Query 023595
Match_columns 280
No_of_seqs 93 out of 95
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 05:13:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023595.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023595hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11152 DUF2930: Protein of u 100.0 1.7E-74 3.6E-79 512.4 19.5 194 62-277 1-195 (195)
2 PF13492 GAF_3: GAF domain; PD 95.3 0.099 2.2E-06 40.0 7.4 105 151-278 11-125 (129)
3 PF13185 GAF_2: GAF domain; PD 94.8 0.057 1.2E-06 42.4 4.9 72 192-278 74-145 (148)
4 smart00065 GAF Domain present 93.4 0.36 7.7E-06 35.6 6.5 80 186-278 57-137 (149)
5 PF01590 GAF: GAF domain; Int 92.9 0.21 4.6E-06 39.4 5.0 83 185-278 56-152 (154)
6 PRK11061 fused phosphoenolpyru 92.9 1.1 2.3E-05 47.8 11.5 127 137-278 17-152 (748)
7 TIGR01817 nifA Nif-specific re 88.8 3.9 8.4E-05 41.2 10.5 82 184-278 72-154 (534)
8 TIGR02851 spore_V_T stage V sp 88.6 7.4 0.00016 34.6 11.0 145 113-278 24-177 (180)
9 PRK15429 formate hydrogenlyase 86.9 5.2 0.00011 41.7 10.4 84 184-278 255-339 (686)
10 PRK05022 anaerobic nitric oxid 79.0 19 0.0004 36.4 10.4 131 135-278 16-154 (509)
11 PF00360 PHY: Phytochrome regi 67.9 8.5 0.00019 33.9 4.4 78 149-236 25-104 (182)
12 COG1956 GAF domain-containing 64.6 17 0.00036 32.5 5.5 75 187-278 84-158 (163)
13 PF10605 3HBOH: 3HB-oligomer h 54.4 12 0.00025 39.9 3.2 39 52-90 607-645 (690)
14 PRK13558 bacterio-opsin activa 52.2 23 0.0005 36.0 4.9 45 226-278 389-433 (665)
15 KOG0429 Ubiquitin-conjugating 34.8 17 0.00037 34.2 0.8 23 44-66 63-87 (258)
16 PF13334 DUF4094: Domain of un 26.7 51 0.0011 26.7 2.2 25 93-117 4-28 (95)
17 TIGR02916 PEP_his_kin putative 24.4 1.2E+02 0.0026 31.3 5.0 46 225-278 409-455 (679)
No 1
>PF11152 DUF2930: Protein of unknown function (DUF2930); InterPro: IPR021325 This family of proteins has no known function.
Probab=100.00 E-value=1.7e-74 Score=512.44 Aligned_cols=194 Identities=37% Similarity=0.544 Sum_probs=186.5
Q ss_pred hhHHHHHHHHHHHHhhhhccCCCCChhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCCCCCCCCCCCeeceEeccCchHH
Q 023595 62 LPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDA 141 (280)
Q Consensus 62 LP~~vG~l~g~Lll~N~~~s~a~~t~aQ~RsevLg~~Laa~~v~l~l~G~~w~~~~P~~~~~v~l~geq~F~l~~~Lsd~ 141 (280)
||+++|+++++++++||++++ .+||||+||||||++||+++ +++|++|++++|++++.+++.|+|+|+|++||||+
T Consensus 1 LPl~vG~l~~~lll~N~~~~~-~~t~sq~RaevLg~~ls~~l---iL~g~lw~~l~p~~~~~v~L~G~~~f~l~~~L~~~ 76 (195)
T PF11152_consen 1 LPLIVGLLGGSLLLLNRLSGA-DATPSQSRAEVLGLILSAVL---ILTGLLWQRLKPRSPEAVDLPGEQGFELSPDLSDA 76 (195)
T ss_pred CceEehHHHHHHHHhhhcccC-CCCHHHHHHHHHHHHHHHHH---HHHHHHHhhccCCCCCccCCCCccceEECCCCCHH
Confidence 799999999999999997776 68999999999999999665 89999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhccccEEEEEECCEEE-EeeeccCCCCCChHHHHHHHHHHhhhcccccCCCcccccCCcccccccc
Q 023595 142 LKENLAWATYVLLRNTNSISVLISIRGELC-VRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEM 220 (280)
Q Consensus 142 ~k~ELAWas~~LLtnT~a~svlV~~~g~ll-~RG~~~~p~~~~~g~i~~r~~~~~~~~~L~~L~~t~lyPgr~E~~~~~~ 220 (280)
+|+|||||||+|||||+|+||+|||||++| +||++++++++++|+||++++++++.+||+|+ .|||||+| |+|
