Query 023804
Match_columns 277
No_of_seqs 113 out of 126
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 06:47:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023804.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023804hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10173 Mit_KHE1: Mitochondri 100.0 6.7E-64 1.4E-68 441.1 17.2 170 4-194 1-187 (187)
2 KOG4539 Uncharacterized conser 100.0 3.8E-61 8.2E-66 433.1 11.9 264 2-273 1-274 (274)
3 PF13443 HTH_26: Cro/C1-type H 73.1 2.2 4.8E-05 30.2 1.5 36 237-275 27-62 (63)
4 COG3655 Predicted transcriptio 55.4 10 0.00022 29.6 2.3 28 248-275 40-67 (73)
5 PF05915 DUF872: Eukaryotic pr 45.5 9.5 0.00021 31.8 0.8 22 165-186 86-107 (115)
6 smart00530 HTH_XRE Helix-turn- 42.9 28 0.0006 21.7 2.6 23 248-270 34-56 (56)
7 PF08104 Antimicrobial_9: Pone 41.4 8.7 0.00019 23.7 -0.0 15 38-52 2-16 (24)
8 PF03428 RP-C: Replication pro 32.3 89 0.0019 27.9 4.9 54 82-142 41-103 (177)
9 cd00093 HTH_XRE Helix-turn-hel 32.2 51 0.0011 20.6 2.6 23 248-270 36-58 (58)
10 PF01527 HTH_Tnp_1: Transposas 31.7 19 0.00041 26.2 0.5 23 253-275 23-45 (76)
11 smart00760 Bac_DnaA_C Bacteria 31.5 31 0.00067 24.8 1.5 19 253-271 3-21 (60)
12 PF05289 BLYB: Borrelia hemoly 31.4 35 0.00076 28.4 2.0 18 169-186 36-53 (105)
13 PF04552 Sigma54_DBD: Sigma-54 30.6 35 0.00076 29.9 2.0 40 236-276 108-149 (160)
14 PF01418 HTH_6: Helix-turn-hel 30.1 42 0.0009 25.3 2.1 19 248-266 43-61 (77)
15 PRK11187 replication initiatio 28.9 89 0.0019 28.4 4.3 36 223-263 140-182 (182)
16 PF12844 HTH_19: Helix-turn-he 28.0 44 0.00096 23.5 1.9 26 248-273 36-61 (64)
17 PF02061 Lambda_CIII: Lambda P 27.9 52 0.0011 23.4 2.1 19 57-75 18-36 (45)
18 PF05121 GvpK: Gas vesicle pro 26.7 42 0.0009 27.2 1.6 19 253-271 58-76 (88)
19 PF14056 DUF4250: Domain of un 26.6 26 0.00056 25.9 0.4 20 253-272 20-39 (55)
20 PF08299 Bac_DnaA_C: Bacterial 25.8 39 0.00085 25.3 1.3 20 253-272 3-22 (70)
21 TIGR02395 rpoN_sigma RNA polym 25.7 57 0.0012 32.7 2.8 39 237-276 379-419 (429)
22 PF14813 NADH_B2: NADH dehydro 24.9 41 0.00089 26.1 1.3 17 169-185 32-48 (71)
23 PF01476 LysM: LysM domain; I 24.0 36 0.00079 22.1 0.7 22 253-274 6-27 (44)
24 PF10956 DUF2756: Protein of u 22.1 35 0.00076 28.4 0.4 27 144-170 2-31 (104)
25 PRK05932 RNA polymerase factor 22.0 75 0.0016 32.2 2.8 39 237-276 403-443 (455)
26 PHA01976 helix-turn-helix prot 21.9 80 0.0017 22.4 2.2 25 248-272 39-63 (67)
27 PF14039 YusW: YusW-like prote 21.5 1.4E+02 0.003 24.0 3.8 38 236-274 48-85 (92)
28 PRK13890 conjugal transfer pro 21.3 88 0.0019 25.8 2.6 28 248-275 42-69 (120)
29 PF01381 HTH_3: Helix-turn-hel 20.4 74 0.0016 21.5 1.7 23 248-270 33-55 (55)
No 1
>PF10173 Mit_KHE1: Mitochondrial K+-H+ exchange-related; InterPro: IPR018786 This entry represents a family of proteins conserved from plants to humans. Their function is not known.
