Query 023083
Match_columns 287
No_of_seqs 94 out of 96
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:19:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023083.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023083hhsearch_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 3.5E-73 7.6E-78 505.6 19.9 194 62-278 1-195 (195)
2 PF13185 GAF_2: GAF domain; PD 95.3 0.026 5.7E-07 44.4 4.2 54 220-281 94-147 (148)
3 PF13492 GAF_3: GAF domain; PD 94.9 0.097 2.1E-06 40.2 6.4 108 152-281 11-127 (129)
4 smart00065 GAF Domain present 91.9 0.5 1.1E-05 34.8 5.5 49 225-281 90-139 (149)
5 PRK11061 fused phosphoenolpyru 91.8 1.6 3.6E-05 46.6 11.3 128 138-280 17-153 (748)
6 PF01590 GAF: GAF domain; Int 90.6 0.33 7.2E-06 38.3 3.7 84 186-279 56-152 (154)
7 TIGR02851 spore_V_T stage V sp 89.5 3.9 8.5E-05 36.5 9.9 146 116-281 26-179 (180)
8 PRK15429 formate hydrogenlyase 85.2 5.3 0.00012 41.8 9.5 85 185-281 255-341 (686)
9 TIGR01817 nifA Nif-specific re 83.0 12 0.00025 38.0 10.6 83 186-281 73-156 (534)
10 COG1956 GAF domain-containing 74.7 6.1 0.00013 35.4 5.0 75 195-283 88-162 (163)
11 PRK05022 anaerobic nitric oxid 73.6 30 0.00065 35.0 10.2 132 136-280 16-155 (509)
12 PF00360 PHY: Phytochrome regi 61.0 14 0.0003 32.7 4.4 78 150-237 25-104 (182)
13 PF10605 3HBOH: 3HB-oligomer h 54.4 12 0.00025 40.1 3.2 38 52-89 607-644 (690)
14 PRK13558 bacterio-opsin activa 51.8 18 0.0004 36.8 4.1 47 227-281 389-435 (665)
15 KOG0429 Ubiquitin-conjugating 34.1 18 0.00039 34.3 0.8 23 44-66 63-87 (258)
16 TIGR02916 PEP_his_kin putative 27.6 1.1E+02 0.0024 31.8 5.3 47 226-280 409-456 (679)
17 COG2203 FhlA FOG: GAF domain [ 21.2 93 0.002 23.6 2.6 54 220-281 108-162 (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=3.5e-73 Score=505.57 Aligned_cols=194 Identities=38% Similarity=0.552 Sum_probs=185.3
Q ss_pred hhHHHHHHHHHHHHhhhhccCCCCChhhHHHHHHHHHHHHHHhhhhhhhhhhhccccCCCCCCCCCCCeeceEeccCchH
Q 023083 62 LPRWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISD 141 (287)
Q Consensus 62 LP~~vG~l~g~Lll~N~~~s~a~~t~aQ~RsevLg~~Laa~lillP~~G~~Lw~~~~P~~~~~v~l~geq~F~l~~~Lsd 141 (287)
||+++|+++++++++||++++ .+||||+||||||++||+++|| +|. +|++++|++++.+++.|+|+|+|++||||
T Consensus 1 LPl~vG~l~~~lll~N~~~~~-~~t~sq~RaevLg~~ls~~liL---~g~-lw~~l~p~~~~~v~L~G~~~f~l~~~L~~ 75 (195)
T PF11152_consen 1 LPLIVGLLGGSLLLLNRLSGA-DATPSQSRAEVLGLILSAVLIL---TGL-LWQRLKPRSPEAVDLPGEQGFELSPDLSD 75 (195)
T ss_pred CceEehHHHHHHHHhhhcccC-CCCHHHHHHHHHHHHHHHHHHH---HHH-HHhhccCCCCCccCCCCccceEECCCCCH
Confidence 799999999999999997776 6899999999999999999999 994 99999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhccccEEEEEECCEEE-EeeeecCCCCCChHHHHHHHHHhhhhcccccCCCcccccCCccccccc
Q 023083 142 ALKENLAWATYVLLRNTNSISVLISIRGELC-VRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWE 220 (287)
Q Consensus 142 ~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll-~RG~~~~p~~~~~g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~ 220 (287)
