Query 036078
Match_columns 285
No_of_seqs 110 out of 348
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 09:12:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036078.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036078hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02396 diverge_rpsU rpsU-di 100.0 1.4E-48 3E-53 344.1 19.3 164 96-260 1-184 (184)
2 COG5590 Uncharacterized conser 100.0 5.7E-34 1.2E-38 253.8 16.9 175 90-264 23-217 (229)
3 PF08511 COQ9: COQ9; InterPro 100.0 6.5E-32 1.4E-36 209.1 4.6 79 180-258 1-79 (79)
4 KOG2969 Uncharacterized conser 100.0 2.2E-27 4.8E-32 210.7 17.1 181 96-276 48-260 (264)
5 PRK00767 transcriptional regul 97.4 0.019 4E-07 49.1 17.1 71 93-163 8-98 (197)
6 TIGR03384 betaine_BetI transcr 97.0 0.055 1.2E-06 45.8 15.9 73 91-163 5-96 (189)
7 PRK14996 TetR family transcrip 96.0 0.59 1.3E-05 40.1 15.8 79 93-171 7-102 (192)
8 PRK15008 HTH-type transcriptio 95.4 0.29 6.3E-06 43.1 11.8 74 93-166 17-108 (212)
9 TIGR03613 RutR pyrimidine util 94.7 0.89 1.9E-05 39.1 12.7 74 93-166 7-98 (202)
10 PRK10668 DNA-binding transcrip 94.7 2.6 5.7E-05 36.6 16.6 74 93-166 10-103 (215)
11 PRK11202 DNA-binding transcrip 94.1 2.6 5.7E-05 36.9 14.4 36 93-128 10-56 (203)
12 PRK09480 slmA division inhibit 93.7 3.8 8.2E-05 34.7 15.5 76 93-169 9-104 (194)
13 PRK09975 DNA-binding transcrip 93.4 4.3 9.2E-05 35.2 14.4 73 91-163 8-100 (213)
14 TIGR02366 DHAK_reg probable di 90.7 7.2 0.00016 32.8 12.3 30 94-123 3-32 (176)
15 PRK13756 tetracycline represso 89.8 2.5 5.4E-05 37.9 9.0 74 95-168 5-95 (205)
16 PRK11552 putative DNA-binding 88.1 0.88 1.9E-05 40.8 5.0 35 93-128 12-56 (225)
17 PRK11640 putative transcriptio 86.3 22 0.00047 31.0 15.9 68 95-162 2-89 (191)
18 PF00440 TetR_N: Bacterial reg 83.1 0.5 1.1E-05 32.3 0.7 25 99-123 1-25 (47)
19 COG1309 AcrR Transcriptional r 66.3 8.9 0.00019 30.3 3.9 30 94-123 12-41 (201)
20 COG3226 Uncharacterized protei 59.6 1E+02 0.0023 28.1 9.7 29 95-123 14-42 (204)
21 cd03204 GST_C_GDAP1 GST_C fami 23.4 2E+02 0.0044 23.4 5.2 59 162-230 3-81 (111)
No 1
>TIGR02396 diverge_rpsU rpsU-divergently transcribed protein. This uncharacterized protein is found in a number of Alphaproteobacteria and, with N-terminal regions long enough to be transit peptides, in eukaryotes. This phylogeny suggests mitochondrial derivation. In several Alphaproteobacteria, the gene for this protein is encoded divergently from rpsU, the gene for ribosomal protein S21. S21 is unusual in being encoded outside the usual long ribosomal protein operons, but rather in contexts that suggest regulation of the initiation of protein translation.