Probab=100.00 E-value=6.7e-64 Score=441.08 Aligned_cols=170 Identities=36% Similarity=0.652 Sum_probs=157.5
Q ss_pred eEEEEeecC-eeeEEeccCCCCCcccccCCCCCchhHHHHhhhccccccCccchHHHHHHHHHHHHHHhhccccCCCCch
Q 023804 4 RLVVFPVKG-RNWCFSRSIDPLSPETASSCNTPTTLKQLWHKLTSSEKHNSNNVELVVDFVSHKMNNAWIGLEKAPQGSM 82 (277)
Q Consensus 4 rl~~iPIt~-r~~iy~~~~~~~~~~~s~~~~~p~t~~~lw~~~~~~~~~~~~k~~~~~d~it~KA~~~W~~~e~a~~Gsw 82 (277)
|||+|||++ |.+|||+|.+..+++ + +.+...++++++||+++||+++|++||+|++| |
T Consensus 1 Rl~~lPi~~~r~~~y~~~~~~~~~~-~-------------------~~~~~~~~~~~~~~i~~ka~~~W~~~~~a~~g-~ 59 (187)
T PF10173_consen 1 RLIALPISTRRWLIYCQHVPPPAAE-S-------------------QLSTPSKAQSLEDKITNKAAKTWAKWEKAPKG-W 59 (187)
T ss_pred CEEEEEeCCCceEEEeecCCcccch-h-------------------hcccchhhhhHHHHHHHHHHHHHHHHhcCchh-H
Confidence 899999998 557999999988765 1 22335568889999999999999999999999 9
Q ss_pred hHHHHHHHHHHHhCCCcchhccccCCCCCC--------------eEEEEcC-CCCChHHHHHHHHHHHHhhhHHHHHHHH
Q 023804 83 KNKIHGLGLKLLSGVKPSEMFLKSISKEVS--------------QVEVTYP-SSLNARLVRRRLRHIAMRGTILHNKYLY 147 (277)
Q Consensus 83 k~ki~~~G~~ll~rIp~EE~~LKsip~~~~--------------~IeV~yP-~sl~~~~v~~~L~~la~~~~~~Hrk~~~ 147 (277)
|+|||++|+++|||||||||+|||||+... +|+|||| +.++++.|+++|++++++|+++|+|||+
T Consensus 60 k~ki~~~g~~ll~rIp~eE~~LKsiP~~~~~~~~~~~~~~~~~~~i~v~yP~~~~~~~~v~~~L~~l~~~~~~~H~k~~~ 139 (187)
T PF10173_consen 60 KRKIVSYGNRLLDRIPYEEWALKSIPSLSHLRRRINEEHESQKKPIEVYYPGSVISPREVLRQLRKLATERQPYHRKRMI 139 (187)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHhcCCCcccccchhhhhccccccceeEecCcccCCHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 999999999999999999999999997544 8999999 6689999999999999999999999999
Q ss_pred HHhhccccccceecccC-CCchHHHHHHHHHHHHHHHhhHHHHHHHhh
Q 023804 148 GSVSLLPLTFVFSVLPL-PNVPFFWILYRTYSHWRALQGSEKLLQLVS 194 (277)
Q Consensus 148 ~~~~~lPLT~P~aLiPl-PNiP~FYl~YRaysH~rAl~GskhL~~Ll~ 194 (277)
+|++|+|||+||+|||| |||||||++|||||||||++|++||++||+
T Consensus 140 ~~~~~~PlT~P~~LiPviPNiP~FYl~yRaysh~rAl~G~k~L~~Lle 187 (187)
T PF10173_consen 140 WCILGIPLTLPFALIPVIPNIPFFYLAYRAYSHWRALQGSKHLQSLLE 187 (187)
T ss_pred HHHHhhhhhcceeeecCCCCccHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 99999999999999998 999999999999999999999999999985
No 2
>KOG4539 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.8e-61 Score=433.05 Aligned_cols=264 Identities=53% Similarity=0.884 Sum_probs=235.3
Q ss_pred cceEEEEeecCeeeEEeccCCCCCcccccCCCCCchhHHHHhhhccccccCccchHHHHHHHHHHHHHHhhccccCCCCc
Q 023804 2 RARLVVFPVKGRNWCFSRSIDPLSPETASSCNTPTTLKQLWHKLTSSEKHNSNNVELVVDFVSHKMNNAWIGLEKAPQGS 81 (277)
Q Consensus 2 ~~rl~~iPIt~r~~iy~~~~~~~~~~~s~~~~~p~t~~~lw~~~~~~~~~~~~k~~~~~d~it~KA~~~W~~~e~a~~Gs 81 (277)
|+|++||||++..|||.+..+..+++ +....+|.+..-+|..+++..++.+..+..+++||.+|+++.|.+|++++. |