T Consensus 77 ~k~ELAWas~~LLt~T~a~svlV~~~g~~llrrG~~~~~~~~~~g~i~~~~~~~~~~~yL~nl---~lyPGr~E---f~~ 150 (195)
T PF11152_consen 77 AKEELAWASYALLTNTNARSVLVYYDGRVLLRRGILGSPSKFKPGPICQRAMESGKLIYLVNL---KLYPGRVE---FDY 150 (195)
T ss_pred HHHHHHHHHHHHHhhCCceEEEEEECCEEEEEeeccCCCCCcchHHHHHHHHhcCCceecccc---ccCCCchh---hhh
Confidence 999999999999999999999999999965 68999989999999999999999999999777 89999999 899
Q ss_pred CCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHHhhh
Q 023595 221 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR 277 (280)
Q Consensus 221 LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R~fT~kDe~WI~~iA~KL~ 277 (280)
||+|||||||||+|+ +||||+|||++||||||||+||++|||||+
T Consensus 151 lP~ntq~VlvqP~g~------------~G~lvlgs~~~R~ft~~D~~Wi~~iA~Kl~ 195 (195)
T PF11152_consen 151 LPENTQSVLVQPLGQ------------NGVLVLGSNSPRAFTKSDEAWIAGIADKLR 195 (195)
T ss_pred cCCCCcEEEEEEcCC------------CeEEEEeeCCccccCHHHHHHHHHHHHhcC
Confidence 999999999999999 699999999999999999999999999996
No 2
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=95.30 E-value=0.099 Score=40.01 Aligned_cols=105 Identities=16% Similarity=0.214 Sum_probs=68.5
Q ss_pred HHHhhhccccEEEEE--ECC-E-E-EEeeeccCCC----C-CChHHHHHHHHHHhhhcccccCCCcccccCCcccccccc
Q 023595 151 YVLLRNTNSISVLIS--IRG-E-L-CVRGYWQTPD----G-ASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEM 220 (280)
Q Consensus 151 ~~LLtnT~a~svlV~--~~g-~-l-l~RG~~~~p~----~-~~~g~i~~r~~~~~~~~~L~~L~~t~lyPgr~E~~~~~~ 220 (280)
+.+...+.+..+.|| .++ . + +..++ .... . .....++.++.++.+..+. |+-.+..+
T Consensus 11 ~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~~~~~~~---------~~~~~~~~--- 77 (129)
T PF13492_consen 11 ELLRELLGADRAALFLLDEDGNRLRVVAGW-GGDPRLSESLPEDDPLIGRALETGEPVSV---------PDIDERDF--- 77 (129)
T ss_dssp HHHHHHST-SEEEEEEEETTCECEEEEEEE-SS-GCGHHCEETTSHHHHHHHHHTS-EEE---------STCCC-TT---
T ss_pred HHHHHHhCCCEEEEEEEECCCCEEEEEEEe-CCCccccccCCCCccHHHHHHhhCCeEEe---------cccccccC---
Confidence 445566666666554 434 2 2 34665 2111 1 1556788888888876444 22222111
Q ss_pred CCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHHhhhh
Q 023595 221 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRD 278 (280)
Q Consensus 221 LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R~fT~kDe~WI~~iA~KL~~ 278 (280)
.+.+++++.||..+ .+.-|+|.+++..++.||++|+..++.+|+-+..
T Consensus 78 --~~~~s~~~vPl~~~--------~~~~Gvl~~~~~~~~~~~~~d~~~l~~~a~~~a~ 125 (129)
T PF13492_consen 78 --LGIRSLLVVPLRSR--------DRVIGVLCLDSREPEEFSDEDLQLLESLANQLAI 125 (129)
T ss_dssp --TTTCEEEEEEEEET--------TEEEEEEEEEECTTCG-SHHHHHHHHHHHHHHHH
T ss_pred --CCCCEEEEEEEeEC--------CEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHH
Confidence 66799999999773 3668999999999999999999999999998764
No 3
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=94.81 E-value=0.057 Score=42.36 Aligned_cols=72 Identities=22% Similarity=0.244 Sum_probs=47.9
Q ss_pred HHHhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHH
Q 023595 192 ERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKA 271 (280)
Q Consensus 192 ~~~~~~~~L~~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R~fT~kDe~WI~~ 271 (280)
.++.+++... .+..-++.. ..+.=.|.+++++.||..+ .+.=|+|.+.+..++.||+.|+.+++.
