Query 023791
Match_columns 277
No_of_seqs 13 out of 15
Neff 1.7
Searched_HMMs 46136
Date Fri Mar 29 06:40:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023791.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023791hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08279 HTH_11: HTH domain; 71.0 0.63 1.4E-05 31.1 -1.6 38 125-162 16-53 (55)
2 COG1654 BirA Biotin operon rep 59.3 2.9 6.2E-05 32.3 -0.2 40 123-162 18-57 (79)
3 PRK12410 glutamylglutaminyl-tR 57.4 14 0.0003 36.1 4.0 49 77-144 56-104 (433)
4 PRK12558 glutamyl-tRNA synthet 44.8 30 0.00066 33.8 4.2 41 90-144 67-107 (445)
5 cd07377 WHTH_GntR Winged helix 38.9 14 0.00031 24.1 0.7 29 130-159 31-59 (66)
6 PF08220 HTH_DeoR: DeoR-like h 36.9 6.4 0.00014 27.5 -1.3 36 131-169 21-56 (57)
7 PF02829 3H: 3H domain; Inter 36.0 24 0.00052 28.2 1.7 47 133-182 2-55 (98)
8 PF07862 Nif11: Nitrogen fixat 34.2 29 0.00062 23.4 1.6 27 119-152 4-30 (49)
9 COG0008 GlnS Glutamyl- and glu 33.1 34 0.00074 33.8 2.6 102 89-206 73-193 (472)
10 PLN03233 putative glutamate-tR 32.7 49 0.0011 33.3 3.6 42 91-146 77-118 (523)
11 PF02082 Rrf2: Transcriptional 30.0 35 0.00076 24.8 1.6 44 125-169 26-69 (83)
12 PRK01406 gltX glutamyl-tRNA sy 28.4 78 0.0017 30.9 4.1 36 95-144 82-117 (476)
13 KOG0913 Thiol-disulfide isomer 27.3 67 0.0015 30.2 3.3 32 169-200 176-207 (248)
14 PF00749 tRNA-synt_1c: tRNA sy 26.9 49 0.0011 30.3 2.3 132 93-251 70-227 (314)
15 smart00420 HTH_DEOR helix_turn 26.3 20 0.00043 22.4 -0.2 34 130-166 20-53 (53)
16 PF01522 Polysacc_deac_1: Poly 25.2 82 0.0018 22.8 2.8 93 89-201 10-102 (123)
17 PLN02627 glutamyl-tRNA synthet 24.2 83 0.0018 31.9 3.5 36 95-144 124-159 (535)
18 PF00325 Crp: Bacterial regula 23.5 36 0.00078 22.7 0.6 24 130-153 8-31 (32)
19 TIGR00463 gltX_arch glutamyl-t 23.2 83 0.0018 31.9 3.3 51 121-172 176-239 (560)
20 PF07739 TipAS: TipAS antibiot 22.4 49 0.0011 24.5 1.2 26 108-133 93-118 (118)
21 TIGR00464 gltX_bact glutamyl-t 22.2 1E+02 0.0022 30.0 3.6 37 93-143 70-106 (470)
22 PRK07114 keto-hydroxyglutarate 22.2 54 0.0012 29.2 1.6 19 119-137 172-190 (222)
23 TIGR03128 RuMP_HxlA 3-hexulose 22.1 47 0.001 27.1 1.1 24 113-136 163-187 (206)
24 PRK14895 gltX glutamyl-tRNA sy 21.7 1E+02 0.0023 30.9 3.6 49 77-144 61-110 (513)
25 TIGR00122 birA_repr_reg BirA b 20.7 62 0.0014 22.6 1.4 40 127-169 16-55 (69)
No 1
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=71.04 E-value=0.63 Score=31.06 Aligned_cols=38 Identities=26% Similarity=0.476 Sum_probs=30.2
Q ss_pred HHhhhheeeccCCcHhHHHHHHhccccccchhhhhccC
Q 023791 125 IDAGVNAYALGCTDEGLRKELTAMKESGVEIDALQSYG 162 (277)
Q Consensus 125 i~AgV~AYalGcteEgLrkEL~~~~~sg~eie~~~~yg 162 (277)
+++.-.|-.+|++..-+++.|..|++.|+.|+..+..|
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~~~~~I~~~~~~G 53 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELREWGIPIESKRGKG 53 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHHTT-EEEEETTTE
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEeeCCCC
Confidence 55666778899999999999999999998888776653
No 2
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=59.28 E-value=2.9 Score=32.34 Aligned_cols=40 Identities=25% Similarity=0.515 Sum_probs=34.8
Q ss_pred HHHHhhhheeeccCCcHhHHHHHHhccccccchhhhhccC
Q 023791 123 EFIDAGVNAYALGCTDEGLRKELTAMKESGVEIDALQSYG 162 (277)
Q Consensus 123 eFi~AgV~AYalGcteEgLrkEL~~~~~sg~eie~~~~yg 162 (277)
+|++--..|=+|||+...+-|-+-.+++.|++||+.+.-|
T Consensus 18 ~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kG 57 (79)
T COG1654 18 NFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKG 57 (79)
T ss_pred CcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCc
