Query 044567
Match_columns 288
No_of_seqs 50 out of 52
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 04:33:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044567.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044567hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00989 PAS: PAS fold; Inter 91.3 0.26 5.6E-06 36.1 3.4 36 183-218 1-36 (113)
2 PF13188 PAS_8: PAS domain; PD 90.2 0.48 1.1E-05 33.2 3.9 33 186-219 4-36 (64)
3 PF08448 PAS_4: PAS fold; Int 84.4 0.84 1.8E-05 33.2 2.4 26 193-218 5-30 (110)
4 PF13426 PAS_9: PAS domain; PD 83.2 1.2 2.5E-05 32.0 2.7 24 195-218 3-26 (104)
5 TIGR00229 sensory_box PAS doma 80.4 3 6.4E-05 27.4 3.6 30 190-219 10-39 (124)
6 cd00130 PAS PAS domain; PAS mo 76.1 3.7 8E-05 25.2 3.0 25 195-219 4-28 (103)
7 TIGR02966 phoR_proteo phosphat 66.9 8 0.00017 33.6 3.9 36 183-218 6-41 (333)
8 PRK11073 glnL nitrogen regulat 64.6 9.4 0.0002 34.4 4.1 38 183-220 7-44 (348)
9 PRK11086 sensory histidine kin 59.9 11 0.00024 35.9 3.8 37 183-219 221-257 (542)
10 PF12860 PAS_7: PAS fold 52.6 20 0.00044 27.6 3.6 26 196-221 8-33 (115)
11 PRK10820 DNA-binding transcrip 44.2 21 0.00045 36.2 3.1 36 185-220 82-117 (520)
12 PRK11006 phoR phosphate regulo 42.9 21 0.00045 33.9 2.7 31 189-219 104-134 (430)
13 PRK13560 hypothetical protein; 37.3 41 0.00088 33.7 3.9 32 187-218 208-239 (807)
14 TIGR02938 nifL_nitrog nitrogen 37.3 30 0.00066 31.9 2.8 36 183-218 4-39 (494)
15 smart00091 PAS PAS domain. PAS 36.7 66 0.0014 18.0 3.4 28 192-219 10-37 (67)
16 TIGR03859 PQQ_PqqD coenzyme PQ 34.4 12 0.00025 29.1 -0.3 33 246-278 6-39 (81)
17 TIGR02040 PpsR-CrtJ transcript 34.3 32 0.00069 32.9 2.5 31 189-219 258-288 (442)
18 PRK11091 aerobic respiration c 34.1 47 0.001 34.3 3.9 31 189-219 161-191 (779)
19 PRK15053 dpiB sensor histidine 32.4 45 0.00098 32.4 3.3 34 186-219 225-258 (545)
20 TIGR02938 nifL_nitrog nitrogen 30.3 61 0.0013 30.0 3.6 32 187-218 134-165 (494)
21 PRK11388 DNA-binding transcrip 30.1 51 0.0011 33.9 3.3 32 188-219 208-239 (638)
22 PRK13559 hypothetical protein; 26.5 79 0.0017 28.9 3.6 37 183-219 43-82 (361)
23 PF03792 PBC: PBC domain; Int 26.1 21 0.00046 32.9 -0.1 9 32-40 147-155 (191)
24 PRK10060 RNase II stability mo 23.3 69 0.0015 33.1 2.9 30 189-218 117-146 (663)
25 PRK09959 hybrid sensory histid 21.1 1.1E+02 0.0024 33.3 3.9 32 189-220 582-613 (1197)
No 1
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=91.34 E-value=0.26 Score=36.13 Aligned_cols=36 Identities=28% Similarity=0.385 Sum_probs=31.8
Q ss_pred HHHhhhcCCCCCCeEeeCCCCcEEEehHHHHHhhCC
Q 044567 183 GERKANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQ 218 (288)
Q Consensus 183 eEv~~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq 218 (288)
|..+.-|+.-.-|.||.|..|+|.++|.|+.+|.|-
T Consensus 1 e~~~~i~~~~~~~i~~~d~~g~I~~~N~a~~~l~g~ 36 (113)
T PF00989_consen 1 ERYRAILENSPDGIFVIDEDGRILYVNQAAEELLGY 36 (113)
T ss_dssp HHHHHHHHCSSSEEEEEETTSBEEEECHHHHHHHSS
T ss_pred CHHHHHHhcCCceEEEEeCcCeEEEECHHHHHHHcc
Confidence 455667778888999999999999999999999986
No 2
>PF13188 PAS_8: PAS domain; PDB: 2JHE_D 3VOL_A.