T Consensus 74 ~~~~~~~~~~--~~~~~~~~~-----~~~~~~~~~s~l~vPl~~~--------~~~~Gvl~l~~~~~~~f~~~~~~~l~~ 138 (148)
T PF13185_consen 74 LRTGEPIIIN--DDDSSFPPW-----ELARHPGIRSILCVPLRSG--------GEVIGVLSLYSKEPNAFSEEDLELLEA 138 (148)
T ss_dssp HHHTS-EEES--CCCGGGSTT-----HHHCCTT-SEEEEEEEEET--------TEEEEEEEEEESSTT---HHHHHHHHH
T ss_pred HhcCceEEEe--Cccccccch-----hhhccccCCEEEEEEEeEC--------CEEEEEEEEeeCCCCCcCHHHHHHHHH
Confidence 6667777663 111122221 2345678999999999873 245799999999999999999999999
Q ss_pred HHHhhhh
Q 023595 272 VSNKFRD 278 (280)
Q Consensus 272 iA~KL~~ 278 (280)
+|+-+..
T Consensus 139 la~~~a~ 145 (148)
T PF13185_consen 139 LADQIAI 145 (148)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9987653
No 4
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=93.36 E-value=0.36 Score=35.55 Aligned_cols=80 Identities=15% Similarity=0.233 Sum_probs=55.2
Q ss_pred HHHHHHHHHhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeC-Cccccchh
Q 023595 186 QLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSHK 264 (280)
Q Consensus 186 ~i~~r~~~~~~~~~L~~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~R~fT~k 264 (280)
.++.+++++.+.....+.... |-..+ ....-..+..+.++.||..+ .+.-|++.+... .+|.|++.
T Consensus 57 ~~~~~~~~~~~~~~~~~~~~~---~~~~~--~~~~~~~~~~s~~~~Pl~~~--------~~~~G~l~~~~~~~~~~~~~~ 123 (149)
T smart00065 57 GLAGRVAETGRPLNIPDVEAD---PVFAL--DLLGRYQGVRSFLAVPLVAD--------GELVGVLALHNKDSPRPFTEE 123 (149)
T ss_pred ChHHHHHHcCCeEEeechhhC---Ccccc--ccccceeceeeEEEeeeeec--------CEEEEEEEEEecCCCCCCCHH
Confidence 678888888777766544221 21111 11111233899999998762 234699999988 89999999
Q ss_pred hHHHHHHHHHhhhh
Q 023595 265 DRAWIKAVSNKFRD 278 (280)
Q Consensus 265 De~WI~~iA~KL~~ 278 (280)
|+..++.+|+.+..
T Consensus 124 ~~~~l~~~~~~i~~ 137 (149)
T smart00065 124 DEELLQALANQLAI 137 (149)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999988754
No 5
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=92.93 E-value=0.21 Score=39.36 Aligned_cols=83 Identities=18% Similarity=0.192 Sum_probs=59.1
Q ss_pred HHHHHHHHHHhhhcccccCCCcccccCCcccc-ccccC------------CCCCceeEEEeccCCCCCCcccccccceEE
Q 023595 185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAG-QWEML------------PKGTCSVFVQPVIQAPNPSAVEVEKIEGFV 251 (280)
Q Consensus 185 g~i~~r~~~~~~~~~L~~L~~t~lyPgr~E~~-~~~~L------------P~ntqsVlvQPig~~~~~~~~~~~~~~Gvl 251 (280)
..++..+.+..+...+.|. .-.|-..+.. .-..+ ..+..++++-||.. ..+.-|+|
T Consensus 56 ~~~~~~~~~~~~~~~i~d~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~--------~g~~~G~l 124 (154)
T PF01590_consen 56 ESICGQVLQSREPIVISDV---AADPRFAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIIS--------GGRLIGVL 124 (154)
T ss_dssp SSHHHHHHHHTSCEEESSS---GGSTTSSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEE--------TTEEEEEE
T ss_pred ccHHHHHHhCCCeEeeccc---cccccccccccccccccccccccccccccccCceeeEeeeec--------ccCcEEEE
Confidence 4568899999998887666 3333322100 00112 56999999999865 23457999
Q ss_pred EEeeCCc-cccchhhHHHHHHHHHhhhh
Q 023595 252 LLASSMT-YAYSHKDRAWIKAVSNKFRD 278 (280)
Q Consensus 252 vlgs~s~-R~fT~kDe~WI~~iA~KL~~ 278 (280)
.+....+ |.||+.|...++.+|+.+..