Probab=100.00 E-value=1.4e-48 Score=344.13 Aligned_cols=164 Identities=41% Similarity=0.697 Sum_probs=148.3
Q ss_pred HHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHHH---HH-------HHHHHhhcCCCCCCCChHHHHHHH
Q 036078 96 QARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDDC---LQ-------RLIDRIDSGEDLKDLIPSQRISKL 155 (285)
Q Consensus 96 r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~~---~~-------~L~~~iD~~~~l~~l~~rERI~~l 155 (285)
+++||+++|+|||++||++.+|.++|++ +|+++. .+ .+.+.+.. .++..++++|||+.+
T Consensus 1 ~~~iL~aal~~vp~~Gwt~~al~~aa~~lgl~~~~~~~~~~~g~~dLv~~~~~~~d~l~~~~~~-~~~~~~~~reri~~l 79 (184)
T TIGR02396 1 KAKILDAALEHVPFLGWTNEALLLAARELGYSDSTPGILPPEGAADLIEFFEDYCNALLASLKS-SDLEVLKVSEKIELA 79 (184)
T ss_pred ChHHHHHHHHhhhhcCCCHHHHHHHHHHcCCCHHHHHHhCCchHHHHHHHHHHHHHHHHHHHhc-cccccCCHHHHHHHH
Confidence 4689999999999999999999999998 444432 22 33333321 356778999999999
Q ss_pred HHHHHhhccchhhhHHHHHHhhcCCCCchHHHHHHHHHHHHHHHHhCCCCCCchhHHHHHHHHHHHHHHHHHHhcCCCCC
Q 036078 156 VRIRLEMQAPYISKWPQALSIQAQPLNVPTSFKQRAMLVDEIWHAVGDEASDIDWYVKRTVLGGIYSTTEIYMLTDSSPD 235 (285)
Q Consensus 156 L~~RLe~l~P~~e~~~qaLa~lalP~n~~~sl~~l~~laD~Iw~~AGD~StD~~wYtKRa~La~IY~stel~wL~D~S~d 235 (285)
|+.||++++||+++|+++++++++|+|++.+++++|+++|+||+++||+|+||||||||++|++||++|++|||+|+|||
T Consensus 80 i~~RL~~~~p~~~~~~~ala~~~~P~n~~~~~~~l~~l~D~iw~~aGD~s~D~~wYtKRa~L~~vY~st~l~~l~D~S~~ 159 (184)
T TIGR02396 80 VWIRLKMNIPIIQHLPQALAFLAQPLNLITSLRLLARLSDAIWYLAGDKSTDFNWYTKRAILSGVYSSTELFMLQDKSEG 159 (184)
T ss_pred HHHHHHhcccHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHhCCCcccchHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Q 036078 236 FCDTSRFLDDRVRDAFDLKKTFQEA 260 (285)
Q Consensus 236 ~~~T~aFLdrRL~~a~~l~~~~~~~ 260 (285)
|++||+||||||+++++|++.++++
T Consensus 160 ~~~T~~FLdrri~~v~~~~~~k~~~ 184 (184)
T TIGR02396 160 FEDTWSFLDSRIDNAVKLQKFKARL 184 (184)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999999999999999999988753
No 2
>COG5590 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.7e-34 Score=253.77 Aligned_cols=175 Identities=22% Similarity=0.399 Sum_probs=156.4
Q ss_pred CCCchHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHHHHHH---HHHHhhc-------CCCCCCCChH
Q 036078 90 VEYRDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDDCLQR---LIDRIDS-------GEDLKDLIPS 149 (285)
Q Consensus 90 ~~~e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~~~~~---L~~~iD~-------~~~l~~l~~r 149 (285)
..+...+..+++++|+|||++||++..|.++... .||++..+- +.++.|. ..+....+++
T Consensus 23 ~k~s~kk~~~l~~llelvP~~gwnn~li~eal~a~Gys~~~s~ilfP~g~~eLi~f~~~~~d~~aL~~lk~~dvtp~kir 102 (229)
T COG5590 23 EKESIKKIVFLQSLLELVPFNGWNNRLIVEALEALGYSKGYSLILFPEGPMELIKFLEVYLDAYALESLKNIDVTPQKIR 102 (229)
T ss_pred hhhcHHHHHHHHHHHHhccccccchhHHHHHHHhcCcccchhhhcCCCCHHHHHHHHHHHhHHHHHhcCCccccchHHHH
Confidence 3444568999999999999999999999999887 788886442 3344442 1344566789
Q ss_pred HHHHHHHHHHHhhccchhhhHHHHHHhhcCCCCchHHHHHHHHHHHHHHHHhCCCCCCchhHHHHHHHHHHHHHHHHHHh
Q 036078 150 QRISKLVRIRLEMQAPYISKWPQALSIQAQPLNVPTSFKQRAMLVDEIWHAVGDEASDIDWYVKRTVLGGIYSTTEIYML 229 (285)
Q Consensus 150 ERI~~lL~~RLe~l~P~~e~~~qaLa~lalP~n~~~sl~~l~~laD~Iw~~AGD~StD~~wYtKRa~La~IY~stel~wL 229 (285)
+||..+|..||+++.|.-.++++.+++++.|.|+..+++.+|+++|+||++|||+++||||||||+.|++||.++++||+
T Consensus 103 ~ri~~~v~~Rl~~~~pi~~~L~~l~A~lafpsn~~~~l~~~~rssDaIwr~AgDks~Dfn~YtKRa~lssiyisS~lf~~ 182 (229)
T COG5590 103 ERISLLVKKRLKTDKPIGGHLHSLNAQLAFPSNLIQGLAVLHRSSDAIWRYAGDKSLDFNWYTKRAALSSIYISSILFMI 182 (229)
T ss_pred HHHHHHHHHHHHhcCchhhhhHHHHHHHhccchHHHHHHHHHHhhHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 036078 230 TDSSPDFCDTSRFLDDRVRDAFDLKKTFQEATYLA 264 (285)
Q Consensus 230 ~D~S~d~~~T~aFLdrRL~~a~~l~~~~~~~~~~a 264 (285)
+|+|++|.+|..|++.+|.++++++..++++..++
T Consensus 183 qd~S~ny~etd~fi~~~i~~~~~~~~~~~~~le~~ 217 (229)
T COG5590 183 QDESENYIETDTFIETKIHNIKKLGELYNKTLEFS 217 (229)
T ss_pred hccchhHHHHHHHHHHHHHHHHHHhhhhhhhhhhh
Confidence 99999999999999999999999999998887654
No 3
>PF08511 COQ9: COQ9; InterPro: IPR013718 COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q []. It may either catalyse a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role. ; PDB: 3NI7_B.