T Consensus 1 ~~r~v~~p~~~~~~~~~~~~~mra~~-~pl~~~~~~v~lh~~pi~~~~kpIt~h~d~l~n~I~~k~~K~W~~l~ksp~-s 78 (274)
T KOG4539|consen 1 RARLVVFPIKGKKWCFSRSVDMRAAQ-SPLGVTPTTVRLHWKPISSESKPITAHADLLVNFISDKMNKAWVGLEKSPD-S 78 (274)
T ss_pred CcceEEecCCCcchhhhhccchhhhc-CcCCCCcceEEEEeccchheeechhhhHHHHHHHHHHHHHHHHHHHhhChH-H
Confidence 68999999999999999999998887 777889999999999999999999999999999999999999999999999 8
Q ss_pred hhHHHHHHHHHHHhCCCcchhccccCCC--------CCCeEEEEcCCCCChHHHHHHHHHHHHhhhHHHHHHHHHHhhcc
Q 023804 82 MKNKIHGLGLKLLSGVKPSEMFLKSISK--------EVSQVEVTYPSSLNARLVRRRLRHIAMRGTILHNKYLYGSVSLL 153 (277)
Q Consensus 82 wk~ki~~~G~~ll~rIp~EE~~LKsip~--------~~~~IeV~yP~sl~~~~v~~~L~~la~~~~~~Hrk~~~~~~~~l 153 (277)
.|+|||.+|+++|.+.||+|++|++|++ +.+++.|+||+++.++.|+++|+++++.|..+|++|+++|++|+
T Consensus 79 ~k~KIvs~g~~lL~~tp~sEnfL~sI~~vKklnDtE~~q~l~V~yPP~l~s~~~lr~l~~~~q~g~i~Hkkylvg~v~gL 158 (274)
T KOG4539|consen 79 IKNKIVSFGLKLLARTPPSENFLKSISKVKKLNDTEEVQSLQVTYPPSLDSRLVLRRLRHIAQSGTILHKKYLVGSVTGL 158 (274)
T ss_pred HHHHHHHHHHHHHhcCChhhhHHHhccccccccchhhcceeEEEcCCCCChHHHHHHHHHHHhhcchhhhheeeeeeecC
Confidence 9999999999999999999999999997 67899999999999999999999999999999999999999999
Q ss_pred ccccceecccC-CCchHHHHHHHHHHHHHHHhhHHHHHHHhhCCCCCCccccccCCCCccccCCCccccccCCCCc-ccc
Q 023804 154 PLTFVFSVLPL-PNVPFFWILYRTYSHWRALQGSEKLLQLVSNDSHTQNFGFSNVKGSEAEHNNSECETSNLQGVP-SIL 231 (277)
Q Consensus 154 PLT~P~aLiPl-PNiP~FYl~YRaysH~rAl~GskhL~~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 231 (277)
|||+||+|||+ |||||||++|||||||||++|++||..|+++....+..+..+.+..-+++|.. .+ +...+| ..|
T Consensus 159 PLTipfiliPLiPNiPgFyl~yRaY~n~rA~qGs~~L~~lis~~~N~~~~es~~~~~~~K~s~t~-~~--qk~~~~~~~L 235 (274)
T KOG4539|consen 159 PLTIPFILIPLIPNIPGFYLLYRAYSNWRALQGSEKLLKLISNEANPDKPESTDDADESKNSNTK-PE--QKSQSPTCIL 235 (274)
T ss_pred cccchheeeccCCCCCcceehhhhhhhHHHHhhHHHHHHHHhcccCcCcccccchHHHhhcccCC-cc--ccccCCCcee
Confidence 99999999996 99999999999999999999999999999987777766554433333322111 22 333444 889
Q ss_pred CCchhHHHHHhhCCCCCCCCCHHHHHHHHhhhCCCccccccc
Q 023804 232 VPSGELEELIHSGGKTDDGLSKCAILNICTIYKLNPIDVLKY 273 (277)
Q Consensus 232 ~~s~~l~~~~~~~~~~~~~l~~~~i~~ic~~~~l~~~d~~k~ 273 (277)
-|++++-.|+. +.. .+++.+++|.++|+. +++++|++||
T Consensus 236 l~n~~~~pLi~-~~~-e~~~~e~~~~~i~~q-e~~k~~~~K~ 274 (274)
T KOG4539|consen 236 LPNEELYPLIR-EAS-EEGLDEATIIEICKQ-ELNKNDVLKY 274 (274)
T ss_pred ccCcchhHHHH-HHh-hCcchHHHHHHHHHH-HhhhhhhhcC
Confidence 99999877765 333 578899999999999 9999999997
No 3
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=73.10 E-value=2.2 Score=30.24 Aligned_cols=36 Identities=14% Similarity=0.287 Sum_probs=23.8
Q ss_pred HHHHHhhCCCCCCCCCHHHHHHHHhhhCCCccccccccc
Q 023804 237 LEELIHSGGKTDDGLSKCAILNICTIYKLNPIDVLKYRN 275 (277)
Q Consensus 237 l~~~~~~~~~~~~~l~~~~i~~ic~~~~l~~~d~~k~~~ 275 (277)
+.++++.. ...++-++|..||+.||++.+||+.|..