++|+|||||||+|||||+|+||+|||||++| +||++++++++++|+||++++++++.+||+|+ .|||||+| |+
T Consensus 76 ~~k~ELAWas~~LLt~T~a~svlV~~~g~~llrrG~~~~~~~~~~g~i~~~~~~~~~~~yL~nl---~lyPGr~E---f~ 149 (195)
T PF11152_consen 76 AAKEELAWASYALLTNTNARSVLVYYDGRVLLRRGILGSPSKFKPGPICQRAMESGKLIYLVNL---KLYPGRVE---FD 149 (195)
T ss_pred HHHHHHHHHHHHHHhhCCceEEEEEECCEEEEEeeccCCCCCcchHHHHHHHHhcCCceecccc---ccCCCchh---hh
Confidence 9999999999999999999999999999966 58999888999999999999998888888777 89999999 89
Q ss_pred cCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhc
Q 023083 221 MLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFR 278 (287)
Q Consensus 221 ~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~ 278 (287)
|||+|||||||||+|+ +||||+|||++||||+|||+||++|||||+
T Consensus 150 ~lP~ntq~VlvqP~g~------------~G~lvlgs~~~R~ft~~D~~Wi~~iA~Kl~ 195 (195)
T PF11152_consen 150 YLPENTQSVLVQPLGQ------------NGVLVLGSNSPRAFTKSDEAWIAGIADKLR 195 (195)
T ss_pred hcCCCCcEEEEEEcCC------------CeEEEEeeCCccccCHHHHHHHHHHHHhcC
Confidence 9999999999999999 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=95.28 E-value=0.026 Score=44.41 Aligned_cols=54 Identities=19% Similarity=0.234 Sum_probs=41.8
Q ss_pred ccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083 220 EMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS 281 (287)
Q Consensus 220 ~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~ 281 (287)
.+.=.|.+++++.||..+ .+.=|+|.+.+..++.||+.|+.+++.+|+-+..++
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=94.91 E-value=0.097 Score=40.17 Aligned_cols=108 Identities=17% Similarity=0.211 Sum_probs=67.3
Q ss_pred HHHhhhccccEEEEE--ECC-E-E-EEeeeecCCC---C-CChHHHHHHHHHhhhhcccccCCCcccccCCccccccccC
Q 023083 152 YVLLRNTNSISVLIS--IRG-E-L-CVRGYWQTPD---G-ASKTQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEML 222 (287)
Q Consensus 152 ~~LLtnT~a~svlV~--~~g-~-l-l~RG~~~~p~---~-~~~g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~L 222 (287)
+.+...+.+..+.|| .++ . + +..++-+.+. . .....++.++.++.+..+ .|+-.+..+
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 445566666665554 434 2 2 2366511111 1 144567667777665432 233222111
Q ss_pred CCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083 223 PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS 281 (287)
Q Consensus 223 P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~ 281 (287)
.+.+++++.||..+ .+.-|+|.+++..++.||++|+..++.+|+-+..+.
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 366899999999999999999999999999876554
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=91.86 E-value=0.5 Score=34.82 Aligned_cols=49 Identities=16% Similarity=0.350 Sum_probs=40.9
Q ss_pred CCceeEEEeccCCCCCCcccccccceEEEEeeC-CccccchhhHHHHHHHHhhhcccc
Q 023083 225 GTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSHKDRAWIKAVSNKFRGKS 281 (287)
Q Consensus 225 ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~RafT~kDe~WI~~iA~KL~~~~ 281 (287)
+..+.++.||..+ .+.-|++.+... .+|.|+..|+..++.+|+.+..+.