Confidence 3666667788999999999999999999999999987744
No 3
>PRK12410 glutamylglutaminyl-tRNA synthetase; Provisional
Probab=57.36 E-value=14 Score=36.09 Aligned_cols=49 Identities=22% Similarity=0.276 Sum_probs=34.7
Q ss_pred CCCccccccCCCCCCCcccccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHHH
Q 023791 77 PSKKWLCRSHDPISPDNEYRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRKE 144 (277)
Q Consensus 77 ~~~~wl~~~~~~~s~dde~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrkE 144 (277)
.+-+||. +..|+.|+.|.++. +|+.+ +++.++.| .||.|-||.|+|.+.
T Consensus 56 ~~L~WlG-----l~wDe~y~QSeR~~-----~Y~~~--------a~~Li~~G-~AY~C~cs~eel~~~ 104 (433)
T PRK12410 56 EILNLFG-----ISWDKLVYQSENLK-----FHRQM--------AEKLLSEK-KAFACFCSEEELEAK 104 (433)
T ss_pred HHHHHcC-----CCCCCCeehhccHH-----HHHHH--------HHHHHHcC-CeeeecCCHHHHHHH
Confidence 3446773 34567799998864 56654 45677777 599999999988654
No 4
>PRK12558 glutamyl-tRNA synthetase; Provisional
Probab=44.78 E-value=30 Score=33.81 Aligned_cols=41 Identities=27% Similarity=0.336 Sum_probs=29.0
Q ss_pred CCCcccccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHHH
Q 023791 90 SPDNEYRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRKE 144 (277)
Q Consensus 90 s~dde~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrkE 144 (277)
..|..|+.|..+ .+|+.+ ++..++.|. ||.|-||.|+|.+.
T Consensus 67 ~~De~y~QSer~-----~~y~~~--------~e~L~e~G~-AY~C~Ct~eel~~~ 107 (445)
T PRK12558 67 NWDRTFRQSDRF-----DRYDEA--------AEKLKAAGR-LYPCYETPEELELK 107 (445)
T ss_pred CCCccccHHHHH-----HHHHHH--------HHHHHHCCC-EEEecCchHHHHHH
Confidence 355567766655 356554 467788887 99999999988543
No 5
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=38.94 E-value=14 Score=24.08 Aligned_cols=29 Identities=21% Similarity=0.394 Sum_probs=24.1
Q ss_pred heeeccCCcHhHHHHHHhccccccchhhhh
Q 023791 130 NAYALGCTDEGLRKELTAMKESGVEIDALQ 159 (277)
Q Consensus 130 ~AYalGcteEgLrkEL~~~~~sg~eie~~~ 159 (277)
.|-.+|.+.+-+++.|..|.+.|+ |+..+
T Consensus 31 la~~~~is~~~v~~~l~~L~~~G~-i~~~~ 59 (66)
T cd07377 31 LAEELGVSRTTVREALRELEAEGL-VERRP 59 (66)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCC-EEecC
Confidence 455679999999999999999998 76553
No 6
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=36.93 E-value=6.4 Score=27.54 Aligned_cols=36 Identities=22% Similarity=0.458 Sum_probs=29.1
Q ss_pred eeeccCCcHhHHHHHHhccccccchhhhhccCCcccccc
Q 023791 131 AYALGCTDEGLRKELTAMKESGVEIDALQSYGGGTSLKS 169 (277)
Q Consensus 131 AYalGcteEgLrkEL~~~~~sg~eie~~~~yggsts~ks 169 (277)
|=.+|+++.-+|+.|..|.+.|+ .-+.+||-...++
T Consensus 21 a~~~~VS~~TiRRDl~~L~~~g~---i~r~~GG~~~~~~ 56 (57)
T PF08220_consen 21 AEEFGVSEMTIRRDLNKLEKQGL---IKRTHGGAVLNDS 56 (57)
T ss_pred HHHHCcCHHHHHHHHHHHHHCCC---EEEEcCEEEeCCC
Confidence 44689999999999999999998 4567888766554
No 7
>PF02829 3H: 3H domain; InterPro: IPR004173 The 3H domain is named after its three highly conserved histidine residues. The 3H domain appears to be a small molecule-binding domain, based on its occurrence with other domains []. Several proteins carrying this domain are transcriptional regulators from the biotin repressor family. The transcription regulator TM1602 from Thermotoga maritima is a DNA-binding protein thought to belong to a family of de novo NAD synthesis pathway regulators. TM1602 has an N-terminal DNA-binding domain and a C-terminal 3H regulatory domain. The N-terminal domain appears to bind to the NAD promoter region and repress the de novo NAD biosynthesis operon, while the C-terminal 3H domain may bind to nicotinamide, nicotinic acid, or other substrate/products []. The 3H domain has a 2-layer alpha/beta sandwich fold.; GO: 0005488 binding; PDB: 1J5Y_A.