T Consensus 27 l~~~~~~~---~~~~~~~~l~~ia~~l~~~~~el~~~~~ 62 (63)
T PF13443_consen 27 LSRILNGK---PSNPSLDTLEKIAKALNCSPEELFEYEP 62 (63)
T ss_dssp HHHHHTTT--------HHHHHHHHHHHT--HHHCTECCE
T ss_pred HHHHHhcc---cccccHHHHHHHHHHcCCCHHHHhhcCC
Confidence 46666622 2579999999999999999999998865
No 4
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=55.39 E-value=10 Score=29.58 Aligned_cols=28 Identities=21% Similarity=0.433 Sum_probs=25.7
Q ss_pred CCCCCHHHHHHHHhhhCCCccccccccc
Q 023804 248 DDGLSKCAILNICTIYKLNPIDVLKYRN 275 (277)
Q Consensus 248 ~~~l~~~~i~~ic~~~~l~~~d~~k~~~ 275 (277)
..+|.=+|++.||+.++-.+.|++-|..
T Consensus 40 ~k~I~~~tL~~iC~~LeCqpgDiley~~ 67 (73)
T COG3655 40 VKAIRLSTLEKICKALECQPGDILEYVP 67 (73)
T ss_pred cceeeHHHHHHHHHHcCCChhheeEEec
Confidence 6789999999999999999999999954
No 5
>PF05915 DUF872: Eukaryotic protein of unknown function (DUF872); InterPro: IPR008590 This entry represents several uncharacterised eukaryotic transmembrane proteins. The function of this currently unknown.
Probab=45.54 E-value=9.5 Score=31.84 Aligned_cols=22 Identities=27% Similarity=0.516 Sum_probs=18.9
Q ss_pred CCchHHHHHHHHHHHHHHHhhH
Q 023804 165 PNVPFFWILYRTYSHWRALQGS 186 (277)
Q Consensus 165 PNiP~FYl~YRaysH~rAl~Gs 186 (277)
==|||||-++-+|+-||.+.|-
T Consensus 86 ~fIPG~Y~~~i~y~a~rg~~Gy 107 (115)
T PF05915_consen 86 CFIPGFYHTRIAYYAWRGYKGY 107 (115)
T ss_pred HHhccHHHHHHHHHHHcCCCCC
Confidence 4578999999999999988874
No 6
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=42.95 E-value=28 Score=21.73 Aligned_cols=23 Identities=4% Similarity=-0.018 Sum_probs=19.1
Q ss_pred CCCCCHHHHHHHHhhhCCCcccc
Q 023804 248 DDGLSKCAILNICTIYKLNPIDV 270 (277)
Q Consensus 248 ~~~l~~~~i~~ic~~~~l~~~d~ 270 (277)
...++.+++..||+.||++.+++
T Consensus 34 ~~~~~~~~~~~i~~~~~~~~~~~ 56 (56)
T smart00530 34 KRKPSLETLKKLAKALGVSLDEL 56 (56)
T ss_pred CCCCCHHHHHHHHHHhCCChhhC
Confidence 34569999999999999997764
No 7
>PF08104 Antimicrobial_9: Ponericin L family; InterPro: IPR012528 This family consists of the ponericin L family of antimicrobial peptides that are isolated from the venom of the predatory ant Pachycondyla goeldii (Ponerine ant). Ponericin L family shares similarities with dermaseptins. Ponericin L may adopt an amphipathic alpha-helical structure in polar environments and these peptides exhibit a defensive role against microbial pathogens arising from prey introduction and/or ingestion [].; GO: 0045087 innate immune response, 0005576 extracellular region
Probab=41.40 E-value=8.7 Score=23.70 Aligned_cols=15 Identities=40% Similarity=0.751 Sum_probs=11.1
Q ss_pred hHHHHhhhccccccC
Q 023804 38 LKQLWHKLTSSEKHN 52 (277)
Q Consensus 38 ~~~lw~~~~~~~~~~ 52 (277)
+++||++|.+.++..
T Consensus 2 lkelwtkikgagkav 16 (24)
T PF08104_consen 2 LKELWTKIKGAGKAV 16 (24)
T ss_pred hHHHHHHhccchHHH
Confidence 578999998765544
No 8
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=32.34 E-value=89 Score=27.89 Aligned_cols=54 Identities=22% Similarity=0.373 Sum_probs=43.8
Q ss_pred hhHHHHHHHHHHHhCCCcchhccccCCCCCCeEEEEcCCC---------CChHHHHHHHHHHHHhhhHHH
Q 023804 82 MKNKIHGLGLKLLSGVKPSEMFLKSISKEVSQVEVTYPSS---------LNARLVRRRLRHIAMRGTILH 142 (277)
Q Consensus 82 wk~ki~~~G~~ll~rIp~EE~~LKsip~~~~~IeV~yP~s---------l~~~~v~~~L~~la~~~~~~H 142 (277)
.+.+...+.+.|++-.|.++|. ....+|+||++ ++++.++++|..|+.-|....