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 5
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=91.82 E-value=1.6 Score=46.58 Aligned_cols=128 Identities=11% Similarity=0.170 Sum_probs=80.2
Q ss_pred CchHHHHHHHHHHHHHHhhhccccEEEEEECCE--EEEeeeecCC------CCCC-hHHHHHHHHHhhhhcccccCCCcc
Q 023083 138 NISDALKENLAWATYVLLRNTNSISVLISIRGE--LCVRGYWQTP------DGAS-KTQLLEWFERQIENIGLSDLKDSL 208 (287)
Q Consensus 138 ~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~--ll~RG~~~~p------~~~~-~g~i~~~~~~~~~~~~Lv~L~~t~ 208 (287)
++.+.+..=+..+...+ +...+++.+++.+. +..+...+.+ -.+. ..-++.++.++.+.....|.....
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 2223222211 1122 233678888888888887775433
Q ss_pred cccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccc
Q 023083 209 YFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK 280 (287)
Q Consensus 209 lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~ 280 (287)
.|..+.+ ..-+++.|+++.||-.. .+.=|+|-+....+|.||+.|+.++..+|.-+..+
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 3432222 12467999999999752 24579999999999999999999999999877544
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=90.55 E-value=0.33 Score=38.33 Aligned_cols=84 Identities=18% Similarity=0.223 Sum_probs=55.4
Q ss_pred HHHHHHHHHhhhhcccccCCCcccccCCccccccccC------------CCCCceeEEEeccCCCCCCcccccccceEEE
Q 023083 186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEML------------PKGTCSVFVQPVIQAPNPSAVEVEKIEGFVL 253 (287)
Q Consensus 186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~L------------P~ntqsVlvQPig~~~~~~~~~~~~~~Gvlv 253 (287)
..++..+.+..+...+.+......+...... -..+ ..+..++++-||.. ..+.-|+|.
T Consensus 56 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~--------~g~~~G~l~ 125 (154)
T PF01590_consen 56 ESICGQVLQSREPIVISDVAADPRFAPQIAA--QSALRALSSAERPFLAEYGVRSYLCVPIIS--------GGRLIGVLS 125 (154)
T ss_dssp SSHHHHHHHHTSCEEESSSGGSTTSSCHHHH--HHTTBTTTHHHHHHHHTTTESEEEEEEEEE--------TTEEEEEEE
T ss_pred ccHHHHHHhCCCeEeeccccccccccccccc--cccccccccccccccccccCceeeEeeeec--------ccCcEEEEE
Confidence 3456666676666665555322222221110 0112 56999999999865 234579999
Q ss_pred EeeCCc-cccchhhHHHHHHHHhhhcc
Q 023083 254 LASSMT-YAYSHKDRAWIKAVSNKFRG 279 (287)
Q Consensus 254 lgs~s~-RafT~kDe~WI~~iA~KL~~ 279 (287)
+....+ |.||+.|+..++.+|+.+..
T Consensus 126 l~~~~~~~~~~~~d~~ll~~~a~~~a~ 152 (154)
T PF01590_consen 126 LYRTRPGRPFTEEDLALLESFAQQLAI 152 (154)
T ss_dssp EEEESSSSS--HHHHHHHHHHHHHHHH
T ss_pred EEECCCCCCcCHHHHHHHHHHHHHHHh
Confidence 999999 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=89.49 E-value=3.9 Score=36.49 Aligned_cols=146 Identities=11% Similarity=0.026 Sum_probs=85.5
Q ss_pred cccCCCCCCCCCCCe-eceEeccCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEEE-eeeecCCCCCChHHHHHHHH
Q 023083 116 GASPVSQKSLPESGE-QIFVMSQNISDALKENLAWATYVLLRNTNSISVLISIRGELCV-RGYWQTPDGASKTQLLEWFE 193 (287)
Q Consensus 116 ~~~P~~~~~v~l~ge-q~F~l~~~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll~-RG~~~~p~~~~~g~i~~~~~ 193 (287)
+++++++..+...++ ++..-.-+.-....+...=....|...|.+ +|.|-...++++ -|.-.. ...++++-+...