Probab=99.97 E-value=6.5e-32 Score=209.13 Aligned_cols=79 Identities=49% Similarity=0.874 Sum_probs=33.0
Q ss_pred CCCchHHHHHHHHHHHHHHHHhCCCCCCchhHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHH
Q 036078 180 PLNVPTSFKQRAMLVDEIWHAVGDEASDIDWYVKRTVLGGIYSTTEIYMLTDSSPDFCDTSRFLDDRVRDAFDLKKTFQ 258 (285)
Q Consensus 180 P~n~~~sl~~l~~laD~Iw~~AGD~StD~~wYtKRa~La~IY~stel~wL~D~S~d~~~T~aFLdrRL~~a~~l~~~~~ 258 (285)
|+|++.+++++|+++|+||++|||+|+|++|||||++|++||+++|+|||+|+|+||++||+||||||+++++|+++|+
T Consensus 1 P~n~~~sl~~l~~l~D~iw~~aGD~S~D~~wYtKR~~L~~iY~st~l~~l~d~S~~~~~T~~Fl~rri~~v~~~~k~k~ 79 (79)
T PF08511_consen 1 PQNAPTSLKLLWRLADDIWYAAGDKSTDFNWYTKRAILAAIYASTELYMLQDKSPDFEDTWAFLDRRIDDVMQFGKAKA 79 (79)
T ss_dssp ------------------------------------HHHHHHHHHHHHHHT--SGGGHHHHHHHHHHHHHH--------
T ss_pred CccccccccccccccccccccccccchhhhhhHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHhhhcccccCC
Confidence 8999999999999999999999999999999999999999999999999999999999999999999999999999763
No 4
>KOG2969 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.95 E-value=2.2e-27 Score=210.69 Aligned_cols=181 Identities=25% Similarity=0.404 Sum_probs=151.6
Q ss_pred HHHHHHHHHhHHhhcCccHHHHHHHHHH---------hccHH-----------HHH----HHHHHhh---cC--CCCCCC
Q 036078 96 QARVLEASLRHVAKHGWGEAAMIAGARD---------FFMDD-----------CLQ----RLIDRID---SG--EDLKDL 146 (285)
Q Consensus 96 r~rIL~aAL~lVp~~GWt~~AL~~aA~d---------~F~~~-----------~~~----~L~~~iD---~~--~~l~~l 146 (285)
+.-|++.+++|||++||++.+|.++..+ .|+.+ ..+ +|.+..- ++ ++....
T Consensus 48 kaliaena~efVPehGFsE~aIVeg~naLGYpn~mia~~ga~n~~~ffh~~~a~melikfqlvdka~rl~eg~~pdi~~q 127 (264)
T KOG2969|consen 48 KALIAENALEFVPEHGFSEDAIVEGGNALGYPNLMIALFGAGNMDLFFHFFLAQMELIKFQLVDKALRLLEGHLPDIPEQ 127 (264)
T ss_pred hHHHHHHHHHhchhcCCcHHHHHhhhhhcCCchhHHHhcCCCCccHHHHHHHHHHHHHHHHHHHHHHHhhcCcCCCCCcc
Confidence 6778889999999999999999999987 22222 111 1222211 11 233333
Q ss_pred ChHHHHHHHHHHHHhhccchhhhHHHHHHhhcCC--CCchHHHHHHHHHHHHHHHHhCCC-CCCchhHHHHHHHHHHHHH
Q 036078 147 IPSQRISKLVRIRLEMQAPYISKWPQALSIQAQP--LNVPTSFKQRAMLVDEIWHAVGDE-ASDIDWYVKRTVLGGIYST 223 (285)
Q Consensus 147 ~~rERI~~lL~~RLe~l~P~~e~~~qaLa~lalP--~n~~~sl~~l~~laD~Iw~~AGD~-StD~~wYtKRa~La~IY~s 223 (285)
.-+..|.++|+.||++..|...++++++++.+.| .+.-.++.++++++|+|.|.+.|+ +.|+.||+||+.+++||..