Probab=90.18 E-value=0.48 Score=33.18 Aligned_cols=33 Identities=21% Similarity=0.375 Sum_probs=25.9
Q ss_pred hhhcCCCCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 186 KANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 186 ~~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
+.-++.-..+-+|.| .++|.++|.|+.+|.|-+
T Consensus 4 ~~l~~~~~~~i~i~d-~~~i~~~N~~~~~l~g~~ 36 (64)
T PF13188_consen 4 RSLFDNSPDGILIID-GGRIIYVNPAFEELFGYS 36 (64)
T ss_dssp HHHHCCSSSEEEEEE-TSBEEEE-HHHHHHHCS-
T ss_pred HHHHHcCccceEEEE-CCChHHhhHHHHHHhCCC
Confidence 444566677889999 889999999999999943
No 3
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=84.42 E-value=0.84 Score=33.21 Aligned_cols=26 Identities=27% Similarity=0.418 Sum_probs=22.0
Q ss_pred CCCeEeeCCCCcEEEehHHHHHhhCC
Q 044567 193 TCPGFISDEFGRVTWTNEAYNKMVGQ 218 (288)
Q Consensus 193 t~P~fISDg~nRV~wvN~AYkrMVgq 218 (288)
..+.+|-|..++|.|+|.||.++.|.
T Consensus 5 p~~i~v~D~~~~i~~~N~~~~~~~~~ 30 (110)
T PF08448_consen 5 PDGIFVIDPDGRIVYANQAAAELFGV 30 (110)
T ss_dssp SSEEEEEETTSBEEEE-HHHHHHHTS
T ss_pred CceeEEECCCCEEEEEHHHHHHHhCC
Confidence 45778999999999999999998875
No 4
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=83.22 E-value=1.2 Score=31.98 Aligned_cols=24 Identities=33% Similarity=0.582 Sum_probs=21.2
Q ss_pred CeEeeCCCCcEEEehHHHHHhhCC
Q 044567 195 PGFISDEFGRVTWTNEAYNKMVGQ 218 (288)
Q Consensus 195 P~fISDg~nRV~wvN~AYkrMVgq 218 (288)
+-||.|..|+|.++|.|+.+|.|-
T Consensus 3 ~i~i~d~~g~i~~~N~~~~~~~g~ 26 (104)
T PF13426_consen 3 GIFILDPDGRILYVNPAFERLFGY 26 (104)
T ss_dssp EEEEEETTSBEEEE-HHHHHHHTS
T ss_pred EEEEECCcCcEEehhHHHHHHHCc
Confidence 568999999999999999999985
No 5
>TIGR00229 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator.
Probab=80.39 E-value=3 Score=27.39 Aligned_cols=30 Identities=17% Similarity=0.289 Sum_probs=24.9
Q ss_pred CCCCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 190 GRDTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 190 E~Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
+.-..+.++.|..+++.++|.+|.++.|.+
T Consensus 10 ~~~~~~~~~~d~~~~i~~~n~~~~~~~g~~ 39 (124)
T TIGR00229 10 ESSPDAIIVIDLEGNILYVNPAFEEIFGYS 39 (124)
T ss_pred hhCCceEEEEcCCCcEEEEchHHHHHhCCC
Confidence 333446789999999999999999999864
No 6
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=76.09 E-value=3.7 Score=25.24 Aligned_cols=25 Identities=24% Similarity=0.373 Sum_probs=22.2
Q ss_pred CeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 195 PGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 195 P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
+.++.|..+++.++|.+|.++.|..
