Query 023149
Match_columns 286
No_of_seqs 94 out of 96
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 08:47:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023149.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023149hhsearch_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 2E-73 4.4E-78 506.9 19.6 194 62-277 1-195 (195)
2 PF13185 GAF_2: GAF domain; PD 95.2 0.027 5.8E-07 44.3 4.2 54 219-280 94-147 (148)
3 PF13492 GAF_3: GAF domain; PD 95.0 0.093 2E-06 40.3 6.4 108 151-280 11-127 (129)
4 PRK11061 fused phosphoenolpyru 92.6 1.1 2.4E-05 47.8 11.2 128 137-279 17-153 (748)
5 smart00065 GAF Domain present 92.0 0.48 1E-05 34.9 5.6 49 224-280 90-139 (149)
6 PF01590 GAF: GAF domain; Int 90.3 0.39 8.6E-06 37.9 3.9 83 185-278 56-152 (154)
7 TIGR02851 spore_V_T stage V sp 89.4 4.1 8.8E-05 36.4 10.0 148 113-280 24-179 (180)
8 PRK15429 formate hydrogenlyase 85.2 5.4 0.00012 41.7 9.5 85 184-280 255-341 (686)
9 TIGR01817 nifA Nif-specific re 82.6 12 0.00026 37.8 10.5 82 185-279 73-155 (534)
10 COG1956 GAF domain-containing 74.7 6.1 0.00013 35.4 5.0 75 194-282 88-162 (163)
11 PRK05022 anaerobic nitric oxid 73.6 30 0.00064 35.1 10.2 132 135-279 16-155 (509)
12 PF00360 PHY: Phytochrome regi 60.4 14 0.00031 32.6 4.4 78 149-236 25-104 (182)
13 PF10605 3HBOH: 3HB-oligomer h 55.7 11 0.00023 40.3 3.2 39 52-90 607-645 (690)
14 PRK13558 bacterio-opsin activa 51.2 19 0.00041 36.7 4.1 47 226-280 389-435 (665)
15 KOG0429 Ubiquitin-conjugating 34.4 18 0.00038 34.3 0.8 23 44-66 63-87 (258)
16 TIGR02916 PEP_his_kin putative 28.6 1E+02 0.0022 32.0 5.3 47 225-279 409-456 (679)
17 PF13334 DUF4094: Domain of un 27.2 50 0.0011 26.8 2.2 25 93-117 4-28 (95)
18 COG2203 FhlA FOG: GAF domain [ 20.8 96 0.0021 23.5 2.6 54 219-280 108-162 (175)
No 1
>PF11152 DUF2930: Protein of unknown function (DUF2930); InterPro: IPR021325 This family of proteins has no known function.
Probab=100.00 E-value=2e-73 Score=506.90 Aligned_cols=194 Identities=37% Similarity=0.544 Sum_probs=185.2
Q ss_pred hhHHHHHHHHHHHHhhhhccCCCCChhhHHHHHHHHHHHHhhhhhhhhhhhhcccCCCCCCCCCCCCeeceEeccCchHH
Q 023149 62 LPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKGASPVSQKSLPESGEQIFVMSQNISDA 141 (286)
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 (286)
||+++|+++++++++||++++ .+||||+||||||++||+++ +++|++|++++|++++.+++.|+|+|+|++||||+
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 68999999999999999555 89999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhccccEEEEEECCEEE-EeeeecCCCCCChHHHHHHHHHhhhhcccccCCCcccccCCcccccccc
Q 023149 142 LKENLAWATYVLLRNTNSISVLISIRGELC-VRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEM 220 (286)
Q Consensus 142 ~k~ELAWaS~~LLtnT~a~svlV~~~g~ll-~RG~~~~p~~~~~g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~ 220 (286)
+|+|||||||+|||||+|+||+|||||++| +||++++++++++|+||++++++++.+||+|+ .|||||+| |+|
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 999999999999999999999999999966 58999888999999999999999888888877 89999999 899
Q ss_pred CCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhc
Q 023149 221 LPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR 277 (286)
Q Consensus 221 LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~ 277 (286)