T Consensus 128 ~~lpslehLilkRLe~dk~IggHL~elia~~aiPsaflfekaipeL~eLSDdiiYfandKdh~D~aWYaKRaAiSaiYia 207 (264)
T KOG2969|consen 128 SGLPSLEHLILKRLEGDKDIGGHLPELIAICAIPSAFLFEKAIPELAELSDDIIYFANDKDHADFAWYAKRAAISAIYIA 207 (264)
T ss_pred cCCchHHHHHHHHHhcCCchhhhHHHHHHHHhCchHHHHHHhhHHHHhhchhheecccccccchHHHHHHHHHHHHHHHH
Confidence 3345699999999999999999999999999999 778899999999999999999998 8999999999999999999
Q ss_pred HHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHh
Q 036078 224 TEIYMLTDSSPDFCDTSRFLDDRVRDAFDLKKTFQEATYLAEAVGAGMGSSLQ 276 (285)
Q Consensus 224 tel~wL~D~S~d~~~T~aFLdrRL~~a~~l~~~~~~~~~~a~~~~~g~g~~~~ 276 (285)
++|||-+|+|++|++|..|.+.+|..+++++.+.++++.+++.-.+...+.++
T Consensus 208 SeLFMaqDkShNfeaTfnFakdkih~a~aLgd~~NdteEfa~fqLmat~niik 260 (264)
T KOG2969|consen 208 SELFMAQDKSHNFEATFNFAKDKIHHAKALGDLRNDTEEFASFQLMATRNIIK 260 (264)
T ss_pred HHHHHhccCCCchHHHhhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999998877665555443
No 5
>PRK00767 transcriptional regulator BetI; Validated
Probab=97.42 E-value=0.019 Score=49.11 Aligned_cols=71 Identities=18% Similarity=0.333 Sum_probs=48.7
Q ss_pred chHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHHH--HHHHHHH----hhcC--CCC--CCCChHHHH
Q 036078 93 RDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDDC--LQRLIDR----IDSG--EDL--KDLIPSQRI 152 (285)
Q Consensus 93 e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~~--~~~L~~~----iD~~--~~l--~~l~~rERI 152 (285)
+..|++||++|++++.+.||...++.+.|++ ||+++- ...++++ +... ..+ ....+.++|
T Consensus 8 ~~~r~~Il~aA~~lf~~~G~~~~s~~~Ia~~aGvs~gslY~~F~~Ke~L~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l 87 (197)
T PRK00767 8 PIRRQQLIDATLRAIGEVGLLDATIAQIARRAGVSTGIISHYFGGKDGLLEATMRHLLRQLGDAVLARLAAAADTPRARL 87 (197)
T ss_pred hhHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHH
Confidence 4579999999999999999999999999998 787662 2222222 1111 111 234678888
Q ss_pred HHHHHHHHhhc
Q 036078 153 SKLVRIRLEMQ 163 (285)
Q Consensus 153 ~~lL~~RLe~l 163 (285)
...+..-+...
T Consensus 88 ~~~~~~~~~~~ 98 (197)
T PRK00767 88 RAIVEANFDAS 98 (197)
T ss_pred HHHHHHhccHh
Confidence 88887545433
No 6
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=97.05 E-value=0.055 Score=45.78 Aligned_cols=73 Identities=16% Similarity=0.304 Sum_probs=49.1
Q ss_pred CCchHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHHH--HHHHH----HHhhcC--CCC-CCCChHHH
Q 036078 91 EYRDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDDC--LQRLI----DRIDSG--EDL-KDLIPSQR 151 (285)
Q Consensus 91 ~~e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~~--~~~L~----~~iD~~--~~l-~~l~~rER 151 (285)
..+.-+++||++|++++.++||+..++.+.|++ ||+++- ...++ +.+... ..+ ....+.++
T Consensus 5 ~~~~rr~~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~~ly~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (189)
T TIGR03384 5 MEPIRRAELIDATIESIGERGSLDVTIAQIARRAGVSSGIISHYFGGKQGLLEATMRHLLSELRAAVVARLAKASSPRER 84 (189)
T ss_pred chhHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHH
Confidence 335678999999999999999999999999998 787662 22222 221110 111 12467888
Q ss_pred HHHHHHHHHhhc
Q 036078 152 ISKLVRIRLEMQ 163 (285)
Q Consensus 152 I~~lL~~RLe~l 163 (285)
|..++..-+...
T Consensus 85 l~~~~~~~~~~~ 96 (189)
T TIGR03384 85 LEAIVEANFDDS 96 (189)
T ss_pred HHHHHHHHhhhh
Confidence 888887545443
No 7
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=96.00 E-value=0.59 Score=40.14 Aligned_cols=79 Identities=16% Similarity=0.261 Sum_probs=51.3
Q ss_pred chHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHHH--HH----HHHHHhhcC-CCCCCCChHHHHHHH
Q 036078 93 RDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDDC--LQ----RLIDRIDSG-EDLKDLIPSQRISKL 155 (285)
Q Consensus 93 e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~~--~~----~L~~~iD~~-~~l~~l~~rERI~~l 155 (285)
+..|++||++|++++.++||...++.+.|+. ||+++- .. .+++.+... ......++.++|...