T Consensus 41 l~~~~l~vL~aLls~~~~~d~~-------~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~r 103 (177)
T PF03428_consen 41 LSDRALAVLDALLSFTPPDDWE-------PGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEAGLIVR 103 (177)
T ss_pred CChhHHHHHHHHHHhCCccccc-------CCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeee
Confidence 7789999999999999999882 23457999985 367889999999998885443
No 9
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=32.18 E-value=51 Score=20.61 Aligned_cols=23 Identities=4% Similarity=-0.006 Sum_probs=19.4
Q ss_pred CCCCCHHHHHHHHhhhCCCcccc
Q 023804 248 DDGLSKCAILNICTIYKLNPIDV 270 (277)
Q Consensus 248 ~~~l~~~~i~~ic~~~~l~~~d~ 270 (277)
...++.+.+..||+.|+++.+++
T Consensus 36 ~~~~~~~~~~~i~~~~~~~~~~l 58 (58)
T cd00093 36 KRNPSLETLEKLAKALGVSLDEL 58 (58)
T ss_pred CCCCCHHHHHHHHHHhCCChhhC
Confidence 34799999999999999987653
No 10
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=31.67 E-value=19 Score=26.17 Aligned_cols=23 Identities=13% Similarity=0.407 Sum_probs=18.3
Q ss_pred HHHHHHHHhhhCCCccccccccc
Q 023804 253 KCAILNICTIYKLNPIDVLKYRN 275 (277)
Q Consensus 253 ~~~i~~ic~~~~l~~~d~~k~~~ 275 (277)
..+|.++|+.||++..-|-+|++
T Consensus 23 g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 23 GESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCceEeeecccccccccccHHHH
Confidence 46899999999999888877753
No 11
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=31.54 E-value=31 Score=24.79 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=16.7
Q ss_pred HHHHHHHHhhhCCCccccc
Q 023804 253 KCAILNICTIYKLNPIDVL 271 (277)
Q Consensus 253 ~~~i~~ic~~~~l~~~d~~ 271 (277)
+++|+..|+.|+++.+|+.
T Consensus 3 ~~I~~~Va~~~~i~~~~i~ 21 (60)
T smart00760 3 EEIIEAVAEYFGVKPEDLK 21 (60)
T ss_pred HHHHHHHHHHhCCCHHHHh
Confidence 5789999999999998875
No 12
>PF05289 BLYB: Borrelia hemolysin accessory protein; InterPro: IPR007953 This entry represents the borrelial prophage-encoded protein BlyB. Originally BlyB and its partner, the membrane-bound protein BlyA, were thought to comprise a haemolysis system. It is now thought, however, that BlyA and BlyB function instead as a holin or holin-like system [].
Probab=31.39 E-value=35 Score=28.42 Aligned_cols=18 Identities=33% Similarity=0.687 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHhhH
Q 023804 169 FFWILYRTYSHWRALQGS 186 (277)
Q Consensus 169 ~FYl~YRaysH~rAl~Gs 186 (277)
|||++|-+|+||.-.--+
T Consensus 36 Gf~Lv~~LYs~y~~IYk~ 53 (105)
T PF05289_consen 36 GFFLVYDLYSHYTLIYKS 53 (105)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 899999999999987544
No 13
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=30.60 E-value=35 Score=29.88 Aligned_cols=40 Identities=28% Similarity=0.341 Sum_probs=29.6
Q ss_pred hHHHHHhhCCCCCCCCCHHHHHHHHhhhCCC--cccccccccC
Q 023804 236 ELEELIHSGGKTDDGLSKCAILNICTIYKLN--PIDVLKYRNS 276 (277)
Q Consensus 236 ~l~~~~~~~~~~~~~l~~~~i~~ic~~~~l~--~~d~~k~~~~ 276 (277)
.+.+++..|+. ...||.+.|.++.++-|++ +--|.|||+.