||+|||||||||+|+ +||||+|||++||||+|||+||++|||||+
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 599999999999999999999999999996
No 2
>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=95.25 E-value=0.027 Score=44.32 Aligned_cols=54 Identities=19% Similarity=0.234 Sum_probs=41.8
Q ss_pred ccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023149 219 EMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS 280 (286)
Q Consensus 219 ~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~ 280 (286)
.+.=.|.+++++.||..+ .+.=|+|.+.+..++.||+.|+.+++.+|+-+..++
T Consensus 94 ~~~~~~~~s~l~vPl~~~--------~~~~Gvl~l~~~~~~~f~~~~~~~l~~la~~~a~ai 147 (148)
T PF13185_consen 94 LARHPGIRSILCVPLRSG--------GEVIGVLSLYSKEPNAFSEEDLELLEALADQIAIAI 147 (148)
T ss_dssp HHCCTT-SEEEEEEEEET--------TEEEEEEEEEESSTT---HHHHHHHHHHHHHHHHHH
T ss_pred hhccccCCEEEEEEEeEC--------CEEEEEEEEeeCCCCCcCHHHHHHHHHHHHHHHHHh
Confidence 345678999999999873 245799999999999999999999999999876554
No 3
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=94.96 E-value=0.093 Score=40.28 Aligned_cols=108 Identities=17% Similarity=0.211 Sum_probs=67.6
Q ss_pred HHHhhhccccEEEEE--ECC-E-E-EEeeeecCCC---C-CChHHHHHHHHHhhhhcccccCCCcccccCCccccccccC
Q 023149 151 YVLLRNTNSISVLIS--IRG-E-L-CVRGYWQTPD---G-ASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEML 221 (286)
Q Consensus 151 ~~LLtnT~a~svlV~--~~g-~-l-l~RG~~~~p~---~-~~~g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~L 221 (286)
+.+...+.+..+.|| .++ . + +..++-+.+. . .....++.++.++.+..+ .|+-.+..+
T Consensus 11 ~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~---------~~~~~~~~~---- 77 (129)
T PF13492_consen 11 ELLRELLGADRAALFLLDEDGNRLRVVAGWGGDPRLSESLPEDDPLIGRALETGEPVS---------VPDIDERDF---- 77 (129)
T ss_dssp HHHHHHST-SEEEEEEEETTCECEEEEEEESS-GCGHHCEETTSHHHHHHHHHTS-EE---------ESTCCC-TT----
T ss_pred HHHHHHhCCCEEEEEEEECCCCEEEEEEEeCCCccccccCCCCccHHHHHHhhCCeEE---------ecccccccC----
Confidence 445566666666554 434 2 2 2366511111 1 145567677777665432 233222111
Q ss_pred CCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023149 222 PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS 280 (286)
Q Consensus 222 P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~ 280 (286)
.+.+++++.||..+ .+.-|+|.+++..++.||++|+..++.+|+-+..++
T Consensus 78 -~~~~s~~~vPl~~~--------~~~~Gvl~~~~~~~~~~~~~d~~~l~~~a~~~a~al 127 (129)
T PF13492_consen 78 -LGIRSLLVVPLRSR--------DRVIGVLCLDSREPEEFSDEDLQLLESLANQLAIAL 127 (129)
T ss_dssp -TTTCEEEEEEEEET--------TEEEEEEEEEECTTCG-SHHHHHHHHHHHHHHHHHH
T ss_pred -CCCCEEEEEEEeEC--------CEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHh
Confidence 66799999999873 356899999999999999999999999999876554
No 4
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=92.61 E-value=1.1 Score=47.79 Aligned_cols=128 Identities=11% Similarity=0.172 Sum_probs=79.7
Q ss_pred CchHHHHHHHHHHHHHHhhhccccEEEEEECCE--EEEeeeecC------CCCCC-hHHHHHHHHHhhhhcccccCCCcc
Q 023149 137 NISDALKENLAWATYVLLRNTNSISVLISIRGE--LCVRGYWQT------PDGAS-KTQLLEWFERQIENIGLSDLKDSL 207 (286)
Q Consensus 137 ~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~--ll~RG~~~~------p~~~~-~g~I~~~~~~~~~~~~Lv~L~~t~ 207 (286)
++.+.+..=+..+...+ +...+++.+++.+. +..+...+. +-.+. ..-++.++.++.+.....|.....