T Consensus 7 ~~~R~~Il~aA~~lf~e~G~~~tSi~~Ia~~aGvsk~~lY~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 86 (192)
T PRK14996 7 DERREVILQAAMRVALAEGFAAMTVRRIASEAQVAAGQVHHHFSSAGELKALAFIHLIRQLLDAEQVPQTASWRERLHAM 86 (192)
T ss_pred HHHHHHHHHHHHHHHHhcChhhccHHHHHHHhCCCcHHHHHHcCCHHHHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHH
Confidence 5569999999999999999999999999998 787762 11 222222111 112234678888888
Q ss_pred HHHHHhhccchhhhHH
Q 036078 156 VRIRLEMQAPYISKWP 171 (285)
Q Consensus 156 L~~RLe~l~P~~e~~~ 171 (285)
+........|+...|.
T Consensus 87 ~~~~~~~~~~~~~l~~ 102 (192)
T PRK14996 87 LGSEDGRFEPYIRLWR 102 (192)
T ss_pred HhCchhhhhHHHHHHH
Confidence 7643333344444443
No 8
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=95.42 E-value=0.29 Score=43.07 Aligned_cols=74 Identities=18% Similarity=0.299 Sum_probs=51.5
Q ss_pred chHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHH--HHHHHHHH----hhcC--CCCCCCChHHHHHH
Q 036078 93 RDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDD--CLQRLIDR----IDSG--EDLKDLIPSQRISK 154 (285)
Q Consensus 93 e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~--~~~~L~~~----iD~~--~~l~~l~~rERI~~ 154 (285)
+..|++||++|+.++.++||...++.+.|+. ||.++ ...+++++ +... .-....++.++|+.
T Consensus 17 ~~~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gtiY~hF~sKe~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 96 (212)
T PRK15008 17 SAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKE 96 (212)
T ss_pred HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHH
Confidence 5579999999999999999999999999998 78776 22222222 1110 11123457788888
Q ss_pred HHHHHHhhccch
Q 036078 155 LVRIRLEMQAPY 166 (285)
Q Consensus 155 lL~~RLe~l~P~ 166 (285)
.+..-++....+
T Consensus 97 ~i~~~~~~~~~~ 108 (212)
T PRK15008 97 YIRLKLEVSRDY 108 (212)
T ss_pred HHHHHHHHHHHC
Confidence 887766665544
No 9
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=94.75 E-value=0.89 Score=39.13 Aligned_cols=74 Identities=19% Similarity=0.287 Sum_probs=52.0
Q ss_pred chHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHH--HHHHHHHHhhc----C--CCCCCCChHHHHHH
Q 036078 93 RDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDD--CLQRLIDRIDS----G--EDLKDLIPSQRISK 154 (285)
Q Consensus 93 e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~--~~~~L~~~iD~----~--~~l~~l~~rERI~~ 154 (285)
+..+++||++|++++.+.||...++.+.|+. ||.++ ...++++.+.. . .-.....+.++|..
T Consensus 7 ~~~r~~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~lY~hF~sKe~L~~av~~~~~~~~~~~~~~~~~~~~~~e~l~~ 86 (202)
T TIGR03613 7 EAKRKAILSAALDTFSRFGFHGTSLEQIAELAGVSKTNLLYYFPSKDALYLAVLRQILDIWLSPLKAFTEDFAPLAAIKA 86 (202)
T ss_pred HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHH
Confidence 5679999999999999999999999999998 77766 22222222110 0 11123467889999
Q ss_pred HHHHHHhhccch
Q 036078 155 LVRIRLEMQAPY 166 (285)
Q Consensus 155 lL~~RLe~l~P~ 166 (285)
++...++...-+
T Consensus 87 ~~~~~~~~~~~~ 98 (202)
T TIGR03613 87 YIRAKLEMSRDH 98 (202)
T ss_pred HHHHHHHHHHHC
Confidence 998877665444
No 10
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=94.71 E-value=2.6 Score=36.62 Aligned_cols=74 Identities=15% Similarity=0.211 Sum_probs=51.8
Q ss_pred chHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHH--HHHHHHHHhhc--------CCCCCCCChHHHH
Q 036078 93 RDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDD--CLQRLIDRIDS--------GEDLKDLIPSQRI 152 (285)
Q Consensus 93 e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~--~~~~L~~~iD~--------~~~l~~l~~rERI 152 (285)
+..|++|+++|+.++.++||...++.++|++ ||.++ ....++++... ........+.++|
T Consensus 10 ~~~R~~Il~AA~~lf~e~G~~~~t~~~Ia~~agvs~~tlY~~F~sKe~Ll~~v~~~~~~~~~~~~~~~~~~~~~~~~~~l 89 (215)
T PRK10668 10 QETRQHILDAALRLFSQQGVSATSLADIAKAAGVTRGAIYWHFKNKSDLFSEIWELSESKIGELELEYQAKFPDDPLSVL 89 (215)
T ss_pred HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCChHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCCHHHHH
Confidence 5579999999999999999999999999998 78766 22333322111 0111223578889
Q ss_pred HHHHHHHHhhccch
Q 036078 153 SKLVRIRLEMQAPY 166 (285)
Q Consensus 153 ~~lL~~RLe~l~P~ 166 (285)
+.++..-++.....