Probab=35.95 E-value=24 Score=28.16 Aligned_cols=47 Identities=21% Similarity=0.365 Sum_probs=34.0
Q ss_pred eccCCcHhHHHHHHhccccccchhhh----hccCCcccccccc---chhhhhhHHHH
Q 023791 133 ALGCTDEGLRKELTAMKESGVEIDAL----QSYGGGTSLKSKI---FSEEVDECILW 182 (277)
Q Consensus 133 alGcteEgLrkEL~~~~~sg~eie~~----~~yggsts~kski---~s~Ev~ECIlw 182 (277)
++-++.+++++||.-|-+.|-.|.+. +.|| .++.++ ...||+++|-=
T Consensus 2 ~v~H~~~~~~~EL~~IVd~Gg~V~DV~veHp~YG---~i~~~L~i~sr~Dv~~Fi~~ 55 (98)
T PF02829_consen 2 AVKHTPDEIEDELEIIVDNGGRVLDVIVEHPVYG---EITGNLNISSRRDVDKFIEK 55 (98)
T ss_dssp EEE--GGGHHHHHHHHHHTT-EEEEEEEEETTTE---EEEEEEEE-SHHHHHHHHHH
T ss_pred eeECCHHHHHHHHHHHHHCCCEEEEEEEeCCCCc---EEEEEEecCCHHHHHHHHHH
Confidence 46689999999999999999998875 5677 666666 45778876643
No 8
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=34.22 E-value=29 Score=23.40 Aligned_cols=27 Identities=30% Similarity=0.519 Sum_probs=20.9
Q ss_pred cchHHHHHhhhheeeccCCcHhHHHHHHhccccc
Q 023791 119 DNLKEFIDAGVNAYALGCTDEGLRKELTAMKESG 152 (277)
Q Consensus 119 ~nlkeFi~AgV~AYalGcteEgLrkEL~~~~~sg 152 (277)
++|+.|+.+.. ++++||++|.+.++..
T Consensus 4 ~~l~~Fl~~~~-------~d~~l~~~l~~~~~~~ 30 (49)
T PF07862_consen 4 ESLKAFLEKVK-------SDPELREQLKACQNPE 30 (49)
T ss_pred HHHHHHHHHHh-------cCHHHHHHHHhcCCHH
Confidence 46888888764 8999999999876433
No 9
>COG0008 GlnS Glutamyl- and glutaminyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=33.05 E-value=34 Score=33.75 Aligned_cols=102 Identities=23% Similarity=0.358 Sum_probs=61.1
Q ss_pred CCCCc-ccccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCc---HhHHHHHHhccc---------cccch
Q 023791 89 ISPDN-EYRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTD---EGLRKELTAMKE---------SGVEI 155 (277)
Q Consensus 89 ~s~dd-e~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcte---EgLrkEL~~~~~---------sg~ei 155 (277)
...|+ -||.|... -+|+.+ +++.|+.| .||.|-||. |.+|++-.+.++ .+++.