T Consensus 125 ~l~~~~~~~~~~~~d~~ll~~~a~~~a~ 152 (154)
T PF01590_consen 125 SLYRTRPGRPFTEEDLALLESFAQQLAI 152 (154)
T ss_dssp EEEEESSSSS--HHHHHHHHHHHHHHHH
T ss_pred EEEECCCCCCcCHHHHHHHHHHHHHHHh
Confidence 9999999 99999999999999998763
No 6
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=92.91 E-value=1.1 Score=47.84 Aligned_cols=127 Identities=13% Similarity=0.219 Sum_probs=80.5
Q ss_pred CchHHHHHHHHHHHHHHhhhccccEEEEEECCE--EEE---eeeccC---CCCCC-hHHHHHHHHHHhhhcccccCCCcc
Q 023595 137 NISDALKENLAWATYVLLRNTNSISVLISIRGE--LCV---RGYWQT---PDGAS-KTQLLEWFERQIENIGLSDLKDSL 207 (280)
Q Consensus 137 ~Lsd~~k~ELAWas~~LLtnT~a~svlV~~~g~--ll~---RG~~~~---p~~~~-~g~i~~r~~~~~~~~~L~~L~~t~ 207 (280)
++.+....=+..+...+ +...+++.+++.+. +.. .|+-.. +-.+. ..-+|.++.++.+++.+.|.....
T Consensus 17 dL~e~L~~Iv~~~~~~l--~~d~~sI~L~D~~~~~L~~~as~Gl~~~~~~~~~l~~geGi~G~Va~tg~pV~V~Dv~~dp 94 (748)
T PRK11061 17 RLNEALDILVTETCLAM--DTEVCSVYLADHDRRCYYLMATRGLKKPRGRTVTLAFDEGIVGLVGRLAEPINLADAQKHP 94 (748)
T ss_pred CHHHHHHHHHHHHHHHh--CCCEEEEEEEECCCCEEEEEEeeCCChHhccceeccCCcchHHHHhccCceEEECCcccCc
Confidence 44444444444444444 55556666665443 222 443100 11222 234789999999999998875433
Q ss_pred cccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHHhhhh
Q 023595 208 YFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRD 278 (280)
Q Consensus 208 lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R~fT~kDe~WI~~iA~KL~~ 278 (280)
.|..+.+ ..-+++.|+++.||-.+ .+.=|+|-+....+|.||+.|+.++..+|+-+..
T Consensus 95 rf~~~~~-----~~~~~~~S~L~VPL~~~--------geVIGVL~v~~~~~~~Fs~~d~~lL~~LA~~aAi 152 (748)
T PRK11061 95 SFKYIPS-----VKEERFRAFLGVPIIYR--------RQLLGVLVVQQRELRQFDESEESFLVTLATQLAA 152 (748)
T ss_pred ccccCcc-----ccCccceEEEEEEEeeC--------CEEEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHH
Confidence 3322222 12467999999999752 2457999999999999999999999999987643
No 7
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=88.81 E-value=3.9 Score=41.21 Aligned_cols=82 Identities=9% Similarity=0.131 Sum_probs=58.7
Q ss_pred hHHHHHHHHHHhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCC-ccccc
Q 023595 184 KTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSM-TYAYS 262 (280)
Q Consensus 184 ~g~i~~r~~~~~~~~~L~~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s-~R~fT 262 (280)
...++.++.++.+++-+.|..+..-|-... .....+++|++|.||..+ .+.=|+|.+.+.. ++.||
T Consensus 72 ~~gi~g~v~~~~~pvii~Dv~~d~~~~~~~-----~~~~~~~~S~l~VPL~~~--------g~viGvL~v~s~~~~~~ft 138 (534)
T TIGR01817 72 GEGAIGQIVATGNSLVVPDVAAEPLFLDRL-----SLYDPGPVPFIGVPIKAD--------SETIGVLAADRDFRSRERL 138 (534)
T ss_pred CccHHHHHHhcCCeEEecccccCchhhhcc-----ccccCCcceEEEEEEcCC--------CEEEEEEEEEecccccccc
Confidence 356889999999988887663221111111 123457899999999752 2347999999875 57789
Q ss_pred hhhHHHHHHHHHhhhh
Q 023595 263 HKDRAWIKAVSNKFRD 278 (280)
Q Consensus 263 ~kDe~WI~~iA~KL~~ 278 (280)
+.|..+++.+|+.+..