T Consensus 90 ~~~~~~~~~~~~~~ 103 (215)
T PRK10668 90 REILIYILEATVTD 103 (215)
T ss_pred HHHHHHHHHHHhcC
Confidence 99888777655543
No 11
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=94.07 E-value=2.6 Score=36.87 Aligned_cols=36 Identities=17% Similarity=0.310 Sum_probs=31.6
Q ss_pred chHHHHHHHHHHh-HHhhcCccHHHHHHHHHH----------hccHH
Q 036078 93 RDEQARVLEASLR-HVAKHGWGEAAMIAGARD----------FFMDD 128 (285)
Q Consensus 93 e~~r~rIL~aAL~-lVp~~GWt~~AL~~aA~d----------~F~~~ 128 (285)
+..|++||++|+. +..++||...++.+.|++ ||.++
T Consensus 10 ~~~R~~Il~aA~~~l~~~~G~~~~si~~IA~~Agvs~~t~Y~hF~sK 56 (203)
T PRK11202 10 EKTRRALIDAAFSQLSAERSFSSLSLREVAREAGIAPTSFYRHFRDM 56 (203)
T ss_pred HHHHHHHHHHHHHHHHhcCCcccCCHHHHHHHhCCCcchHHHHCCCH
Confidence 4568999999997 779999999999999998 78666
No 12
>PRK09480 slmA division inhibitor protein; Provisional
Probab=93.72 E-value=3.8 Score=34.69 Aligned_cols=76 Identities=14% Similarity=0.167 Sum_probs=49.0
Q ss_pred chHHHHHHHHHHhHHhhc-CccHHHHHHHHHH----------hccHHH--HHHHHHHhhc----C--CCC-CCCChHHHH
Q 036078 93 RDEQARVLEASLRHVAKH-GWGEAAMIAGARD----------FFMDDC--LQRLIDRIDS----G--EDL-KDLIPSQRI 152 (285)
Q Consensus 93 e~~r~rIL~aAL~lVp~~-GWt~~AL~~aA~d----------~F~~~~--~~~L~~~iD~----~--~~l-~~l~~rERI 152 (285)
+..+++||+++++++.+. | +..++.+.|++ ||.++. ...+++.+.. . ..+ ....+.+++
T Consensus 9 ~~~r~~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~v~~~~~~~~~~~~~~~~~~~~~~~~~l 87 (194)
T PRK09480 9 GERREQILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEESLFSRINQILKDEKDTLARA 87 (194)
T ss_pred hhHHHHHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHH
Confidence 456999999999998765 8 99999999998 787763 2223222211 0 011 122477788
Q ss_pred HHHHHHHHhhccchhhh
Q 036078 153 SKLVRIRLEMQAPYISK 169 (285)
Q Consensus 153 ~~lL~~RLe~l~P~~e~ 169 (285)
...+..-++....+...
T Consensus 88 ~~~~~~~~~~~~~~~~~ 104 (194)
T PRK09480 88 RLILLLLLGFAERNPGM 104 (194)
T ss_pred HHHHHHHHHHHHhChhH
Confidence 88877766665544433
No 13
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=93.40 E-value=4.3 Score=35.16 Aligned_cols=73 Identities=14% Similarity=0.164 Sum_probs=48.7
Q ss_pred CCchHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHHH--HHHHH-------HHhhcC-CCCCCCChHH
Q 036078 91 EYRDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDDC--LQRLI-------DRIDSG-EDLKDLIPSQ 150 (285)
Q Consensus 91 ~~e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~~--~~~L~-------~~iD~~-~~l~~l~~rE 150 (285)
+.+..|++|+++|++++.++|+...++.++|++ ||.++- ...+. +.++.. .........+
T Consensus 8 ~~~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~sKe~Ll~~v~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (213)
T PRK09975 8 EALKTRQELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYWHFENKTQLFNEMWLQQPPLRELIQEHLTAGLEHDPLQ 87 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHHHcCCHHHHHHHHHHHhhhHHHHHHHHhhhcccCCHHH
Confidence 346679999999999999999999999999998 776662 22222 122211 1112234567
Q ss_pred HHHHHHHHHHhhc
Q 036078 151 RISKLVRIRLEMQ 163 (285)
Q Consensus 151 RI~~lL~~RLe~l 163 (285)
+++..+..-++..