T Consensus 73 l~wde~~~~QS~r~-----~~Y~~~--------~~~Li~~G-~AY~c~ct~eele~~R~~~~~~g~~p~~y~r~~~~L~~ 138 (472)
T COG0008 73 LDWDEGPYYQSERF-----DIYYEY--------AEKLIEKG-KAYVCYCTPEELEEMRELRGALGEPPPSYDRDERNLTL 138 (472)
T ss_pred CCCCCceeehhhhH-----HHHHHH--------HHHHHHCC-CeEEecCCHHHHHHHHHHHhhcCCCCCCCCchhhccch
Confidence 34555 37877764 456655 35677777 599999999 777776666553 33444
Q ss_pred hhhhcc---CCccccccccchhhhhhHHHHHHHhhhhhhccC--CC-ceEeecCCCC
Q 023791 156 DALQSY---GGGTSLKSKIFSEEVDECILWLSIIFITILCTP--QP-TIVRWSSTPP 206 (277)
Q Consensus 156 e~~~~y---ggsts~kski~s~Ev~ECIlwlsIvfITIlctP--qp-tivRWSsTp~ 206 (277)
+.-+.+ ||.-.+..|+-..+... .|-=.|.--|...| .- ++.||.-.|.
T Consensus 139 ~~~~~~~~~~~~~viR~k~~~~~~~~--~~~D~v~g~i~~~~~~~~dv~~r~dg~pt 193 (472)
T COG0008 139 FEKMADLGEGGPAVVRLKIPMAHPGP--VFRDLVRGRIVFAPKHPDFVILRYDGYPT 193 (472)
T ss_pred HHHHhhcccCCCeEEEEeCCCCCCCC--ccccceeeeEecCccCCcceeecCCCCcc
Confidence 333444 77777888877432222 34444444444444 22 6777776654
No 10
>PLN03233 putative glutamate-tRNA ligase; Provisional
Probab=32.66 E-value=49 Score=33.29 Aligned_cols=42 Identities=26% Similarity=0.285 Sum_probs=29.2
Q ss_pred CCcccccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHHHHH
Q 023791 91 PDNEYRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRKELT 146 (277)
Q Consensus 91 ~dde~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrkEL~ 146 (277)
.|..|+.|... .+|+.. .++.|+.| .||.|-||.|.|+++-.
T Consensus 77 wD~~~~qSdr~-----~~y~~~--------a~~Li~~G-~AY~C~cs~eel~~~r~ 118 (523)
T PLN03233 77 PDSVSFTSDYF-----EPIRCY--------AIILIEEG-LAYMDDTPQEEMKKERA 118 (523)
T ss_pred CCCCccccccH-----HHHHHH--------HHHHHHcC-CeEecCCCHHHHHHHHh
Confidence 44567777663 455544 45677777 59999999999976643
No 11
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=29.98 E-value=35 Score=24.85 Aligned_cols=44 Identities=32% Similarity=0.462 Sum_probs=35.7
Q ss_pred HHhhhheeeccCCcHhHHHHHHhccccccchhhhhccCCcccccc
Q 023791 125 IDAGVNAYALGCTDEGLRKELTAMKESGVEIDALQSYGGGTSLKS 169 (277)
Q Consensus 125 i~AgV~AYalGcteEgLrkEL~~~~~sg~eie~~~~yggsts~ks 169 (277)
++.--.|-.+|.+..-++|=|..+++.|+ |+..+--+||..|.-
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gl-i~s~~G~~GGy~L~~ 69 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKKAGL-IESSRGRGGGYRLAR 69 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHHTTS-EEEETSTTSEEEESS
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhCCe-eEecCCCCCceeecC
Confidence 33444567899999999999999999999 888888889888764
No 12
>PRK01406 gltX glutamyl-tRNA synthetase; Reviewed
Probab=28.39 E-value=78 Score=30.87 Aligned_cols=36 Identities=31% Similarity=0.586 Sum_probs=26.6
Q ss_pred cccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHHH
Q 023791 95 YRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRKE 144 (277)
Q Consensus 95 ~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrkE 144 (277)
||.|.+.. +|+.+ +++.++.| .||.|-||.|+|.+.