T Consensus 26 ~i~~gd~~~~~~~~~~~iil~k~~~~~~~~~~A~~~aeII~~~t~~-aVaITDr~~ILA~~G~g~d--~~~~~~is~~t~ 102 (180)
T TIGR02851 26 RIREGDPLEIFTDREGEVILKKYSPIGELGDFAKEYAESLYQSLGH-IVLITDRDTVIAVAGVSKK--EYLNKPISDELE 102 (180)
T ss_pred CCCCCCeEEEEEeCCCEEEEEECCcccchHHHHHHHHHHHHHHhCC-EEEEECCCcEEEEECCChh--hcCCCccCHHHH
Confidence 667777766643332 222222222233444555567899999999 999999999887 786631 111112222233
Q ss_pred Hhhhhccc--ccCCCcccccCCccccccccCCCC--CceeEEEeccCCCCCCcccccccceEEEEeeCCcc--ccchhhH
Q 023083 194 RQIENIGL--SDLKDSLYFPQSADAGQWEMLPKG--TCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY--AYSHKDR 267 (287)
Q Consensus 194 ~~~~~~~L--v~L~~t~lyPgr~E~~~~~~LP~n--tqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R--afT~kDe 267 (287)
+.++.... ++-.+..+||=.. -++ ..+.+|.||-.+ .++-|.|.+- ...+ .+|+.++
T Consensus 103 ~~i~~gk~~~~~~~~~~~i~c~~--------~~~~~l~s~ii~Pl~~~--------g~viGtLkly-~k~~~~~~~~~e~ 165 (180)
T TIGR02851 103 DTMEERKTVILSDTKDGPIEIID--------GQEFEYTSQVIAPIIAE--------GDPIGAVIIF-SKEPGEKLGEVEQ 165 (180)
T ss_pred HHHHcCCEEEecCCccceecccc--------CCCCCcceEEEEEEEEC--------CeEEEEEEEE-ECCccCCCCHHHH
Confidence 33333222 1111111122110 122 579999999763 2346877777 6666 9999999
Q ss_pred HHHHHHHhhhcccc
Q 023083 268 AWIKAVSNKFRGKS 281 (287)
Q Consensus 268 ~WI~~iA~KL~~~~ 281 (287)
.+..++|+=|...+
T Consensus 166 ~la~glA~lLS~QL 179 (180)
T TIGR02851 166 KAAETAAAFLGKQM 179 (180)
T ss_pred HHHHHHHHHHHHhh
Confidence 99999999876543
No 8
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=85.24 E-value=5.3 Score=41.75 Aligned_cols=85 Identities=11% Similarity=0.198 Sum_probs=60.2
Q ss_pred hHHHHHHHHHhhhhcccccCCC-ccccc-CCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcccc
Q 023083 185 KTQLLEWFERQIENIGLSDLKD-SLYFP-QSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAY 262 (287)
Q Consensus 185 ~g~i~~~~~~~~~~~~Lv~L~~-t~lyP-gr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~Raf 262 (287)
.+.+..++.+..+...+ +..+ ..+.+ ++.. .+....++.++++.||... .++-|||.+++...+.|
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 1122 3445678999999999762 34579999998889999
Q ss_pred chhhHHHHHHHHhhhcccc
Q 023083 263 SHKDRAWIKAVSNKFRGKS 281 (287)
Q Consensus 263 T~kDe~WI~~iA~KL~~~~ 281 (287)
+++|..-++.+|+....+.
T Consensus 323 ~~~dl~lL~~iA~~~A~Ai 341 (686)
T PRK15429 323 TTTNLKLLRQIAERVAIAV 341 (686)
T ss_pred CHHHHHHHHHHHHHHHHHH
Confidence 9999999999999887654
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=83.01 E-value=12 Score=37.96 Aligned_cols=83 Identities=8% Similarity=0.123 Sum_probs=57.3
Q ss_pred HHHHHHHHHhhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCC-ccccch
Q 023083 186 TQLLEWFERQIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSM-TYAYSH 264 (287)
Q Consensus 186 g~i~~~~~~~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s-~RafT~ 264 (287)
..++.++.+..++.-+.|..+..-|-.+. .....+++|++|.||..+ .+.=|+|.+.+.. ++.||+
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 hhHHHHHHHHhhhcccc
Q 023083 265 KDRAWIKAVSNKFRGKS 281 (287)
Q Consensus 265 kDe~WI~~iA~KL~~~~ 281 (287)
.|...+..+|+.+..+.