T Consensus 139 ~~d~~lL~~lA~~ia~ 154 (534)
T TIGR01817 139 EEEVRFLEMVANLIGQ 154 (534)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999998764
No 8
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=88.59 E-value=7.4 Score=34.62 Aligned_cols=145 Identities=13% Similarity=0.045 Sum_probs=89.6
Q ss_pred hcccCCCCCCCCCCCCe-eceEeccCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEEE-eeeccC---CCCCChHHH
Q 023595 113 LKGASPVSQKSLPESGE-QIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCV-RGYWQT---PDGASKTQL 187 (280)
Q Consensus 113 w~~~~P~~~~~v~l~ge-q~F~l~~~Lsd~~k~ELAWas~~LLtnT~a~svlV~~~g~ll~-RG~~~~---p~~~~~g~i 187 (280)
=.+++++++..+...++ ++..-.-+.-....+...=....|...|.+ +|.|-...++++ -|.-.. +. ...+.
T Consensus 24 ~l~i~~gd~~~~~~~~~~~iil~k~~~~~~~~~~A~~~aeII~~~t~~-aVaITDr~~ILA~~G~g~d~~~~~--~is~~ 100 (180)
T TIGR02851 24 TLRIREGDPLEIFTDREGEVILKKYSPIGELGDFAKEYAESLYQSLGH-IVLITDRDTVIAVAGVSKKEYLNK--PISDE 100 (180)
T ss_pred HcCCCCCCeEEEEEeCCCEEEEEECCcccchHHHHHHHHHHHHHHhCC-EEEEECCCcEEEEECCChhhcCCC--ccCHH
Confidence 34677777766643332 222222222234445555567899999999 999999999886 887321 11 13345
Q ss_pred HHHHHHHhhhcccccCCCcccccCCccccccccCCCC--CceeEEEeccCCCCCCcccccccceEEEEeeCCcc--ccch
Q 023595 188 LEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKG--TCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY--AYSH 263 (280)
Q Consensus 188 ~~r~~~~~~~~~L~~L~~t~lyPgr~E~~~~~~LP~n--tqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R--~fT~ 263 (280)
.++++++.+.....+ .+..+||=.. -++ ..+.+|.||-.+ .++-|.|.+- ...+ .+|+
T Consensus 101 t~~~i~~gk~~~~~~-~~~~~i~c~~--------~~~~~l~s~ii~Pl~~~--------g~viGtLkly-~k~~~~~~~~ 162 (180)
T TIGR02851 101 LEDTMEERKTVILSD-TKDGPIEIID--------GQEFEYTSQVIAPIIAE--------GDPIGAVIIF-SKEPGEKLGE 162 (180)
T ss_pred HHHHHHcCCEEEecC-Cccceecccc--------CCCCCcceEEEEEEEEC--------CeEEEEEEEE-ECCccCCCCH
Confidence 666666665543311 1111122211 122 579999999763 2346877777 6666 9999
Q ss_pred hhHHHHHHHHHhhhh
Q 023595 264 KDRAWIKAVSNKFRD 278 (280)
Q Consensus 264 kDe~WI~~iA~KL~~ 278 (280)
.++.+..++|+=|..
T Consensus 163 ~e~~la~glA~lLS~ 177 (180)
T TIGR02851 163 VEQKAAETAAAFLGK 177 (180)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999997765
No 9
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=86.89 E-value=5.2 Score=41.73 Aligned_cols=84 Identities=10% Similarity=0.154 Sum_probs=59.9
Q ss_pred hHHHHHHHHHHhhhcccccCCCccccc-CCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccc
Q 023595 184 KTQLLEWFERQIENIGLSDLKDSLYFP-QSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYS 262 (280)
Q Consensus 184 ~g~i~~r~~~~~~~~~L~~L~~t~lyP-gr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R~fT 262 (280)
.+.+..++.++.++..+.+-....+.+ ++.. .+....++.++++.||... .++-|||.+++...+.|+
T Consensus 255 ~~~l~g~V~~~~~p~lv~~~~~d~~~~~~~~~---~~~~~~~~~s~l~vPL~~~--------~~v~GvL~l~~~~~~~F~ 323 (686)
T PRK15429 255 AGTLTERVFKSKEMLLINLHERDDLAPYERML---FDTWGNQIQTLCLLPLMSG--------DTMLGVLKLAQCEEKVFT 323 (686)
T ss_pred ccchHHHHHhcCceEEEECccCcccchhhhhh---hhcccccceEEEEEeEEEC--------CEEEEEEEEeeCCCCcCC
Confidence 346889999999887553321111211 1112 3445678999999999762 345799999988889999
Q ss_pred hhhHHHHHHHHHhhhh
Q 023595 263 HKDRAWIKAVSNKFRD 278 (280)
Q Consensus 263 ~kDe~WI~~iA~KL~~ 278 (280)
++|..-++.+|+..+.