T Consensus 82 y~QS~r~~-----~y~~~--------~~~L~~~g-~aY~C~cs~eel~~~ 117 (476)
T PRK01406 82 YRQSERLD-----IYKEY--------AEQLLEEG-KAYYCYCTPEELEAM 117 (476)
T ss_pred eehhcCHH-----HHHHH--------HHHHHHcC-CeeecCCCHHHHHHH
Confidence 88888864 56654 35666777 599999999988543
No 13
>KOG0913 consensus Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=27.34 E-value=67 Score=30.16 Aligned_cols=32 Identities=16% Similarity=0.018 Sum_probs=28.3
Q ss_pred cccchhhhhhHHHHHHHhhhhhhccCCCceEe
Q 023791 169 SKIFSEEVDECILWLSIIFITILCTPQPTIVR 200 (277)
Q Consensus 169 ski~s~Ev~ECIlwlsIvfITIlctPqptivR 200 (277)
.-+..+++-+|+.|+.|++++.++-+++-+++
T Consensus 176 ~a~v~~~~~~~l~~~~i~~~d~~~p~~~~~~~ 207 (248)
T KOG0913|consen 176 FAGVTEFVGEALGLLTIMTTDQGPPGKDGVTQ 207 (248)
T ss_pred hhhHHHHHHHHHhhhhhheecccCCCccCccc
Confidence 34567889999999999999999999998888
No 14
>PF00749 tRNA-synt_1c: tRNA synthetases class I (E and Q), catalytic domain; InterPro: IPR020058 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure []. ; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016876 ligase activity, forming aminoacyl-tRNA and related compounds, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 2HZ7_A 2CFO_A 4A91_A 1NZJ_A 1N78_A 1G59_C 2CV2_A 2CV1_A 2CV0_B 1GLN_A ....
Probab=26.92 E-value=49 Score=30.26 Aligned_cols=132 Identities=23% Similarity=0.364 Sum_probs=73.2
Q ss_pred cccccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHHHHHhccccc----------------cchh
Q 023791 93 NEYRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRKELTAMKESG----------------VEID 156 (277)
Q Consensus 93 de~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrkEL~~~~~sg----------------~eie 156 (277)
..|+.|..++ +|+.. +++.++.| .||.|-||.|+|+++-......| -+++
T Consensus 70 ~~~~QS~r~~-----~Y~~~--------~~~L~~~g-~aY~C~Csr~~l~~~r~~~~~~~~~~~~~y~~~c~~~~~~~~~ 135 (314)
T PF00749_consen 70 GPYYQSDRLE-----IYQEA--------AEKLIDKG-KAYPCFCSREELKAAREAQEGAGCPHRPRYPGTCRELTEEEMR 135 (314)
T ss_dssp CEEEGGGGHH-----HHHHH--------HHHHHHTT-SEEEEESEHHHHHHHHHHHHHTTSTTTTSBHHHHHCHHHHHHH
T ss_pred eEEeHHHHHH-----HHHHH--------HHHHhhcC-CCccccCCHHHHHHHHHHhhccCCCccccchhhhhhhhHHHHH
Confidence 5667776654 45543 45667666 68999999999988765532222 1122
Q ss_pred hhhccCCccccccccchhhhhhHHHHHHHhhhhhhccCCCceEeecCCCCCCHHHHhhhhh-----HHHHHHhHH-----
Q 023791 157 ALQSYGGGTSLKSKIFSEEVDECILWLSIIFITILCTPQPTIVRWSSTPPVSDEIRLQWKG-----FCALIANAY----- 226 (277)
Q Consensus 157 ~~~~yggsts~kski~s~Ev~ECIlwlsIvfITIlctPqptivRWSsTp~VS~e~~~qWkG-----FcalIaNaY----- 226 (277)
+...-|+...+..|+-.+.- +.|-=.|.--|...|. .+.|-++..|.| |+..|=.+.
T Consensus 136 ~~~~~~~~~~iRlk~~~~~~---~~~~D~v~g~i~~~~~----------~~~D~vi~r~dg~ptY~fA~vVDD~~~gITH 202 (314)
T PF00749_consen 136 AGLAKGGPAVIRLKVPMESP---IAFRDLVRGRIIFDPS----------DLGDFVIRRSDGYPTYHFAVVVDDHLMGITH 202 (314)
T ss_dssp HHHHTTTSEEEEE-SSSTCC---EEEEETTTEEEEEEGG----------GSBTEEEESTTSEB-HHHHHHHHHHHTT-SE
T ss_pred hhhccCCceeeeeecccccc---cccccCcceeeeeccc----------cCCchhccccccCcccccceeecccccccCe
Confidence 23445666666666654421 1111112222222220 123334444444 555555543
Q ss_pred HhhcceeeeecccchhhhhhcccCC
Q 023791 227 YVRGMAWLPVKTLQLEQMAVVGCAE 251 (277)
Q Consensus 227 y~rgMAWlPvktLQLEqmAV~G~ae 251 (277)
-.||.-|++-...|+-.....|...