T Consensus 108 ~i~~lI~~Ed~-~~PlSD~~i~~~L~~~gi~isRRTVaKYR~~ 149 (160)
T PF04552_consen 108 RIKELIEEEDK-KKPLSDQEIAELLKEEGIKISRRTVAKYREE 149 (160)
T ss_dssp HHHHHHTTS-T-TS---HHHHHHHHTTTTS---HHHHHHHHHH
T ss_pred HHHHHHHhcCC-CCCCCHHHHHHHHHHcCCCccHHHHHHHHHH
Confidence 35889998877 7889999999999998888 7789999863
No 14
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=30.06 E-value=42 Score=25.27 Aligned_cols=19 Identities=21% Similarity=0.515 Sum_probs=16.8
Q ss_pred CCCCCHHHHHHHHhhhCCC
Q 023804 248 DDGLSKCAILNICTIYKLN 266 (277)
Q Consensus 248 ~~~l~~~~i~~ic~~~~l~ 266 (277)
..++|+.+|.++|+++|.+
T Consensus 43 ~~~vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 43 KAGVSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HCTS-HHHHHHHHHHCTTT
T ss_pred HcCCCHHHHHHHHHHhCCC
Confidence 6789999999999999998
No 15
>PRK11187 replication initiation regulator SeqA; Provisional
Probab=28.95 E-value=89 Score=28.39 Aligned_cols=36 Identities=19% Similarity=0.474 Sum_probs=27.7
Q ss_pred cCCCCc-cccCCchh------HHHHHhhCCCCCCCCCHHHHHHHHhhh
Q 023804 223 NLQGVP-SILVPSGE------LEELIHSGGKTDDGLSKCAILNICTIY 263 (277)
Q Consensus 223 ~~~~~~-~~~~~s~~------l~~~~~~~~~~~~~l~~~~i~~ic~~~ 263 (277)
|+-.+| |+..+.-- |+++.+ .-|.+.+.|+.+|..+
T Consensus 140 ~Ip~TpfWViTNtNT~RKr~ml~~vm~-----~mg~p~~liekV~~~i 182 (182)
T PRK11187 140 HIPGTPFWVITNTNTGRKRSMLEHVMQ-----SMGFPAELIEKVCGTI 182 (182)
T ss_pred cCCCCCeeEEeCCCcHHHHHHHHHHHH-----HcCCCHHHHHHHHhcC
Confidence 677788 88766532 577777 7789999999999753
No 16
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=27.99 E-value=44 Score=23.48 Aligned_cols=26 Identities=8% Similarity=0.023 Sum_probs=19.6
Q ss_pred CCCCCHHHHHHHHhhhCCCccccccc
Q 023804 248 DDGLSKCAILNICTIYKLNPIDVLKY 273 (277)
Q Consensus 248 ~~~l~~~~i~~ic~~~~l~~~d~~k~ 273 (277)
+--++.+++..||+.|+++.++++..
T Consensus 36 ~~~~~~~~l~~i~~~~~v~~~~l~~~ 61 (64)
T PF12844_consen 36 KRKPSVSTLKKIAEALGVSLDELFDG 61 (64)
T ss_dssp SS--BHHHHHHHHHHHTS-HHHHCCC
T ss_pred CcCCCHHHHHHHHHHhCCCHHHHhcc
Confidence 44789999999999999998887643
No 17
>PF02061 Lambda_CIII: Lambda Phage CIII; InterPro: IPR013056 Bacteriophage lambda regulatory protein CIII is a small protein that plays a role in stabilising the CII transcriptional activator, via a mechanism that is not yet fully understood [, ]. Stabilised CII activates CI, the gene for the repressor protein that prevents transcription of proteins required for lytic development. The central portion of the protein is well conserved and is both necessary and sufficient for the activity of the protein []. Comparative analysis of the CIII sequence in lambda, Bacteriophage HK022 and the lambdoid Enterobacteria phage P22 has led to the suggestion that this central region assumes an amphipathic alpha-helical structure []. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=27.88 E-value=52 Score=23.40 Aligned_cols=19 Identities=26% Similarity=0.555 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHhhccc
Q 023804 57 ELVVDFVSHKMNNAWIGLE 75 (277)
Q Consensus 57 ~~~~d~it~KA~~~W~~~e 75 (277)
+++.|+|++|+-..|..+.
T Consensus 18 ESLLdrItRklr~gwKRl~ 36 (45)
T PF02061_consen 18 ESLLDRITRKLRDGWKRLW 36 (45)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5799999999999997664
No 18
>PF05121 GvpK: Gas vesicle protein K ; InterPro: IPR007805 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins containing this domain are involved in the formation of gas vesicles [].; GO: 0031412 gas vesicle organization
Probab=26.75 E-value=42 Score=27.18 Aligned_cols=19 Identities=26% Similarity=0.525 Sum_probs=15.4
Q ss_pred HHHHHHHHhhhCCCccccc
Q 023804 253 KCAILNICTIYKLNPIDVL 271 (277)
Q Consensus 253 ~~~i~~ic~~~~l~~~d~~ 271 (277)
++.|.+||+.||++.+|+.