T Consensus 324 ~~dl~lL~~iA~~~A~ 339 (686)
T PRK15429 324 TTNLKLLRQIAERVAI 339 (686)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999987754
No 10
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=78.99 E-value=19 Score=36.39 Aligned_cols=131 Identities=11% Similarity=-0.003 Sum_probs=81.6
Q ss_pred ccCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEE--E-eeeccCCC----CCChHHHHHHHHHHhhhcccccCC-Cc
Q 023595 135 SQNISDALKENLAWATYVLLRNTNSISVLISIRGELC--V-RGYWQTPD----GASKTQLLEWFERQIENIGLSDLK-DS 206 (280)
Q Consensus 135 ~~~Lsd~~k~ELAWas~~LLtnT~a~svlV~~~g~ll--~-RG~~~~p~----~~~~g~i~~r~~~~~~~~~L~~L~-~t 206 (280)
+.++.+.+..=+.++.+.+- ....++.++.++.+. + .|...... ....|+++..++++++.+-..+.. ..
T Consensus 16 s~d~~e~L~~vl~~l~~~l~--~~~~~l~l~~~~~l~~~as~gl~~~~~~~~~~~geGP~l~av~~~g~~v~v~~~~~~p 93 (509)
T PRK05022 16 GLPHQDRFQRLLTTLRQVLP--CDASALLRLDGDQLVPLAIDGLSPDVLGRRFALEEHPRLEAILRAGDPVRFPADSELP 93 (509)
T ss_pred CCCHHHHHHHHHHHHHHHcC--CCEEEEEecCCCcEEEEEEcCCChHhhCCccCCCcchHHHHHHhcCCeEEEecCCCCC
Confidence 45777888888889999883 355556656555432 2 44321111 234456778887766665333321 11
Q ss_pred ccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHHhhhh
Q 023595 207 LYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRD 278 (280)
Q Consensus 207 ~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R~fT~kDe~WI~~iA~KL~~ 278 (280)
.+|++.... .-.-.|..|+|+.||--. .+.-|+|-+-+..+..|++.|...++.+|+-+..
T Consensus 94 ~~~~~~~~~---~~~~~gi~S~l~vPL~~~--------~~~~GvL~l~~~~~~~f~~~~~~~l~~~a~~~a~ 154 (509)
T PRK05022 94 DPYDGLIPG---VQESLPVHDCMGLPLFVD--------GRLIGALTLDALDPGQFDAFSDEELRALAALAAA 154 (509)
T ss_pred ccccccccc---ccccCCcceEEEEEEEEC--------CEEEEEEEEeeCCCCcCCHHHHHHHHHHHHHHHH
Confidence 123332220 112347789999998552 2347999999988999999999999999875543
No 11
>PF00360 PHY: Phytochrome region; InterPro: IPR013515 Phytochrome belongs to a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions []. The protein undergoes reversible photochemical conversion between a biologically-inactive red light-absorbing form and the active far-red light-absorbing form. Phytochrome is a dimer of identical 124 kDa subunits, each of which contains a linear tetrapyrrole chromophore, covalently-attached via a Cys residue. This domain represents a region specific to phytochrome proteins.; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3C2W_G 3NHQ_B 3G6O_B 3IBR_A 2VEA_A 3ZQ5_A.