T Consensus 4 ~i~~~d~~~~~~~~n~~~~~~~g~~ 28 (103)
T cd00130 4 GVIVLDLDGRILYANPAAEQLLGYS 28 (103)
T ss_pred eEEEECCCCcEEEECHHHHHHhCCC
Confidence 5678999999999999999999864
No 7
>TIGR02966 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154).
Probab=66.91 E-value=8 Score=33.64 Aligned_cols=36 Identities=22% Similarity=0.339 Sum_probs=31.4
Q ss_pred HHHhhhcCCCCCCeEeeCCCCcEEEehHHHHHhhCC
Q 044567 183 GERKANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQ 218 (288)
Q Consensus 183 eEv~~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq 218 (288)
++.+.-++.-..+.++.|..|++.|+|.|..+|.|-
T Consensus 6 ~~l~~~~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~ 41 (333)
T TIGR02966 6 SRFRAAAQALPDAVVVLDEEGQIEWCNPAAERLLGL 41 (333)
T ss_pred HHHHHHHHhCcCcEEEECCCCcEEEEcHHHHHHhCC
Confidence 455666777788999999999999999999999986
No 8
>PRK11073 glnL nitrogen regulation protein NR(II); Provisional
Probab=64.58 E-value=9.4 Score=34.44 Aligned_cols=38 Identities=13% Similarity=0.108 Sum_probs=31.7
Q ss_pred HHHhhhcCCCCCCeEeeCCCCcEEEehHHHHHhhCCCC
Q 044567 183 GERKANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQEE 220 (288)
Q Consensus 183 eEv~~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~e 220 (288)
.+.+.=|+.-....+|-|..|+|.|+|.|++++.|.+.
T Consensus 7 ~~~~~il~~~~~gi~~~d~~~~i~~~N~a~~~~~g~~~ 44 (348)
T PRK11073 7 PDAGQILNSLINSILLLDDDLAIHYANPAAQQLLAQSS 44 (348)
T ss_pred chHHHHHhcCcCeEEEECCCCeEeeEcHHHHHHhCCCH
Confidence 45556667777789999999999999999999998753
No 9
>PRK11086 sensory histidine kinase DcuS; Provisional
Probab=59.86 E-value=11 Score=35.92 Aligned_cols=37 Identities=22% Similarity=0.219 Sum_probs=29.7
Q ss_pred HHHhhhcCCCCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 183 GERKANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 183 eEv~~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
++++.-|+.-.-.-++.|..|||.++|.|+.+|.|.+
T Consensus 221 ~~~~~il~~~~~gIi~~D~~g~I~~~N~~a~~llg~~ 257 (542)
T PRK11086 221 EQRQAMLQSIKEGVIAVDDRGEVTLINDEAKRLFNYK 257 (542)
T ss_pred HHHHHHHHHhcCcEEEECCCCeEEEEhHHHHHHhCCC
Confidence 4455566665557899999999999999999999754
No 10
>PF12860 PAS_7: PAS fold
Probab=52.60 E-value=20 Score=27.61 Aligned_cols=26 Identities=19% Similarity=0.334 Sum_probs=22.7
Q ss_pred eEeeCCCCcEEEehHHHHHhhCCCCC
Q 044567 196 GFISDEFGRVTWTNEAYNKMVGQEEG 221 (288)
Q Consensus 196 ~fISDg~nRV~wvN~AYkrMVgq~e~ 221 (288)
-.|-|..+|+...|.+|.+|.+-+..
