Query 022619
Match_columns 294
No_of_seqs 92 out of 94
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:55:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022619.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022619hhsearch_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 1.1E-80 2.3E-85 555.3 19.9 195 66-276 1-195 (195)
2 PF13185 GAF_2: GAF domain; PD 96.9 0.0095 2.1E-07 47.0 8.9 71 208-280 73-148 (148)
3 smart00065 GAF Domain present 96.8 0.0081 1.8E-07 44.6 7.8 80 203-282 57-142 (149)
4 PF13492 GAF_3: GAF domain; PD 96.8 0.0068 1.5E-07 46.7 7.4 111 156-281 11-129 (129)
5 PF01590 GAF: GAF domain; Int 96.3 0.013 2.8E-07 46.5 6.4 78 202-279 56-154 (154)
6 PRK11061 fused phosphoenolpyru 94.1 0.84 1.8E-05 48.9 13.1 78 204-281 74-156 (748)
7 TIGR01817 nifA Nif-specific re 93.4 0.98 2.1E-05 45.7 11.7 79 202-280 73-157 (534)
8 TIGR02851 spore_V_T stage V sp 92.4 2.4 5.2E-05 38.0 11.4 116 147-279 54-179 (180)
9 PRK15429 formate hydrogenlyase 90.3 3.3 7.2E-05 43.4 11.7 82 200-281 254-343 (686)
10 COG1956 GAF domain-containing 89.8 1.5 3.4E-05 39.3 7.5 74 203-279 83-160 (163)
11 PRK05022 anaerobic nitric oxid 75.1 43 0.00093 34.0 11.8 131 141-280 17-157 (509)
12 PRK13558 bacterio-opsin activa 60.1 15 0.00033 37.5 5.1 45 237-281 389-437 (665)
13 PF12046 DUF3529: Protein of u 54.9 18 0.00039 32.9 4.1 31 27-57 20-54 (173)
14 PRK10963 hypothetical protein; 49.1 46 0.00099 30.5 5.9 48 235-282 168-219 (223)
15 TIGR02916 PEP_his_kin putative 48.0 2.2E+02 0.0048 29.7 11.3 81 201-281 370-459 (679)
16 COG2203 FhlA FOG: GAF domain [ 42.1 38 0.00083 25.8 3.7 77 205-281 81-164 (175)
17 COG3159 Uncharacterized protei 37.9 75 0.0016 30.0 5.5 51 231-281 159-215 (218)
18 PF00360 PHY: Phytochrome regi 37.1 1.1E+02 0.0024 27.0 6.3 76 154-246 25-103 (182)
19 PRK15429 formate hydrogenlyase 35.2 56 0.0012 34.4 4.7 74 206-280 82-162 (686)
20 PF00481 PP2C: Protein phospha 34.4 1.4E+02 0.0029 27.0 6.5 65 191-257 134-211 (254)
21 PF04340 DUF484: Protein of un 34.3 96 0.0021 28.0 5.5 49 234-282 171-223 (225)
22 PF05309 TraE: TraE protein; 22.1 2.5E+02 0.0053 24.8 5.8 61 104-164 25-87 (187)
23 TIGR02761 TraE_TIGR type IV co 21.2 2.9E+02 0.0062 24.5 6.1 62 104-165 25-88 (181)
No 1
>PF11152 DUF2930: Protein of unknown function (DUF2930); InterPro: IPR021325 This family of proteins has no known function.