Probab=67.91 E-value=8.5 Score=33.89 Aligned_cols=78 Identities=24% Similarity=0.335 Sum_probs=49.0
Q ss_pred HHHHHhhhccccEEEEEECCEEEEeeeccCCCCCChHHHHHHHHHH-hhhccc-ccCCCcccccCCccccccccCCCCCc
Q 023595 149 ATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQ-IENIGL-SDLKDSLYFPQSADAGQWEMLPKGTC 226 (280)
Q Consensus 149 as~~LLtnT~a~svlV~~~g~ll~RG~~~~p~~~~~g~i~~r~~~~-~~~~~L-~~L~~t~lyPgr~E~~~~~~LP~ntq 226 (280)
....|++-..|.++.|+++|++...|- .|+.-.--.|++|+.+. .+.++- .+|. ..||+-.. +.+...
T Consensus 25 ~~~~ll~l~~AdG~al~~~g~~~~~G~--~P~~~~i~~L~~wl~~~~~~~v~~T~~L~--~~~p~~~~------~~~~aa 94 (182)
T PF00360_consen 25 QAPDLLDLVDADGVALVIDGEVYTFGE--TPPEEQIRALAEWLREQADGEVFATDSLS--EDYPDAAA------LAERAA 94 (182)
T ss_dssp TCCCHHHCTT-SEEEEEETTEEEEEES--S--HHHHHHHHHHCCCTTT-SEEEESBGG--GTSGGGGG------GCCCHS
T ss_pred ccHHHHhhccCCEEEEEECCEEEEecC--CcCHHHHHHHHHHHHhhCCCccchhhhHh--HhChhhhh------hcccCC
Confidence 455688889999999999999988895 44444444566666633 222221 1222 33665443 457788
Q ss_pred eeEEEeccCC
Q 023595 227 SVFVQPVIQA 236 (280)
Q Consensus 227 sVlvQPig~~ 236 (280)
|||+.||...
T Consensus 95 GvLai~l~~~ 104 (182)
T PF00360_consen 95 GVLAIPLSSE 104 (182)
T ss_dssp EEEEEEECTT
T ss_pred CcEEEECCCC
Confidence 9999999763
No 12
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=64.61 E-value=17 Score=32.54 Aligned_cols=75 Identities=16% Similarity=0.230 Sum_probs=57.7
Q ss_pred HHHHHHHHhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhH
Q 023595 187 LLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDR 266 (280)
Q Consensus 187 i~~r~~~~~~~~~L~~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R~fT~kDe 266 (280)
+|--+-++.+-.-..| ..-|||-+. =| ..++|=||.||-.+ .+.=|+|=+=|.++=.||+.||
T Consensus 84 VCg~A~~~~~t~~V~D---V~~~~ghia---CD---~as~SEIVvPi~~~--------g~~iGvlDiDS~~~~~Fd~~D~ 146 (163)
T COG1956 84 VCGTAAATGETVRVDD---VHAFPGHIA---CD---AASNSEIVVPIFKD--------GKLIGVLDIDSPTPGRFDEEDE 146 (163)
T ss_pred hhHHHHhcCCeEEecc---cccCCCccc---cc---cccCceEEEEEEEC--------CEEEEEEecCCCCcccCCHHHH
Confidence 5777777766665544 489999776 22 45788999999773 2346888899999999999999
Q ss_pred HHHHHHHHhhhh
Q 023595 267 AWIKAVSNKFRD 278 (280)
Q Consensus 267 ~WI~~iA~KL~~ 278 (280)
.||+.+|+-|..
T Consensus 147 ~~Le~~~~~l~~ 158 (163)
T COG1956 147 AGLEKLAALLEK 158 (163)
T ss_pred HHHHHHHHHHHH
Confidence 999999987654
No 13
>PF10605 3HBOH: 3HB-oligomer hydrolase (3HBOH) ; InterPro: IPR016582 This entry represents a group of predicted D-(-)-3-hydroxybutyrate oligomer hydrolases (also known as 3HB-oligomer hydrolase), which function in the degradation of poly-3-hydroxybutyrate (PHB). These enzymes catalyse the hydrolysis of D(-)-3-hydroxybutyrate oligomers (3HB-oligomers) into 3HB-monomers [, ].; GO: 0047989 hydroxybutyrate-dimer hydrolase activity, 0019605 butyrate metabolic process, 0005615 extracellular space
Probab=54.42 E-value=12 Score=39.93 Aligned_cols=39 Identities=18% Similarity=0.365 Sum_probs=34.2
Q ss_pred cCCCCCCCCChhHHHHHHHHHHHHhhhhccCCCCChhhH
Q 023595 52 FGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQL 90 (280)
Q Consensus 52 lgIpg~Dd~~LP~~vG~l~g~Lll~N~~~s~a~~t~aQ~ 90 (280)
++.||||++++|+-.=+.-.+=++-+|+.++.+++|||-
T Consensus 607 ~~~pG~~~r~VPlh~Y~~qALd~M~a~L~~G~~LPpSQV 645 (690)
T PF10605_consen 607 LDFPGFDTRFVPLHPYFFQALDLMWAHLKSGAALPPSQV 645 (690)
T ss_pred ccCCCCCcccccccHHHHHHHHHHHHHhhcCCCCCccce
Confidence 358999999999998888888889999999977899993
No 14
>PRK13558 bacterio-opsin activator; Provisional
Probab=52.20 E-value=23 Score=35.98 Aligned_cols=45 Identities=13% Similarity=0.256 Sum_probs=38.8
Q ss_pred ceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHHhhhh
Q 023595 226 CSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRD 278 (280)
Q Consensus 226 qsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R~fT~kDe~WI~~iA~KL~~ 278 (280)
+|+++-||-.+ .+.=|+|.+.+..++.|+..|+.-++.+|+++..