T Consensus 8 v~v~D~~~rl~~~N~~~~~l~~~~~~ 33 (115)
T PF12860_consen 8 VAVFDSDGRLVFWNQRFRELFGLPPE 33 (115)
T ss_pred EEEEcCCCeEEeEcHHHHHHhCCCHH
Confidence 46889999999999999999987543
No 11
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=44.16 E-value=21 Score=36.23 Aligned_cols=36 Identities=31% Similarity=0.253 Sum_probs=29.7
Q ss_pred HhhhcCCCCCCeEeeCCCCcEEEehHHHHHhhCCCC
Q 044567 185 RKANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQEE 220 (288)
Q Consensus 185 v~~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~e 220 (288)
.+.=|+.=.-|-|+.|..|+|.|+|.|+.++.|-++
T Consensus 82 L~aIL~sm~eGVi~vD~~G~I~~iN~aA~~Llg~~~ 117 (520)
T PRK10820 82 LSALLEALPEPVLSIDMKGKVELANPASCQLFGQSE 117 (520)
T ss_pred HHHHHHhCCCcEEEECCCCeeeHhHHHHHHHHCcCH
Confidence 344566666788999999999999999999998643
No 12
>PRK11006 phoR phosphate regulon sensor protein; Provisional
Probab=42.86 E-value=21 Score=33.86 Aligned_cols=31 Identities=16% Similarity=0.261 Sum_probs=25.6
Q ss_pred cCCCCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 189 LGRDTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 189 LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
+|.-.-+-|+.|..|+|.|+|.|+.+|.|..
T Consensus 104 ~~~~~~~i~~~d~~g~i~~~N~~a~~l~g~~ 134 (430)
T PRK11006 104 AESLPDAVVLTTEEGNIFWCNGLAQQLLGFR 134 (430)
T ss_pred HHhCCCeEEEEcCCCceeHHHHHHHHHhCCC
Confidence 3444456789999999999999999999863
No 13
>PRK13560 hypothetical protein; Provisional
Probab=37.30 E-value=41 Score=33.73 Aligned_cols=32 Identities=28% Similarity=0.189 Sum_probs=27.0
Q ss_pred hhcCCCCCCeEeeCCCCcEEEehHHHHHhhCC
Q 044567 187 ANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQ 218 (288)
Q Consensus 187 ~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq 218 (288)
.-+|.-..+.|+.|..|++.++|.||.+|.|-
T Consensus 208 ~l~e~~~~~i~~~d~~g~i~~~N~~~~~~~G~ 239 (807)
T PRK13560 208 QLLDNIADPAFWKDEDAKVFGCNDAACLACGF 239 (807)
T ss_pred HHHhhCCCeEEEEcCCCCEEEEhHHHHHHhCC
Confidence 34455667789999999999999999999884
No 14
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=37.28 E-value=30 Score=31.92 Aligned_cols=36 Identities=14% Similarity=0.289 Sum_probs=29.2
Q ss_pred HHHhhhcCCCCCCeEeeCCCCcEEEehHHHHHhhCC
Q 044567 183 GERKANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQ 218 (288)
Q Consensus 183 eEv~~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq 218 (288)
+..+.-++.-..+-++-|..|++.++|.+|.+|.|-
T Consensus 4 ~~~~~i~~~~~~~i~~~d~~g~~~~~N~~~~~~~G~ 39 (494)
T TIGR02938 4 EAYRQTVDQAPLAISITDLKANILYANDAFTRITGY 39 (494)
T ss_pred HHHHHHHHhCCceEEEECCCCcEEEEchhheeecCC
Confidence 344555666667889999999999999999999885
No 15
>smart00091 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels ([1]; Ponting & Aravind, in press).
Probab=36.72 E-value=66 Score=18.01 Aligned_cols=28 Identities=25% Similarity=0.303 Sum_probs=22.8
Q ss_pred CCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 192 DTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 192 Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
-..+.++.|..+.+..+|..+.++.|..