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 222322221 11122 233678888888888887775433
Q ss_pred cccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccc
Q 023149 208 YFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK 279 (286)
Q Consensus 208 lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~ 279 (286)
.|..+.+ ..-+++.|+++.||-.. .+.=|+|-+....+|.||+.|+.++..+|.-+..+
T Consensus 95 rf~~~~~-----~~~~~~~S~L~VPL~~~--------geVIGVL~v~~~~~~~Fs~~d~~lL~~LA~~aAiA 153 (748)
T PRK11061 95 SFKYIPS-----VKEERFRAFLGVPIIYR--------RQLLGVLVVQQRELRQFDESEESFLVTLATQLAAI 153 (748)
T ss_pred ccccCcc-----ccCccceEEEEEEEeeC--------CEEEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3322222 12467999999999752 24579999999999999999999999999877544
No 5
>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=91.99 E-value=0.48 Score=34.94 Aligned_cols=49 Identities=16% Similarity=0.350 Sum_probs=40.8
Q ss_pred CCceeEEEeccCCCCCCcccccccceEEEEeeC-CccccchhhHHHHHHHHhhhcccc
Q 023149 224 GTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSHKDRAWIKAVSNKFRGKS 280 (286)
Q Consensus 224 ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~RafT~kDe~WI~~iA~KL~~~~ 280 (286)
+..+.++.||..+ .+.-|++.+... .+|.|+..|+..++.+|+.+..+.
T Consensus 90 ~~~s~~~~Pl~~~--------~~~~G~l~~~~~~~~~~~~~~~~~~l~~~~~~i~~~l 139 (149)
T smart00065 90 GVRSFLAVPLVAD--------GELVGVLALHNKDSPRPFTEEDEELLQALANQLAIAL 139 (149)
T ss_pred ceeeEEEeeeeec--------CEEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3899999998763 234699999988 899999999999999999886554
No 6
>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=90.33 E-value=0.39 Score=37.91 Aligned_cols=83 Identities=18% Similarity=0.189 Sum_probs=55.5
Q ss_pred HHHHHHHHHhhhhcccccCCCcccccCCcccc-ccccC------------CCCCceeEEEeccCCCCCCcccccccceEE
Q 023149 185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAG-QWEML------------PKGTCSVFVQPVIQAPNPSAVEVEKIEGFV 251 (286)
Q Consensus 185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~-~~~~L------------P~ntqsVlvQPig~~~~~~~~~~~~~~Gvl 251 (286)
..++..+.+..+...+.+. .-.|-..+.. .-..+ ..+..++++-||.. ..+.-|+|
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 3456666777666665555 3333322100 00112 56999999999865 23457999
Q ss_pred EEeeCCc-cccchhhHHHHHHHHhhhcc
Q 023149 252 LLASSMT-YAYSHKDRAWIKAVSNKFRG 278 (286)
Q Consensus 252 vlgs~s~-RafT~kDe~WI~~iA~KL~~ 278 (286)
.+....+ |.||+.|+..++.+|+.+..
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 99999999999999998764
No 7
>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=89.43 E-value=4.1 Score=36.38 Aligned_cols=148 Identities=11% Similarity=0.019 Sum_probs=86.5
Q ss_pred hcccCCCCCCCCCCCCe-eceEeccCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEEE-eeeecCCCCCChHHHHHH
Q 023149 113 LKGASPVSQKSLPESGE-QIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCV-RGYWQTPDGASKTQLLEW 190 (286)
Q Consensus 113 w~~~~P~~~~~v~l~ge-q~F~l~~~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll~-RG~~~~p~~~~~g~I~~~ 190 (286)
=.+++++++..+...++ ++..-.-+.-....+...=....|...|.+ +|.|-...++++ -|.-.. ...++++-+.