Probab=100.00 E-value=1.1e-80 Score=555.34 Aligned_cols=195 Identities=43% Similarity=0.677 Sum_probs=190.6
Q ss_pred hhHHHHHHHHHHHHHHhhhcCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHhhhhcccCCCcccCCCCccceeecCCCCH
Q 022619 66 LPIYVGGASLLAVLFNRTVSGIAPVADASSSQSRADLLAISLAVTSILTGLVWLSIRPKSITVVNPKGVECQMICSYLPD 145 (294)
Q Consensus 66 LP~~vG~l~~~llL~Nr~lsgiAp~~~~t~aQ~RaevLgl~Lsa~liL~Gllw~~~~P~~~~~V~L~G~e~f~l~~~Lsd 145 (294)
||+++|+++++++++||+++ +++||||+|||+||++||++|||+|++|+++||+++++|+|+|+|+|+|++||||
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 LPLIVGLLGGSLLLLNRLSG-----ADATPSQSRAEVLGLILSAVLILTGLLWQRLKPRSPEAVDLPGEQGFELSPDLSD 75 (195)
T ss_pred CceEehHHHHHHHHhhhccc-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCccCCCCccceEECCCCCH
Confidence 69999999999999999776 8999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHhhhccccEEEEEECCeEEEEEeeccCCCCCccchhhcccccchhhHHHHHhhccCceecccccccCC
Q 022619 146 SVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPG 225 (294)
Q Consensus 146 ~~k~ELAWas~~LLtnT~a~svlV~~~G~vllrRG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~nl~lyPG 225 (294)
++|+||||+||+|||||+|+||+|||||+++||||+++++ ++|+||+||+++|++++++||+|++||||
T Consensus 76 ~~k~ELAWas~~LLt~T~a~svlV~~~g~~llrrG~~~~~-----------~~~~~g~i~~~~~~~~~~~yL~nl~lyPG 144 (195)
T PF11152_consen 76 AAKEELAWASYALLTNTNARSVLVYYDGRVLLRRGILGSP-----------SKFKPGPICQRAMESGKLIYLVNLKLYPG 144 (195)
T ss_pred HHHHHHHHHHHHHHhhCCceEEEEEECCEEEEEeeccCCC-----------CCcchHHHHHHHHhcCCceeccccccCCC
Confidence 9999999999999999999999999999999999999864 38999999999999999999999999999
Q ss_pred CCCCCCCCCCCCeeEEEecCCCeEEEEecCCCcccChhhHHHHHHHHHHHH
Q 022619 226 RSELPFLPSNTQAVILQPLGDKGIAIIGGDTIRGFTTSDQSWIAFIGEKLD 276 (294)
Q Consensus 226 r~Ef~~LP~ntqsVlvQPig~~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~ 276 (294)
|+||+|||+|||||||||+|++||+|+|||++||||||||+||++|||||+
T Consensus 145 r~Ef~~lP~ntq~VlvqP~g~~G~lvlgs~~~R~ft~~D~~Wi~~iA~Kl~ 195 (195)
T PF11152_consen 145 RVEFDYLPENTQSVLVQPLGQNGVLVLGSNSPRAFTKSDEAWIAGIADKLR 195 (195)
T ss_pred chhhhhcCCCCcEEEEEEcCCCeEEEEeeCCccccCHHHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999999999999999999985
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=96.85 E-value=0.0095 Score=47.00 Aligned_cols=71 Identities=11% Similarity=0.214 Sum_probs=51.7
Q ss_pred HhhccCceecc-cccccCCCCCCCCCCCCCCeeEEEecCCC----eEEEEecCCCcccChhhHHHHHHHHHHHHHHHh
Q 022619 208 VMRSKAQRYLA-NLLLYPGRSELPFLPSNTQAVILQPLGDK----GIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLA 280 (294)
Q Consensus 208 ~~~~~~~iyL~-nl~lyPGr~Ef~~LP~ntqsVlvQPig~~----Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~ 280 (294)
+++++++++.. +..-+++ .....-.|.+++++.||-.+ |+|.+.+..++.||+.|+.+++.+|+-+...|+
T Consensus 73 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~s~l~vPl~~~~~~~Gvl~l~~~~~~~f~~~~~~~l~~la~~~a~aie 148 (148)