T Consensus 58 e~~~~~l~~~~gl~~~dLn 76 (88)
T PF05121_consen 58 EEAMEELCERFGLTPEDLN 76 (88)
T ss_pred HHHHHHHHHHcCCCHHHhc
Confidence 3567889999999988874
No 19
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=26.60 E-value=26 Score=25.93 Aligned_cols=20 Identities=10% Similarity=0.340 Sum_probs=16.5
Q ss_pred HHHHHHHHhhhCCCcccccc
Q 023804 253 KCAILNICTIYKLNPIDVLK 272 (277)
Q Consensus 253 ~~~i~~ic~~~~l~~~d~~k 272 (277)
.+.++++|..||++++++.+
T Consensus 20 ~~sLd~Lc~~~~id~~~l~~ 39 (55)
T PF14056_consen 20 YSSLDELCYDYDIDKEELEE 39 (55)
T ss_pred cCCHHHHHHHhCCCHHHHHH
Confidence 45789999999999888754
No 20
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=25.80 E-value=39 Score=25.27 Aligned_cols=20 Identities=10% Similarity=0.149 Sum_probs=15.3
Q ss_pred HHHHHHHHhhhCCCcccccc
Q 023804 253 KCAILNICTIYKLNPIDVLK 272 (277)
Q Consensus 253 ~~~i~~ic~~~~l~~~d~~k 272 (277)
+++|+.+|+.|+++.+|+..
T Consensus 3 ~~Ii~~Va~~~~v~~~~i~s 22 (70)
T PF08299_consen 3 EDIIEAVAEYFGVSVEDIRS 22 (70)
T ss_dssp HHHHHHHHHHTT--HHHHHS
T ss_pred HHHHHHHHHHHCCCHHHHhC
Confidence 46889999999999999873
No 21
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=25.67 E-value=57 Score=32.71 Aligned_cols=39 Identities=28% Similarity=0.338 Sum_probs=35.1
Q ss_pred HHHHHhhCCCCCCCCCHHHHHHHHhhhCCC--cccccccccC
Q 023804 237 LEELIHSGGKTDDGLSKCAILNICTIYKLN--PIDVLKYRNS 276 (277)
Q Consensus 237 l~~~~~~~~~~~~~l~~~~i~~ic~~~~l~--~~d~~k~~~~ 276 (277)
+.++++.|+. ...||...|.++.+.-|++ +--|-|||..
T Consensus 379 I~~lI~~E~~-~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe~ 419 (429)
T TIGR02395 379 IKELIAAEDK-RKPLSDQKIAELLKEKGIKIARRTVAKYREE 419 (429)
T ss_pred HHHHHHhcCC-CCCCCHHHHHHHHHhcCCCeehHHHHHHHHH
Confidence 5889998888 8889999999999999999 8889999974
No 22
>PF14813 NADH_B2: NADH dehydrogenase 1 beta subcomplex subunit 2
Probab=24.93 E-value=41 Score=26.14 Aligned_cols=17 Identities=29% Similarity=0.790 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHhh
Q 023804 169 FFWILYRTYSHWRALQG 185 (277)
Q Consensus 169 ~FYl~YRaysH~rAl~G 185 (277)
-||++||+|-++-++.|
T Consensus 32 W~WIlwh~whd~~hvlG 48 (71)
T PF14813_consen 32 WFWILWHFWHDPDHVLG 48 (71)
T ss_pred HHHHHHHHhcChhhhcC
Confidence 79999999999999988
No 23
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=24.01 E-value=36 Score=22.13 Aligned_cols=22 Identities=9% Similarity=0.231 Sum_probs=15.9
Q ss_pred HHHHHHHHhhhCCCcccccccc
Q 023804 253 KCAILNICTIYKLNPIDVLKYR 274 (277)
Q Consensus 253 ~~~i~~ic~~~~l~~~d~~k~~ 274 (277)
.|++..|++.|+++.+++.++-
T Consensus 6 gDtl~~IA~~~~~~~~~l~~~N 27 (44)
T PF01476_consen 6 GDTLWSIAKRYGISVDELMELN 27 (44)
T ss_dssp T--HHHHHHHTTS-HHHHHHHC
T ss_pred CCcHHHHHhhhhhhHhHHHHhc
Confidence 4689999999999988887764
No 24
>PF10956 DUF2756: Protein of unknown function (DUF2756); InterPro: IPR020158 This entry contains proteins with no known function.