T Consensus 24 ~l~i~~gd~~~~~~~~~~~iil~k~~~~~~~~~~A~~~aeII~~~t~~-aVaITDr~~ILA~~G~g~d--~~~~~~is~~ 100 (180)
T TIGR02851 24 TLRIREGDPLEIFTDREGEVILKKYSPIGELGDFAKEYAESLYQSLGH-IVLITDRDTVIAVAGVSKK--EYLNKPISDE 100 (180)
T ss_pred HcCCCCCCeEEEEEeCCCEEEEEECCcccchHHHHHHHHHHHHHHhCC-EEEEECCCcEEEEECCChh--hcCCCccCHH
Confidence 34677777766643332 222222222233444555567899999999 999999999887 886631 1111122222
Q ss_pred HHHhhhhccc--ccCCCcccccCCccccccccCCCC--CceeEEEeccCCCCCCcccccccceEEEEeeCCcc--ccchh
Q 023149 191 FERQIENIGL--SDLKDSLYFPQSADAGQWEMLPKG--TCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY--AYSHK 264 (286)
Q Consensus 191 ~~~~~~~~~L--v~L~~t~lyPgr~E~~~~~~LP~n--tqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R--afT~k 264 (286)
..+.++.... ++-.+..+||=.. -++ ..+.+|.||-.+ .++-|.|.+- ...+ .+|+.
T Consensus 101 t~~~i~~gk~~~~~~~~~~~i~c~~--------~~~~~l~s~ii~Pl~~~--------g~viGtLkly-~k~~~~~~~~~ 163 (180)
T TIGR02851 101 LEDTMEERKTVILSDTKDGPIEIID--------GQEFEYTSQVIAPIIAE--------GDPIGAVIIF-SKEPGEKLGEV 163 (180)
T ss_pred HHHHHHcCCEEEecCCccceecccc--------CCCCCcceEEEEEEEEC--------CeEEEEEEEE-ECCccCCCCHH
Confidence 3333333222 1111111122110 122 579999999763 2346877777 6666 99999
Q ss_pred hHHHHHHHHhhhcccc
Q 023149 265 DRAWIKAVSNKFRGKS 280 (286)
Q Consensus 265 De~WI~~iA~KL~~~~ 280 (286)
++.+..++|+=|...+
T Consensus 164 e~~la~glA~lLS~QL 179 (180)
T TIGR02851 164 EQKAAETAAAFLGKQM 179 (180)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 9999999999876543
No 8
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=85.20 E-value=5.4 Score=41.72 Aligned_cols=85 Identities=11% Similarity=0.198 Sum_probs=60.2
Q ss_pred hHHHHHHHHHhhhhcccccCCC-ccccc-CCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcccc
Q 023149 184 KTQLLEWFERQIENIGLSDLKD-SLYFP-QSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAY 261 (286)
Q Consensus 184 ~g~I~~~~~~~~~~~~Lv~L~~-t~lyP-gr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~Raf 261 (286)
.+.+..++.+..++..+ +..+ ..+.+ ++.. .+....++.++++.||... .++-|||.+++...+.|
T Consensus 255 ~~~l~g~V~~~~~p~lv-~~~~~d~~~~~~~~~---~~~~~~~~~s~l~vPL~~~--------~~v~GvL~l~~~~~~~F 322 (686)
T PRK15429 255 AGTLTERVFKSKEMLLI-NLHERDDLAPYERML---FDTWGNQIQTLCLLPLMSG--------DTMLGVLKLAQCEEKVF 322 (686)
T ss_pred ccchHHHHHhcCceEEE-ECccCcccchhhhhh---hhcccccceEEEEEeEEEC--------CEEEEEEEEeeCCCCcC
Confidence 34677888888876644 4432 11111 1112 3445678999999999762 34579999998889999
Q ss_pred chhhHHHHHHHHhhhcccc
Q 023149 262 SHKDRAWIKAVSNKFRGKS 280 (286)
Q Consensus 262 T~kDe~WI~~iA~KL~~~~ 280 (286)
+++|..-++.+|+....+.