T Consensus 203 ViRG~D~l~~t~~Q~~L~~~Lg~~~ 227 (314)
T PF00749_consen 203 VIRGEDLLSSTPRQILLYEALGWPP 227 (314)
T ss_dssp EEEEGGGTTCHHHHHHHHHHCTSSS
T ss_pred EEEccccccccHHHHHHHHHhCCCC
Confidence 3588999998888888887777654
No 15
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=26.29 E-value=20 Score=22.42 Aligned_cols=34 Identities=29% Similarity=0.563 Sum_probs=25.9
Q ss_pred heeeccCCcHhHHHHHHhccccccchhhhhccCCccc
Q 023791 130 NAYALGCTDEGLRKELTAMKESGVEIDALQSYGGGTS 166 (277)
Q Consensus 130 ~AYalGcteEgLrkEL~~~~~sg~eie~~~~yggsts 166 (277)
.|-.+|.+...+++.|..|.+.|+ |+ +.+||.+|
T Consensus 20 l~~~l~~s~~tv~~~l~~L~~~g~-i~--~~~~~~~~ 53 (53)
T smart00420 20 LAELLGVSEMTIRRDLNKLEEQGL-LT--RVHGGAVS 53 (53)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCC-EE--EeecCccC
Confidence 344479999999999999999988 44 35576654
No 16
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=25.24 E-value=82 Score=22.80 Aligned_cols=93 Identities=22% Similarity=0.285 Sum_probs=46.6
Q ss_pred CCCCcccccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHHHHHhccccccchhhhhccCCccccc
Q 023791 89 ISPDNEYRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRKELTAMKESGVEIDALQSYGGGTSLK 168 (277)
Q Consensus 89 ~s~dde~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrkEL~~~~~sg~eie~~~~yggsts~k 168 (277)
.+.||.+++...-++.++++|.--. +-+-.|-..+.-.++|.+|.++|.||- +.|=+-.--
T Consensus 10 ltfDdg~~~~~~~~~~~l~~~~i~a----------------t~fv~~~~~~~~~~~l~~l~~~G~ei~---~H~~~H~~~ 70 (123)
T PF01522_consen 10 LTFDDGYRDNYDRLLPLLKKYGIPA----------------TFFVIGSWVERYPDQLRELAAAGHEIG---NHGWSHPNL 70 (123)
T ss_dssp EEEESHCHTHHHHHHHHHHHTT--E----------------EEEE-HHHHHHHHHHHHHHHHTT-EEE---EE-SSSSCG
T ss_pred EEEecCchhhHHHHHHHHHhcccce----------------eeeecccccccccccchhHHHHHHHHH---hcCCccccc
Confidence 4678888888888888888885211 111111123333778888888898863 222222222
Q ss_pred cccchhhhhhHHHHHHHhhhhhhccCCCceEee
Q 023791 169 SKIFSEEVDECILWLSIIFITILCTPQPTIVRW 201 (277)
Q Consensus 169 ski~s~Ev~ECIlwlsIvfITIlctPqptivRW 201 (277)
.....+++++-|..-.-.+-.++-. .|+..|+
T Consensus 71 ~~~~~~~~~~ei~~~~~~l~~~~g~-~~~~f~~ 102 (123)
T PF01522_consen 71 STLSPEELRREIERSREILEEITGR-PPKGFRY 102 (123)
T ss_dssp GGS-HHHHHHHHHHHHHHHHHHHSS-EESEEE-
T ss_pred ccCCHHHHHHHHHHHHHHHHHHhCC-CCcEEEC
Confidence 3444444444444433333333333 4445555
No 17
>PLN02627 glutamyl-tRNA synthetase
Probab=24.24 E-value=83 Score=31.86 Aligned_cols=36 Identities=31% Similarity=0.579 Sum_probs=25.9
Q ss_pred cccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHHH
Q 023791 95 YRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRKE 144 (277)
Q Consensus 95 ~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrkE 144 (277)
|+.|..+ .+|+.+ ++..++.| .||.|-||.|+|.+.