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 (67)
T smart00091 10 LPDGIFVLDLDGRILYANPAAEELLGYS 37 (67)
T ss_pred CCceEEEEcCCCeEEEECHHHHHHhCCC
Confidence 3445678899999999999999998753
No 16
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=34.35 E-value=12 Score=29.06 Aligned_cols=33 Identities=21% Similarity=0.321 Sum_probs=27.0
Q ss_pred EEEEEEeeCCeeeeeecceeeEEeec-CeeeEEe
Q 044567 246 RVRLQYSYGKEKNSLTLPCDVWRMDG-GGFAWRL 278 (288)
Q Consensus 246 rVRiqw~~~~ek~s~tvPCDVwRLd~-GgFaWRl 278 (288)
-||+||.......-+..|=.+++|+. |+|+|++
T Consensus 6 ~~r~~~~~v~~~~Vl~~p~~~~~Ln~~g~~Iw~l 39 (81)
T TIGR03859 6 GYRLQWERAQDCYVLLYPEGMVKLNDSAGEILEL 39 (81)
T ss_pred CeeeeeccccCcEEEEcCCceeeeChHHHHHHHH
Confidence 47999988777777888888999975 7799976
No 17
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=34.27 E-value=32 Score=32.92 Aligned_cols=31 Identities=19% Similarity=0.187 Sum_probs=26.6
Q ss_pred cCCCCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 189 LGRDTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 189 LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
+|.-.-+-||.|..|+|..+|.||-+|.|.+
T Consensus 258 ~e~~~d~I~v~D~~G~I~~~N~a~~~l~G~~ 288 (442)
T TIGR02040 258 YHEAPDAIVFSDADGTIRGANEAFLELTDSS 288 (442)
T ss_pred HHhCCceEEEEcCCCcEEehhHHHHHHhCCC
Confidence 4555557789999999999999999999974
No 18
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=34.11 E-value=47 Score=34.25 Aligned_cols=31 Identities=19% Similarity=0.230 Sum_probs=25.7
Q ss_pred cCCCCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 189 LGRDTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 189 LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
|+.-.-+-|+.|..|+|.++|.|+.+|.|-+
T Consensus 161 l~~~~~~i~~~D~~g~i~~~N~a~~~l~G~~ 191 (779)
T PRK11091 161 LDASPDLVYYRNEDGEFSGCNRAMELLTGKS 191 (779)
T ss_pred HhcCcceEEEECCCCcEEeEcHHHHHHhCcC
Confidence 3444456789999999999999999999864
No 19
>PRK15053 dpiB sensor histidine kinase DpiB; Provisional
Probab=32.38 E-value=45 Score=32.39 Aligned_cols=34 Identities=24% Similarity=0.149 Sum_probs=26.9
Q ss_pred hhhcCCCCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 186 KANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 186 ~~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
+.-|+.-.=+-++-|..|+|.++|.|+.+|.|.+
T Consensus 225 ~~il~~~~egii~~D~~g~I~~~N~~a~~ll~~~ 258 (545)
T PRK15053 225 EALFSSVYEGLIAVDPHGYITAINRNARKMLGLS 258 (545)
T ss_pred HHHHHHhCceEEEECCCCeEEeecHHHHHHhCCC
Confidence 3344444456789999999999999999999863
No 20
>TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes.
Probab=30.28 E-value=61 Score=29.96 Aligned_cols=32 Identities=22% Similarity=0.327 Sum_probs=26.7
Q ss_pred hhcCCCCCCeEeeCCCCcEEEehHHHHHhhCC
Q 044567 187 ANLGRDTCPGFISDEFGRVTWTNEAYNKMVGQ 218 (288)
Q Consensus 187 ~~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq 218 (288)
.-++.-..+.++.|..|++.++|.+|.+|.|.
T Consensus 134 ~~~~~~~~~i~~~d~~~~i~~~N~~~~~~~g~ 165 (494)
T TIGR02938 134 SVVDAAPVAFVLLDPTGRVILDNQEYKKLATD 165 (494)
T ss_pred HHHhcccceEEEEcCCCCEEEechhHHHhhch
Confidence 34455666789999999999999999999875
No 21
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=30.13 E-value=51 Score=33.91 Aligned_cols=32 Identities=16% Similarity=0.117 Sum_probs=27.1
Q ss_pred hcCCCCCCeEeeCCCCcEEEehHHHHHhhCCC
Q 044567 188 NLGRDTCPGFISDEFGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 188 ~LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~ 219 (288)
-|+.-.-+-++.|..|+|.++|.|+.+|.|..