T Consensus 323 ~~~dl~lL~~iA~~~A~Ai 341 (686)
T PRK15429 323 TTTNLKLLRQIAERVAIAV 341 (686)
T ss_pred CHHHHHHHHHHHHHHHHHH
Confidence 9999999999999877654
No 9
>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=82.60 E-value=12 Score=37.85 Aligned_cols=82 Identities=9% Similarity=0.129 Sum_probs=56.9
Q ss_pred HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCC-ccccch
Q 023149 185 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSM-TYAYSH 263 (286)
Q Consensus 185 g~I~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s-~RafT~ 263 (286)
..++.++.+..++.-+.|..+..-|-.+. .....+++|++|.||..+ .+.=|+|.+.+.. ++.||+
T Consensus 73 ~gi~g~v~~~~~pvii~Dv~~d~~~~~~~-----~~~~~~~~S~l~VPL~~~--------g~viGvL~v~s~~~~~~ft~ 139 (534)
T TIGR01817 73 EGAIGQIVATGNSLVVPDVAAEPLFLDRL-----SLYDPGPVPFIGVPIKAD--------SETIGVLAADRDFRSRERLE 139 (534)
T ss_pred ccHHHHHHhcCCeEEecccccCchhhhcc-----ccccCCcceEEEEEEcCC--------CEEEEEEEEEeccccccccH
Confidence 45777888887777666653221111111 123457899999999752 2347999999875 577899
Q ss_pred hhHHHHHHHHhhhccc
Q 023149 264 KDRAWIKAVSNKFRGK 279 (286)
Q Consensus 264 kDe~WI~~iA~KL~~~ 279 (286)
.|...+..+|+.+..+
T Consensus 140 ~d~~lL~~lA~~ia~a 155 (534)
T TIGR01817 140 EEVRFLEMVANLIGQT 155 (534)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999987654
No 10
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=74.68 E-value=6.1 Score=35.37 Aligned_cols=75 Identities=15% Similarity=0.212 Sum_probs=55.8
Q ss_pred hhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHH
Q 023149 194 QIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVS 273 (286)
Q Consensus 194 ~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA 273 (286)
+.+...-+..-|..-|||-+. =| ..++|=||.||-.+ .+.=|+|=+=|.++=.||+.||.||+.+|
T Consensus 88 A~~~~~t~~V~DV~~~~ghia---CD---~as~SEIVvPi~~~--------g~~iGvlDiDS~~~~~Fd~~D~~~Le~~~ 153 (163)
T COG1956 88 AAATGETVRVDDVHAFPGHIA---CD---AASNSEIVVPIFKD--------GKLIGVLDIDSPTPGRFDEEDEAGLEKLA 153 (163)
T ss_pred HHhcCCeEEecccccCCCccc---cc---cccCceEEEEEEEC--------CEEEEEEecCCCCcccCCHHHHHHHHHHH
Confidence 333333344445589999776 22 45788999999773 23468888999999999999999999999
Q ss_pred hhhccccce
Q 023149 274 NKFRGKSIW 282 (286)
Q Consensus 274 ~KL~~~~~~ 282 (286)
+-|.....|
T Consensus 154 ~~l~~~~~~ 162 (163)
T COG1956 154 ALLEKSLAF 162 (163)
T ss_pred HHHHHHhcc
Confidence 988766554
No 11
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=73.61 E-value=30 Score=35.06 Aligned_cols=132 Identities=11% Similarity=-0.000 Sum_probs=80.2
Q ss_pred ccCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEE--E-eeeecCCC----CCChHHHHHHHHHhhhhcccccCC-Cc
Q 023149 135 SQNISDALKENLAWATYVLLRNTNSISVLISIRGELC--V-RGYWQTPD----GASKTQLLEWFERQIENIGLSDLK-DS 206 (286)
Q Consensus 135 ~~~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll--~-RG~~~~p~----~~~~g~I~~~~~~~~~~~~Lv~L~-~t 206 (286)
+.++.+.+..=+..+.+.+- ....++.++.++.+. + .|...... ....|++++.+.++++..-..+.. ..