T Consensus 124 y~QSeR~-----~~Y~~~--------a~~Li~~G-~AY~CfCs~eel~~~ 159 (535)
T PLN02627 124 YRQSERN-----AIYKQY--------AEKLLESG-HVYPCFCTDEELEAM 159 (535)
T ss_pred eeeeccH-----HHHHHH--------HHHHHHcC-CeeeccCChHHHHHH
Confidence 7888775 356554 45667777 599999999988543
No 18
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=23.53 E-value=36 Score=22.67 Aligned_cols=24 Identities=29% Similarity=0.372 Sum_probs=19.8
Q ss_pred heeeccCCcHhHHHHHHhcccccc
Q 023791 130 NAYALGCTDEGLRKELTAMKESGV 153 (277)
Q Consensus 130 ~AYalGcteEgLrkEL~~~~~sg~ 153 (277)
.|..+|||-|-.-.-|..+++.|+
T Consensus 8 iA~~lG~t~ETVSR~l~~l~~~gl 31 (32)
T PF00325_consen 8 IADYLGLTRETVSRILKKLERQGL 31 (32)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHHhCCcHHHHHHHHHHHHHcCC
Confidence 467899999999999999988875
No 19
>TIGR00463 gltX_arch glutamyl-tRNA synthetase, archaeal and eukaryotic family. The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This alignment models just the eukaryotic cytosolic and archaeal forms of the enzyme. In some eukaryotes, the glutamyl-tRNA synthetase is part of a longer, multifunctional aminoacyl-tRNA ligase. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases may act on both tRNA(gln) and tRNA(glu).
Probab=23.20 E-value=83 Score=31.93 Aligned_cols=51 Identities=20% Similarity=0.367 Sum_probs=31.8
Q ss_pred hHHHHHhhhheeeccCCcHhHHHHHHhcccc---ccchh-------hhh---ccCCccccccccc
Q 023791 121 LKEFIDAGVNAYALGCTDEGLRKELTAMKES---GVEID-------ALQ---SYGGGTSLKSKIF 172 (277)
Q Consensus 121 lkeFi~AgV~AYalGcteEgLrkEL~~~~~s---g~eie-------~~~---~yggsts~kski~ 172 (277)
+++.|+.| .||.|-||.|+|+++-.+-..+ +..+| .|. ..||...+..|+-
T Consensus 176 a~~Li~~G-~AY~C~cs~eei~~~r~~g~~~~cR~~s~eenl~~fe~m~~g~~~~~~~~lR~K~d 239 (560)
T TIGR00463 176 CRKLIEMG-KAYVCDCPPEEFRELRNDGVACACRDRSVEENLEIWEEMLNGTEEGGKVVVRAKTD 239 (560)
T ss_pred HHHHHHcC-CceeecCCHHHHHHHHhCCCCCCccCCCHHHHHHHHHHHhcccccCCCeEEEEECC
Confidence 45667777 4999999999998875432211 12222 232 2367777888763
No 20
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=22.44 E-value=49 Score=24.49 Aligned_cols=26 Identities=38% Similarity=0.703 Sum_probs=20.9
Q ss_pred hhhHhccCCCCcchHHHHHhhhheee
Q 023791 108 RYRNVIDRGGGDNLKEFIDAGVNAYA 133 (277)
Q Consensus 108 RY~~Vi~rg~~~nlkeFi~AgV~AYa 133 (277)
|++..++.+.+..+-+||..++.+|+
T Consensus 93 ~~~~~~~~~~~~~~~~fi~~Ai~~y~ 118 (118)
T PF07739_consen 93 RFAAMYDKKFGPGLAEFIEKAIEAYA 118 (118)
T ss_dssp HHHHHHG-GGSTTHHHHHHHHHHHHH
T ss_pred HHHhhccccCCHHHHHHHHHHHHHHC
Confidence 55677787889999999999998885
No 21
>TIGR00464 gltX_bact glutamyl-tRNA synthetase, bacterial family. The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This alignment models just the bacterial and mitochondrial forms of the enzyme. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases may act on both tRNA(gln) and tRNA(glu). This model is highly specific. Proteins with positive scores below the trusted cutoff may be fragments rather than full-length sequences.