T Consensus 208 il~~~~~gVl~vD~~G~I~~~N~aa~~llg~s 239 (638)
T PRK11388 208 LLESMDDGVIAWDEQGNLQFLNAQAARLLRLD 239 (638)
T ss_pred HHhccCCcEEEECCCCeEehhhHHHHHHhCcC
Confidence 44555668999999999999999999999863
No 22
>PRK13559 hypothetical protein; Provisional
Probab=26.45 E-value=79 Score=28.87 Aligned_cols=37 Identities=14% Similarity=0.121 Sum_probs=29.7
Q ss_pred HHHhhhcCCCCCCeEeeCC---CCcEEEehHHHHHhhCCC
Q 044567 183 GERKANLGRDTCPGFISDE---FGRVTWTNEAYNKMVGQE 219 (288)
Q Consensus 183 eEv~~~LE~Dt~P~fISDg---~nRV~wvN~AYkrMVgq~ 219 (288)
+..+.-+|.-..+-+|.|. .|++.++|.||.+|.|-.
T Consensus 43 ~~~~~~~e~~~~~i~i~D~~~~~g~i~~~N~a~~~l~G~~ 82 (361)
T PRK13559 43 RLFEQAMEQTRMAMCITDPHQPDLPIVLANQAFLDLTGYA 82 (361)
T ss_pred hHHHHHHHhCCCcEEEecCCCCCCcEEEEchHHHHHhCCC
Confidence 4455567777788899996 568999999999999963
No 23
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=26.12 E-value=21 Score=32.90 Aligned_cols=9 Identities=67% Similarity=1.298 Sum_probs=7.7
Q ss_pred hcccCCCCC
Q 044567 32 RFRPIAPKP 40 (288)
Q Consensus 32 RFRPIAPKP 40 (288)
|||||+||-
T Consensus 147 ~~RPIs~ke 155 (191)
T PF03792_consen 147 EFRPISPKE 155 (191)
T ss_pred ccCCCCHHH
Confidence 799999973
No 24
>PRK10060 RNase II stability modulator; Provisional
Probab=23.34 E-value=69 Score=33.10 Aligned_cols=30 Identities=17% Similarity=0.179 Sum_probs=25.1
Q ss_pred cCCCCCCeEeeCCCCcEEEehHHHHHhhCC
Q 044567 189 LGRDTCPGFISDEFGRVTWTNEAYNKMVGQ 218 (288)
Q Consensus 189 LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq 218 (288)
+|.-.-.-+|.|..|++.++|.||.+|.|-
T Consensus 117 ~~~~~~gI~i~D~~g~I~~~N~a~~~l~Gy 146 (663)
T PRK10060 117 VSEANSVIVILDSRGNIQRFNRLCEEYTGL 146 (663)
T ss_pred HhhCCceEEEEeCCCCEEEEcHHHHHHHCc
Confidence 344445678999999999999999999985
No 25
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=21.10 E-value=1.1e+02 Score=33.31 Aligned_cols=32 Identities=16% Similarity=0.198 Sum_probs=27.4
Q ss_pred cCCCCCCeEeeCCCCcEEEehHHHHHhhCCCC
Q 044567 189 LGRDTCPGFISDEFGRVTWTNEAYNKMVGQEE 220 (288)
Q Consensus 189 LE~Dt~P~fISDg~nRV~wvN~AYkrMVgq~e 220 (288)
++.=..|-+|.|..|||.++|.|+.++.|...
T Consensus 582 ~~~~~~~i~~~d~~g~i~~~N~~~~~~~g~~~ 613 (1197)
T PRK09959 582 SDSLPNPTYVVNWQGNVISHNSAFEHYFTADY 613 (1197)
T ss_pred HhhCCCcEEEEcCCCcEEEehHHHHHHhCccc
Confidence 45566788999999999999999999998653
Done!