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 355556656555422 2 34322111 233455767776655544222221 11
Q ss_pred ccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccc
Q 023149 207 LYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK 279 (286)
Q Consensus 207 ~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~ 279 (286)
.+|++.... .-.-.|..|+|+.||--. .+.-|+|-+-+..+..|++.|...++.+|+-+..+
T Consensus 94 ~~~~~~~~~---~~~~~gi~S~l~vPL~~~--------~~~~GvL~l~~~~~~~f~~~~~~~l~~~a~~~a~A 155 (509)
T PRK05022 94 DPYDGLIPG---VQESLPVHDCMGLPLFVD--------GRLIGALTLDALDPGQFDAFSDEELRALAALAAAT 155 (509)
T ss_pred ccccccccc---ccccCCcceEEEEEEEEC--------CEEEEEEEEeeCCCCcCCHHHHHHHHHHHHHHHHH
Confidence 123222220 112347789999998552 23479999999889999999999999998765543
No 12
>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=60.38 E-value=14 Score=32.59 Aligned_cols=78 Identities=23% Similarity=0.334 Sum_probs=47.7
Q ss_pred HHHHHhhhccccEEEEEECCEEEEeeeecCCCCCChHHHHHHHHHhhhh-cc-cccCCCcccccCCccccccccCCCCCc
Q 023149 149 ATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIEN-IG-LSDLKDSLYFPQSADAGQWEMLPKGTC 226 (286)
Q Consensus 149 aS~~LLtnT~a~svlV~~~g~ll~RG~~~~p~~~~~g~I~~~~~~~~~~-~~-Lv~L~~t~lyPgr~E~~~~~~LP~ntq 226 (286)
....|++-..|.++.|+++|++...|-. |+.-.--+|.+|+.+.... .+ --+|. ..||+-.. +.+...
T Consensus 25 ~~~~ll~l~~AdG~al~~~g~~~~~G~~--P~~~~i~~L~~wl~~~~~~~v~~T~~L~--~~~p~~~~------~~~~aa 94 (182)
T PF00360_consen 25 QAPDLLDLVDADGVALVIDGEVYTFGET--PPEEQIRALAEWLREQADGEVFATDSLS--EDYPDAAA------LAERAA 94 (182)
T ss_dssp TCCCHHHCTT-SEEEEEETTEEEEEESS----HHHHHHHHHHCCCTTT-SEEEESBGG--GTSGGGGG------GCCCHS
T ss_pred ccHHHHhhccCCEEEEEECCEEEEecCC--cCHHHHHHHHHHHHhhCCCccchhhhHh--HhChhhhh------hcccCC
Confidence 4456888899999999999999888975 3332333455555533222 11 11222 33665443 457788
Q ss_pred eeEEEeccCC
Q 023149 227 SVFVQPVIQA 236 (286)
Q Consensus 227 sVlvQPig~~ 236 (286)
|||+.||...
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 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=55.66 E-value=11 Score=40.27 Aligned_cols=39 Identities=18% Similarity=0.365 Sum_probs=34.3
Q ss_pred cCCCCCCCCChhHHHHHHHHHHHHhhhhccCCCCChhhH
Q 023149 52 FGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQL 90 (286)
Q Consensus 52 lgIpg~Dd~~LP~~vG~l~g~Lll~N~~~s~a~~t~aQ~ 90 (286)
++.||||++++|+-.=+.-.+=++-+|+.++.+++|||-
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 458999999999998888888889999999977899993
No 14
>PRK13558 bacterio-opsin activator; Provisional
Probab=51.24 E-value=19 Score=36.71 Aligned_cols=47 Identities=13% Similarity=0.236 Sum_probs=40.5
Q ss_pred ceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023149 226 CSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS 280 (286)
Q Consensus 226 qsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~ 280 (286)
+|+++-||-.+ .+.=|+|.+.+..++.|+..|+.-++.+|+.+..+.