T Consensus 140 ~d~~lL~~lA~~ia~aI 156 (534)
T TIGR01817 140 EEVRFLEMVANLIGQTV 156 (534)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 99999999999877543
No 10
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=74.70 E-value=6.1 Score=35.40 Aligned_cols=75 Identities=15% Similarity=0.212 Sum_probs=55.9
Q ss_pred hhhhcccccCCCcccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHH
Q 023083 195 QIENIGLSDLKDSLYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVS 274 (287)
Q Consensus 195 ~~~~~~Lv~L~~t~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA 274 (287)
+.+...-+..-|..-|||-+. =| ..++|=||.||-.+ .+.=|+|=+=|.++=.||+.||.||+.+|
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 46788999999773 23468888999999999999999999999
Q ss_pred hhhcccccc
Q 023083 275 NKFRGKSIW 283 (287)
Q Consensus 275 ~KL~~~~~~ 283 (287)
+-|.....|
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=73.56 E-value=30 Score=35.03 Aligned_cols=132 Identities=11% Similarity=-0.012 Sum_probs=80.2
Q ss_pred ccCchHHHHHHHHHHHHHHhhhccccEEEEEECCEEE--E-eeeecCCC----CCChHHHHHHHHHhhhhcccccCC-Cc
Q 023083 136 SQNISDALKENLAWATYVLLRNTNSISVLISIRGELC--V-RGYWQTPD----GASKTQLLEWFERQIENIGLSDLK-DS 207 (287)
Q Consensus 136 ~~~Lsd~~k~ELAWaS~~LLtnT~a~svlV~~~g~ll--~-RG~~~~p~----~~~~g~i~~~~~~~~~~~~Lv~L~-~t 207 (287)
+.++.+.+..=+..+.+.+- ....++.++.++.+. + .|...... ....|++++.+.++++..-..+.. ..
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 355566656555422 2 33322111 233455667776655544222221 11
Q ss_pred ccccCCccccccccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhccc
Q 023083 208 LYFPQSADAGQWEMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGK 280 (287)
Q Consensus 208 ~lyPgr~E~~~~~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~ 280 (287)
.+|++... -.-.-.|..|+|+.||--. .+.-|+|-+-+..+..|++.|...++.+|+-+..+
T Consensus 94 ~~~~~~~~---~~~~~~gi~S~l~vPL~~~--------~~~~GvL~l~~~~~~~f~~~~~~~l~~~a~~~a~A 155 (509)
T PRK05022 94 DPYDGLIP---GVQESLPVHDCMGLPLFVD--------GRLIGALTLDALDPGQFDAFSDEELRALAALAAAT 155 (509)
T ss_pred cccccccc---cccccCCcceEEEEEEEEC--------CEEEEEEEEeeCCCCcCCHHHHHHHHHHHHHHHHH
Confidence 12332222 0112347789999998552 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=60.95 E-value=14 Score=32.69 Aligned_cols=78 Identities=23% Similarity=0.334 Sum_probs=47.8
Q ss_pred HHHHHhhhccccEEEEEECCEEEEeeeecCCCCCChHHHHHHHHHhhhh-cc-cccCCCcccccCCccccccccCCCCCc
Q 023083 150 ATYVLLRNTNSISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIEN-IG-LSDLKDSLYFPQSADAGQWEMLPKGTC 227 (287)
Q Consensus 150 aS~~LLtnT~a~svlV~~~g~ll~RG~~~~p~~~~~g~i~~~~~~~~~~-~~-Lv~L~~t~lyPgr~E~~~~~~LP~ntq 227 (287)
....|++-..|.++.|+++|++...|-. |+.-.--+|.+|+.+.... .+ --+|. ..||+-.. +.+...