T Consensus 88 ~l~~~~~~~~~~~ 100 (213)
T PRK09975 88 QLREKFIAGLQYI 100 (213)
T ss_pred HHHHHHHHHHHHH
Confidence 7877776666543
No 14
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=90.73 E-value=7.2 Score=32.79 Aligned_cols=30 Identities=3% Similarity=-0.003 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHhHHhhcCccHHHHHHHHHH
Q 036078 94 DEQARVLEASLRHVAKHGWGEAAMIAGARD 123 (285)
Q Consensus 94 ~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d 123 (285)
..|++|.+++++++.++||...++.+.|+.
T Consensus 3 ~Tk~~I~~a~~~Ll~~k~~~~ITV~~I~~~ 32 (176)
T TIGR02366 3 ITKKKIAKAFKDLMEVQAFSKISVSDIMST 32 (176)
T ss_pred HHHHHHHHHHHHHHHHCCCccCCHHHHHHH
Confidence 358999999999999999999999999998
No 15
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=89.76 E-value=2.5 Score=37.86 Aligned_cols=74 Identities=12% Similarity=0.069 Sum_probs=50.1
Q ss_pred HHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHH--HHHHHHHHh----hcC-CCCCCCChHHHHHHHHH
Q 036078 95 EQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDD--CLQRLIDRI----DSG-EDLKDLIPSQRISKLVR 157 (285)
Q Consensus 95 ~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~--~~~~L~~~i----D~~-~~l~~l~~rERI~~lL~ 157 (285)
.+++||++|++++.++|+...++.+.|++ ||.++ ..+.+.+.+ ... ....+...+++|.....
T Consensus 5 sre~Il~aA~~l~~e~G~~~lsmr~lA~~lgv~~~slY~hf~~K~~Ll~~~~~~~~~~~~~~~~~~~~~~w~~~l~~~~~ 84 (205)
T PRK13756 5 DKEKVIDSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEILDRHHTHFLPLEGESWQDFLRNNAK 84 (205)
T ss_pred CHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHHHHcCCHHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHH
Confidence 38999999999999999999999999998 77666 233333332 111 11233467888877776
Q ss_pred HHHhhccchhh
Q 036078 158 IRLEMQAPYIS 168 (285)
Q Consensus 158 ~RLe~l~P~~e 168 (285)
.=.+.+..|..
T Consensus 85 ~~~~~l~~~p~ 95 (205)
T PRK13756 85 SFRCALLSYRD 95 (205)
T ss_pred HHHHHHHHCcc
Confidence 55555555543
No 16
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=88.12 E-value=0.88 Score=40.80 Aligned_cols=35 Identities=17% Similarity=0.272 Sum_probs=31.8
Q ss_pred chHHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHH
Q 036078 93 RDEQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDD 128 (285)
Q Consensus 93 e~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~ 128 (285)
+..|++||++|+++..++||. .++.++|+. ||++|
T Consensus 12 ~~~r~~Il~aA~~lF~~~Gy~-~s~~~IA~~AGvsk~tiy~~F~sK 56 (225)
T PRK11552 12 EQAKQQLIAAALAQFGEYGLH-ATTRDIAAQAGQNIAAITYYFGSK 56 (225)
T ss_pred HHHHHHHHHHHHHHHHHhCcc-CCHHHHHHHhCCCHHHHHHHcCCH
Confidence 457999999999999999999 999999998 78776
No 17
>PRK11640 putative transcriptional regulator; Provisional
Probab=86.30 E-value=22 Score=31.02 Aligned_cols=68 Identities=16% Similarity=0.123 Sum_probs=45.9
Q ss_pred HHHHHHHHHHhHHhhcCccHHHHHHHHHH----------hccHHH--HHHHHHH--------hhcCCCCCCCChHHHHHH
Q 036078 95 EQARVLEASLRHVAKHGWGEAAMIAGARD----------FFMDDC--LQRLIDR--------IDSGEDLKDLIPSQRISK 154 (285)
Q Consensus 95 ~r~rIL~aAL~lVp~~GWt~~AL~~aA~d----------~F~~~~--~~~L~~~--------iD~~~~l~~l~~rERI~~ 154 (285)
.|++||++|+.+.-++||+...|.+.++. ||+++- ....+++ ++....-...++.++|..
T Consensus 2 ~r~~il~~A~~lf~~~Gy~~tsi~~I~~~aGv~k~slY~~F~sKe~L~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 81 (191)
T PRK11640 2 QREDVLGEALKLLEQQGLANTTLEMLAERVDYPLDELQRFWPDREALLYDALRYHSQQIDTWRRQLLLDETLSAEQKLLA 81 (191)
T ss_pred hHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 37999999999999999999999999988 787762 1111111 111000123467888888
Q ss_pred HHHHHHhh
Q 036078 155 LVRIRLEM 162 (285)
Q Consensus 155 lL~~RLe~ 162 (285)
++..-.+.