T Consensus 389 ~s~~~vPL~~~--------g~~~GvL~v~~~~~~~f~~~e~~ll~~la~~ia~aI 435 (665)
T PRK13558 389 SAVAAVPLVYR--------ETTYGVLVVYTAEPDEIDDRERVVLEALGRAVGAAI 435 (665)
T ss_pred ceEEEEeEEEC--------CEEEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 39999999652 234799999999999999999999999999987765
No 15
>KOG0429 consensus Ubiquitin-conjugating enzyme-related protein Ft1, involved in programmed cell death [Posttranslational modification, protein turnover, chaperones]
Probab=34.39 E-value=18 Score=34.28 Aligned_cols=23 Identities=52% Similarity=0.785 Sum_probs=19.7
Q ss_pred cceeeeeecCCCC-C-CCCChhHHH
Q 023149 44 NLSVLRFTFGIPG-F-DESYLPRWI 66 (286)
Q Consensus 44 ~~sv~RftlgIpg-~-Dd~~LP~~v 66 (286)
.-+|||||.=||. | ||.+||++|
T Consensus 63 aggVFRFtIliPdnfPdd~dlPrvv 87 (258)
T KOG0429|consen 63 AGGVFRFTILIPDNFPDDSDLPRVV 87 (258)
T ss_pred cCceEEEEEEcCccCCCcCCCCeEE
Confidence 3589999999997 3 799999987
No 16
>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=28.65 E-value=1e+02 Score=32.01 Aligned_cols=47 Identities=21% Similarity=0.378 Sum_probs=36.4
Q ss_pred CceeEEEeccCCCCCCcccccccceEEEEeeC-CccccchhhHHHHHHHHhhhccc
Q 023149 225 TCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSHKDRAWIKAVSNKFRGK 279 (286)
Q Consensus 225 tqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~RafT~kDe~WI~~iA~KL~~~ 279 (286)
..+.+|-|+... .+.-|+++++.+ .++.|+..|..+++.+++.+...
T Consensus 409 ~~~~l~vPL~~~--------~~~~G~l~l~~~~~~~~~~~e~~~lL~~l~~q~a~~ 456 (679)
T TIGR02916 409 PNAWLIVPLISG--------EELVGFVVLARPRTAGEFNWEVRDLLKTAGRQAASY 456 (679)
T ss_pred CCceEEEEeccC--------CEEEEEEEEecCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 456899999763 234799999876 55689999999999998876543
No 17
>PF13334 DUF4094: Domain of unknown function (DUF4094)
Probab=27.16 E-value=50 Score=26.84 Aligned_cols=25 Identities=20% Similarity=0.279 Sum_probs=21.0
Q ss_pred HHHHHHHHHhhhhhhhhhhhhcccC
Q 023149 93 EVLGLSLAAFSVTLPYLGKFLKGAS 117 (286)
Q Consensus 93 evLg~~Laa~~v~L~l~G~~w~~~~ 117 (286)
=++-+|++.||+++.++|++|.--.
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 18
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=20.81 E-value=96 Score=23.54 Aligned_cols=54 Identities=13% Similarity=0.185 Sum_probs=41.3
Q ss_pred ccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcc-ccchhhHHHHHHHHhhhcccc
Q 023149 219 EMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY-AYSHKDRAWIKAVSNKFRGKS 280 (286)
Q Consensus 219 ~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R-afT~kDe~WI~~iA~KL~~~~ 280 (286)
....++..+.++.||... .+.=|.+.+....++ -|++.|+.-+..+|+.+..+.
T Consensus 108 ~~~~~~i~~~l~vPl~~~--------~~~~G~l~~~~~~~~~~~~~~e~~ll~~la~~~a~ai 162 (175)
T COG2203 108 VLLEPPIRSYLGVPLIAQ--------GELLGLLCVHDSEPRRQWSEEELELLEELAEQVAIAI 162 (175)
T ss_pred HHHHHHHHHheeeeeeEC--------CEeeEEeeeeccCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 334444889999998763 134688888888777 599999999999999876553
Done!