Probab=22.17 E-value=1e+02 Score=30.00 Aligned_cols=37 Identities=30% Similarity=0.584 Sum_probs=27.0
Q ss_pred cccccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHH
Q 023791 93 NEYRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRK 143 (277)
Q Consensus 93 de~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrk 143 (277)
..|+.|.++ .+|+.+. +..|+.| .||.|-||.|+|.+
T Consensus 70 ~~~~QS~r~-----~~y~~~~--------~~L~~~g-~aY~C~ct~~~l~~ 106 (470)
T TIGR00464 70 GPYYQSQRL-----DIYKKYA--------KELLEEG-LAYRCYCSKERLER 106 (470)
T ss_pred CeeehhCCH-----HHHHHHH--------HHHHHcC-CEEecCCChHHHHH
Confidence 468888775 4566553 5677777 59999999998853
No 22
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=22.16 E-value=54 Score=29.21 Aligned_cols=19 Identities=37% Similarity=0.737 Sum_probs=16.3
Q ss_pred cchHHHHHhhhheeeccCC
Q 023791 119 DNLKEFIDAGVNAYALGCT 137 (277)
Q Consensus 119 ~nlkeFi~AgV~AYalGct 137 (277)
+|++||.++|+.|..+|-.
T Consensus 172 ~n~~~yl~aGa~avg~Gs~ 190 (222)
T PRK07114 172 ENLKKWFGAGVTCVGMGSK 190 (222)
T ss_pred hcHHHHHhCCCEEEEEChh
Confidence 6999999999888877754
No 23
>TIGR03128 RuMP_HxlA 3-hexulose-6-phosphate synthase. at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. In these species, the enzyme is viewed as a lyase rather than a synthase and is called D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Note that there is some overlap in specificity with the Escherichia coli enzyme 3-keto-L-gulonate 6-phosphate decarboxylase.
Probab=22.06 E-value=47 Score=27.13 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=20.2
Q ss_pred ccCCCC-cchHHHHHhhhheeeccC
Q 023791 113 IDRGGG-DNLKEFIDAGVNAYALGC 136 (277)
Q Consensus 113 i~rg~~-~nlkeFi~AgV~AYalGc 136 (277)
+++|.. +|+++++++|++...+|=
T Consensus 163 v~GGI~~~n~~~~~~~Ga~~v~vGs 187 (206)
T TIGR03128 163 VAGGINLDTIPDVIKLGPDIVIVGG 187 (206)
T ss_pred EECCcCHHHHHHHHHcCCCEEEEee
Confidence 477765 699999999999999974
No 24
>PRK14895 gltX glutamyl-tRNA synthetase; Provisional
Probab=21.74 E-value=1e+02 Score=30.95 Aligned_cols=49 Identities=18% Similarity=0.293 Sum_probs=33.5
Q ss_pred CCCccccccCCCCCCC-cccccchhhHHHHHHhhhHhccCCCCcchHHHHHhhhheeeccCCcHhHHHH
Q 023791 77 PSKKWLCRSHDPISPD-NEYRSSRNIAISLFRRYRNVIDRGGGDNLKEFIDAGVNAYALGCTDEGLRKE 144 (277)
Q Consensus 77 ~~~~wl~~~~~~~s~d-de~rssrniaisL~rRY~~Vi~rg~~~nlkeFi~AgV~AYalGcteEgLrkE 144 (277)
.+-+||.-. .| .-||.|.++. +|+.+ +++.++.| .||.|-||.|+|.+.
T Consensus 61 ~~L~WLGl~-----wDe~py~QSeR~~-----~Y~~~--------a~~Li~~G-~AY~CfCt~eel~~~ 110 (513)
T PRK14895 61 SGLKWLGLD-----WNGEVIFQSKRNN-----LYKEA--------ALKLLQNG-KAYYCFTRQEEIERQ 110 (513)
T ss_pred HHHHHcCCC-----CCCCceeEeCcHH-----HHHHH--------HHHHHHcC-CeEEecCcHHHHHHH
Confidence 345677433 33 3588888864 45544 46777777 599999999988543
No 25
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=20.74 E-value=62 Score=22.58 Aligned_cols=40 Identities=25% Similarity=0.413 Sum_probs=31.6
Q ss_pred hhhheeeccCCcHhHHHHHHhccccccchhhhhccCCcccccc
Q 023791 127 AGVNAYALGCTDEGLRKELTAMKESGVEIDALQSYGGGTSLKS 169 (277)
Q Consensus 127 AgV~AYalGcteEgLrkEL~~~~~sg~eie~~~~yggsts~ks 169 (277)
..-.|-.+|.+....++-+..|.+.|+.|+.- |+|..++.
T Consensus 16 ~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~---~~g~~l~~ 55 (69)
T TIGR00122 16 GEKLGEALGMSRTAVNKHIQTLREWGVDVLTV---GKGYRLPP 55 (69)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec---CCceEecC
Confidence 44557788999999999999999999998775 45555533
Done!