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 4556888899999999999999888975 3333333455555533222 11 11222 33665444 457788
Q ss_pred eeEEEeccCC
Q 023083 228 SVFVQPVIQA 237 (287)
Q Consensus 228 sVlvQPig~~ 237 (287)
|||+.||...
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=54.40 E-value=12 Score=40.07 Aligned_cols=38 Identities=18% Similarity=0.359 Sum_probs=33.9
Q ss_pred cCCCCCCCCChhHHHHHHHHHHHHhhhhccCCCCChhh
Q 023083 52 FGIPGFDESYLPRWIGYGFGSLIVLNHFAFSNSVTSAQ 89 (287)
Q Consensus 52 lgIpg~Dd~~LP~~vG~l~g~Lll~N~~~s~a~~t~aQ 89 (287)
++.||||++++|+-.=+.-.+=++-+|+.++.+++|||
T Consensus 607 ~~~pG~~~r~VPlh~Y~~qALd~M~a~L~~G~~LPpSQ 644 (690)
T PF10605_consen 607 LDFPGFDTRFVPLHPYFFQALDLMWAHLKSGAALPPSQ 644 (690)
T ss_pred ccCCCCCcccccccHHHHHHHHHHHHHhhcCCCCCccc
Confidence 45899999999999888888888999999997789999
No 14
>PRK13558 bacterio-opsin activator; Provisional
Probab=51.76 E-value=18 Score=36.81 Aligned_cols=47 Identities=13% Similarity=0.236 Sum_probs=40.5
Q ss_pred ceeEEEeccCCCCCCcccccccceEEEEeeCCccccchhhHHHHHHHHhhhcccc
Q 023083 227 CSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTYAYSHKDRAWIKAVSNKFRGKS 281 (287)
Q Consensus 227 qsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~RafT~kDe~WI~~iA~KL~~~~ 281 (287)
+|+++-||-.+ .+.=|+|.+.+..++.|+..|+.-++.+|+.+..+.
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=34.12 E-value=18 Score=34.26 Aligned_cols=23 Identities=52% Similarity=0.785 Sum_probs=19.6
Q ss_pred cceeeeeecCCCC-C-CCCChhHHH
Q 023083 44 NLSVLRFTFGIPG-F-DESYLPRWI 66 (287)
Q Consensus 44 ~~sv~RftlgIpg-~-Dd~~LP~~v 66 (287)
.-+|||||.=||. | ||.+||++|
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=27.56 E-value=1.1e+02 Score=31.80 Aligned_cols=47 Identities=21% Similarity=0.378 Sum_probs=36.4
Q ss_pred CceeEEEeccCCCCCCcccccccceEEEEeeC-CccccchhhHHHHHHHHhhhccc
Q 023083 226 TCSVFVQPVIQAPNPSAVEVEKIEGFVLLASS-MTYAYSHKDRAWIKAVSNKFRGK 280 (287)
Q Consensus 226 tqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~-s~RafT~kDe~WI~~iA~KL~~~ 280 (287)
..+.+|-|+... .+.-|+++++.+ .++.|+..|..+++.+++.+...
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
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=21.16 E-value=93 Score=23.61 Aligned_cols=54 Identities=13% Similarity=0.185 Sum_probs=41.3
Q ss_pred ccCCCCCceeEEEeccCCCCCCcccccccceEEEEeeCCcc-ccchhhHHHHHHHHhhhcccc
Q 023083 220 EMLPKGTCSVFVQPVIQAPNPSAVEVEKIEGFVLLASSMTY-AYSHKDRAWIKAVSNKFRGKS 281 (287)
Q Consensus 220 ~~LP~ntqsVlvQPig~~~~~~~~~~~~~~Gvlvlgs~s~R-afT~kDe~WI~~iA~KL~~~~ 281 (287)
....++..+.++.||... .+.=|.+.+....++ -|++.|+.-+..+|+.+..+.
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!