T Consensus 82 ~~~~~~~~ 89 (191)
T PRK11640 82 RYQALSEC 89 (191)
T ss_pred HHHHHHHH
Confidence 87764444
No 18
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=83.11 E-value=0.5 Score=32.33 Aligned_cols=25 Identities=32% Similarity=0.457 Sum_probs=24.1
Q ss_pred HHHHHHhHHhhcCccHHHHHHHHHH
Q 036078 99 VLEASLRHVAKHGWGEAAMIAGARD 123 (285)
Q Consensus 99 IL~aAL~lVp~~GWt~~AL~~aA~d 123 (285)
||+++++++.++||...++.+.|++
T Consensus 1 Il~aa~~l~~~~G~~~~s~~~Ia~~ 25 (47)
T PF00440_consen 1 ILEAALELFAEKGYEAVSIRDIARR 25 (47)
T ss_dssp HHHHHHHHHHHHHTTTSSHHHHHHH
T ss_pred CHHHHHHHHHHhCHHhCCHHHHHHH
Confidence 7999999999999999999999998
No 19
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=66.35 E-value=8.9 Score=30.30 Aligned_cols=30 Identities=27% Similarity=0.492 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHhHHhhcCccHHHHHHHHHH
Q 036078 94 DEQARVLEASLRHVAKHGWGEAAMIAGARD 123 (285)
Q Consensus 94 ~~r~rIL~aAL~lVp~~GWt~~AL~~aA~d 123 (285)
..+.+|+++++.+.-++||...++.+.|+.
T Consensus 12 ~~~~~ii~aa~~l~~~~G~~~~t~~~Ia~~ 41 (201)
T COG1309 12 ERRERILDAALRLFAEKGYAATTVDEIAKA 41 (201)
T ss_pred hHHHHHHHHHHHHHHHcCcCCCCHHHHHHH
Confidence 368999999999999999999999999988
No 20
>COG3226 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.56 E-value=1e+02 Score=28.11 Aligned_cols=29 Identities=17% Similarity=0.219 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhHHhhcCccHHHHHHHHHH
Q 036078 95 EQARVLEASLRHVAKHGWGEAAMIAGARD 123 (285)
Q Consensus 95 ~r~rIL~aAL~lVp~~GWt~~AL~~aA~d 123 (285)
-|++|+++++++|.++|+...+=.+.|.+
T Consensus 14 RRqaIv~Aa~eli~~~Gv~aV~HR~VAa~ 42 (204)
T COG3226 14 RRQAIVQAALELIKRYGVHAVRHRAVAAE 42 (204)
T ss_pred HHHHHHHHHHHHHHhcchhhhhHHHHHHH
Confidence 69999999999999999999988888777
No 21
>cd03204 GST_C_GDAP1 GST_C family, Ganglioside-induced differentiation-associated protein 1 (GDAP1) subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal thioredoxin-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates.
Probab=23.44 E-value=2e+02 Score=23.36 Aligned_cols=59 Identities=22% Similarity=0.110 Sum_probs=36.5
Q ss_pred hccchhhhHHHHHHhhcCCCCchHHHH------HHHHHHHHHH--------------HHhCCCCCCchhHHHHHHHHHHH
Q 036078 162 MQAPYISKWPQALSIQAQPLNVPTSFK------QRAMLVDEIW--------------HAVGDEASDIDWYVKRTVLGGIY 221 (285)
Q Consensus 162 ~l~P~~e~~~qaLa~lalP~n~~~sl~------~l~~laD~Iw--------------~~AGD~StD~~wYtKRa~La~IY 221 (285)
|..-|+.....+=+.++-|.|....-+ ..+...+..+ |.+|| +.+++-||
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l~~~l~~LE~~L~~~~~~~~~~~~~~yL~Gd----------~~TlADi~ 72 (111)
T cd03204 3 LATAYIAKQKKLKSKLLDHDNVEYLKKILDELEMVLDQVEQELQRRKEETEEQKCQLWLCGD----------TFTLADIS 72 (111)
T ss_pred HHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHHHHHHHcCCcccccccCCCccCCC----------CCCHHHHH
Confidence 344566666666677788888664322 2223334433 23343 47899999
Q ss_pred HHHHHHHhc
Q 036078 222 STTEIYMLT 230 (285)
Q Consensus 222 ~stel~wL~ 230 (285)
..+.+.|+.
T Consensus 73 l~~~l~~~~ 81 (111)
T cd03204 73 LGVTLHRLK 81 (111)
T ss_pred HHHHHHHHH
Confidence 999988876
Done!