Probab=22.08 E-value=35 Score=28.36 Aligned_cols=27 Identities=33% Similarity=0.386 Sum_probs=19.5
Q ss_pred HHHHHHhhcccccc---ceecccCCCchHH
Q 023804 144 KYLYGSVSLLPLTF---VFSVLPLPNVPFF 170 (277)
Q Consensus 144 k~~~~~~~~lPLT~---P~aLiPlPNiP~F 170 (277)
|++++-++++||++ |+-.++=||-|||
T Consensus 2 K~ll~laalLPl~~~Aqp~n~~nnpnqpgy 31 (104)
T PF10956_consen 2 KRLLILAALLPLAAMAQPLNTTNNPNQPGY 31 (104)
T ss_pred hHHHHHHHHccHHHHHhHhhcCCCcCCCCC
Confidence 56777788888876 3444555999998
No 25
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=21.95 E-value=75 Score=32.16 Aligned_cols=39 Identities=23% Similarity=0.339 Sum_probs=34.7
Q ss_pred HHHHHhhCCCCCCCCCHHHHHHHHhhhCCC--cccccccccC
Q 023804 237 LEELIHSGGKTDDGLSKCAILNICTIYKLN--PIDVLKYRNS 276 (277)
Q Consensus 237 l~~~~~~~~~~~~~l~~~~i~~ic~~~~l~--~~d~~k~~~~ 276 (277)
+.++++.|+. .-.||...|.++.++-|++ +--|-|||..
T Consensus 403 Ik~lI~~Ed~-~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe~ 443 (455)
T PRK05932 403 IKKLIAAENP-KKPLSDSKIAELLKEQGIDVARRTVAKYREA 443 (455)
T ss_pred HHHHHHhcCC-CCCCCHHHHHHHHHHcCCCeehHHHHHHHHH
Confidence 5889998887 7889999999999999998 8889999974
No 26
>PHA01976 helix-turn-helix protein
Probab=21.88 E-value=80 Score=22.36 Aligned_cols=25 Identities=4% Similarity=-0.146 Sum_probs=21.2
Q ss_pred CCCCCHHHHHHHHhhhCCCcccccc
Q 023804 248 DDGLSKCAILNICTIYKLNPIDVLK 272 (277)
Q Consensus 248 ~~~l~~~~i~~ic~~~~l~~~d~~k 272 (277)
....+.+.+..||+.|+++.++|+.
T Consensus 39 ~~~p~~~~l~~ia~~l~v~~~~l~~ 63 (67)
T PHA01976 39 KRLPNLKTLLRLADALGVTLDWLCG 63 (67)
T ss_pred CCCCCHHHHHHHHHHHCcCHHHHhc
Confidence 4467899999999999999988763
No 27
>PF14039 YusW: YusW-like protein
Probab=21.54 E-value=1.4e+02 Score=23.95 Aligned_cols=38 Identities=24% Similarity=0.358 Sum_probs=26.9
Q ss_pred hHHHHHhhCCCCCCCCCHHHHHHHHhhhCCCcccccccc
Q 023804 236 ELEELIHSGGKTDDGLSKCAILNICTIYKLNPIDVLKYR 274 (277)
Q Consensus 236 ~l~~~~~~~~~~~~~l~~~~i~~ic~~~~l~~~d~~k~~ 274 (277)
+++.++..=.-+..--+.++|+.+.+.|+|++ |+-+|.
T Consensus 48 ~l~~~l~~L~~~~~t~~~evi~~Vl~~f~Ld~-dy~~fe 85 (92)
T PF14039_consen 48 ELEPLLSELSFDSDTSEEEVIDQVLKAFNLDP-DYQEFE 85 (92)
T ss_pred HHHHHHHhCCCCCCCChHHHHHHHHHHhCCCc-cceEEE
Confidence 35666654444344467899999999999998 776653
No 28
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=21.33 E-value=88 Score=25.81 Aligned_cols=28 Identities=11% Similarity=-0.045 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHhhhCCCccccccccc
Q 023804 248 DDGLSKCAILNICTIYKLNPIDVLKYRN 275 (277)
Q Consensus 248 ~~~l~~~~i~~ic~~~~l~~~d~~k~~~ 275 (277)
..-.|.+++..||+.|+++.++++..-+
T Consensus 42 ~~~ps~~~l~kIa~aL~v~~~~L~~~~~ 69 (120)
T PRK13890 42 KANPSLKVMEAIADALETPLPLLLESTD 69 (120)
T ss_pred CCCCCHHHHHHHHHHHCCCHHHHhccCc
Confidence 3458999999999999999988876643
No 29
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=20.41 E-value=74 Score=21.54 Aligned_cols=23 Identities=13% Similarity=0.098 Sum_probs=19.4
Q ss_pred CCCCCHHHHHHHHhhhCCCcccc
Q 023804 248 DDGLSKCAILNICTIYKLNPIDV 270 (277)
Q Consensus 248 ~~~l~~~~i~~ic~~~~l~~~d~ 270 (277)
+..++.+++..||+.||++.+++
T Consensus 33 ~~~~~~~~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 33 KRNPSLDTLKKIAKALGVSPEYL 55 (55)
T ss_dssp SSTSBHHHHHHHHHHHTSEHHHH
T ss_pred CCCCCHHHHHHHHHHHCCCHHHC
Confidence 56799999999999999987654
Done!