T Consensus 389 ~s~~~vPL~~~--------g~~~GvL~v~~~~~~~f~~~e~~ll~~la~~ia~ 433 (665)
T PRK13558 389 SAVAAVPLVYR--------ETTYGVLVVYTAEPDEIDDRERVVLEALGRAVGA 433 (665)
T ss_pred ceEEEEeEEEC--------CEEEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHH
Confidence 39999999652 2347999999999999999999999999998864
No 15
>KOG0429 consensus Ubiquitin-conjugating enzyme-related protein Ft1, involved in programmed cell death [Posttranslational modification, protein turnover, chaperones]
Probab=34.83 E-value=17 Score=34.23 Aligned_cols=23 Identities=52% Similarity=0.785 Sum_probs=19.7
Q ss_pred ccceeeeecCCCC-C-CCCChhHHH
Q 023595 44 NLSVLRFTFGIPG-F-DESYLPRWI 66 (280)
Q Consensus 44 ~~sv~RftlgIpg-~-Dd~~LP~~v 66 (280)
.-+|||||.=||. | ||.+||++|
T Consensus 63 aggVFRFtIliPdnfPdd~dlPrvv 87 (258)
T KOG0429|consen 63 AGGVFRFTILIPDNFPDDSDLPRVV 87 (258)
T ss_pred cCceEEEEEEcCccCCCcCCCCeEE
Confidence 3589999999997 3 799999986
No 16
>PF13334 DUF4094: Domain of unknown function (DUF4094)
Probab=26.73 E-value=51 Score=26.67 Aligned_cols=25 Identities=20% Similarity=0.279 Sum_probs=21.0
Q ss_pred HHHHHHHHHhhhhhhhhhhhhcccC
Q 023595 93 EVLGLSLAAFSVTLPYLGKFLKGAS 117 (280)
Q Consensus 93 evLg~~Laa~~v~l~l~G~~w~~~~ 117 (280)
=++-+|++.||+++.++|++|.--.
T Consensus 4 w~l~Lc~~SF~~G~lft~R~W~~pe 28 (95)
T PF13334_consen 4 WVLLLCIASFCAGMLFTNRMWTVPE 28 (95)
T ss_pred HHHHHHHHHHHHHHHHhcccccCCc
Confidence 3788999999999999999994433
No 17
>TIGR02916 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes.
Probab=24.39 E-value=1.2e+02 Score=31.33 Aligned_cols=46 Identities=22% Similarity=0.402 Sum_probs=35.9
Q ss_pred CceeEEEeccCCCCCCcccccccceEEEEeeC-CccccchhhHHHHHHHHHhhhh
Q 023595 225 TCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSHKDRAWIKAVSNKFRD 278 (280)
Q Consensus 225 tqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~R~fT~kDe~WI~~iA~KL~~ 278 (280)
..+.+|-|+... .+.-|+++++.+ .++.|+..|..+++.+++.+..
T Consensus 409 ~~~~l~vPL~~~--------~~~~G~l~l~~~~~~~~~~~e~~~lL~~l~~q~a~ 455 (679)
T TIGR02916 409 PNAWLIVPLISG--------EELVGFVVLARPRTAGEFNWEVRDLLKTAGRQAAS 455 (679)
T ss_pred CCceEEEEeccC--------CEEEEEEEEecCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 456899999763 234799999876 5568999999999999887653
Done!