.7
Q ss_pred cCCChhhHHHHHHHHHHhhCCCCCCCchHHHHhhHHh
Q 022911 233 VGTRHQIVINEAVDLAKRFCDGAAPRIINGCLRTFVR 269 (290)
Q Consensus 233 ~diP~~vaINEAVeLAK~y~~~~s~~FVNaVLr~i~r 269 (290)
++---..+|.|||.+|++ |.+-+..-||+|=..+-.
T Consensus 24 Le~~RE~aIeeav~~c~~-g~pFs~d~IN~vT~~mN~ 59 (84)
T PF10752_consen 24 LEQQREAAIEEAVSLCKQ-GEPFSTDKINEVTKEMNE 59 (84)
T ss_pred HHHHHHHHHHHHHHHHHC-CCCCcHHHHHHHHHHHHH
Confidence 345567899999999998 456677889999877643
No 21
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=22.85 E-value=74 Score=26.26 Aligned_cols=49 Identities=18% Similarity=0.164 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHhhccC-CChhhHHHHHHHHHHhhCC-CCCCCchHHHHhhH
Q 022911 219 ELSILHLAMSEITVVG-TRHQIVINEAVDLAKRFCD-GAAPRIINGCLRTF 267 (290)
Q Consensus 219 draILRlAiyELlf~d-iP~~vaINEAVeLAK~y~~-~~s~~FVNaVLr~i 267 (290)
|..-+|-|+-.+.-.| +|...||+-|+..|++..+ .-+.+|.-||=.+.
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 7788899999988666 9999999999999998764 33456666665444
Done!