T PF13185_consen 73 VLRTGEPIIINDDDSSFPP--WELARHPGIRSILCVPLRSGGEVIGVLSLYSKEPNAFSEEDLELLEALADQIAIAIE 148 (148)
T ss_dssp HHHHTS-EEESCCCGGGST--THHHCCTT-SEEEEEEEEETTEEEEEEEEEESSTT---HHHHHHHHHHHHHHHHHHH
T ss_pred HHhcCceEEEeCccccccc--hhhhccccCCEEEEEEEeECCEEEEEEEEeeCCCCCcCHHHHHHHHHHHHHHHHHhC
Confidence 37889999998 2222222 22455678999999999654 899999999999999999999999999887764
No 3
>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=96.82 E-value=0.0081 Score=44.58 Aligned_cols=80 Identities=15% Similarity=0.159 Sum_probs=61.0
Q ss_pred hHHHHHhhccCceecccccccCCCCCCCCCC-CCCCeeEEEecCCC----eEEEEecC-CCcccChhhHHHHHHHHHHHH
Q 022619 203 SVYLGVMRSKAQRYLANLLLYPGRSELPFLP-SNTQAVILQPLGDK----GIAIIGGD-TIRGFTTSDQSWIAFIGEKLD 276 (294)
Q Consensus 203 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP-~ntqsVlvQPig~~----Gvlvlgs~-s~R~FT~kDe~WI~~iA~KL~ 276 (294)
+++.+++++++.++..+..-.+-..+....+ .+..+.++.||..+ |++.+... .+|.|++.|+..+..+|+.+.
T Consensus 57 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~Pl~~~~~~~G~l~~~~~~~~~~~~~~~~~~l~~~~~~i~ 136 (149)
T smart00065 57 GLAGRVAETGRPLNIPDVEADPVFALDLLGRYQGVRSFLAVPLVADGELVGVLALHNKDSPRPFTEEDEELLQALANQLA 136 (149)
T ss_pred ChHHHHHHcCCeEEeechhhCCccccccccceeceeeEEEeeeeecCEEEEEEEEEecCCCCCCCHHHHHHHHHHHHHHH
Confidence 5688899999999988876544111112222 23799999998543 78888887 799999999999999999999
Q ss_pred HHHhhc
Q 022619 277 ATLAKY 282 (294)
Q Consensus 277 ~tL~~~ 282 (294)
..+++.
T Consensus 137 ~~l~~~ 142 (149)
T smart00065 137 IALANA 142 (149)
T ss_pred HHHHHH
Confidence 888763
No 4
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=96.78 E-value=0.0068 Score=46.70 Aligned_cols=111 Identities=11% Similarity=0.157 Sum_probs=72.4
Q ss_pred HHHhhhccccEEEEE--ECC--eEEEEEeeccCCCCCccchhhcccccchhhHHHHHhhccCceecccccccCCCCCCCC
Q 022619 156 ESLSAVTCCRSLVVV--YDG--IYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLLLYPGRSELPF 231 (294)
Q Consensus 156 ~~LLtnT~a~svlV~--~~G--~vllrRG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~ 231 (294)
+.+...+.+..+.|+ .++ +..+..+. ........ .++ ..-+++.++.++++.++..+..- +.+
T Consensus 11 ~~l~~~~~~~~~~l~~~d~~~~~~~~~~~~-~~~~~~~~--~l~----~~~~~~~~~~~~~~~~~~~~~~~---~~~--- 77 (129)
T PF13492_consen 11 ELLRELLGADRAALFLLDEDGNRLRVVAGW-GGDPRLSE--SLP----EDDPLIGRALETGEPVSVPDIDE---RDF--- 77 (129)
T ss_dssp HHHHHHST-SEEEEEEEETTCECEEEEEEE-SS-GCGHH--CEE----TTSHHHHHHHHHTS-EEESTCCC----TT---
T ss_pred HHHHHHhCCCEEEEEEEECCCCEEEEEEEe-CCCccccc--cCC----CCccHHHHHHhhCCeEEeccccc---ccC---
Confidence 445566666665543 433 34455665 22111001 111 34577889999999877766422 222
Q ss_pred CCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHHHHhh
Q 022619 232 LPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAK 281 (294)
Q Consensus 232 LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~~ 281 (294)
.+.+++++.||.. -|+|.++....+.||++|+..++.+|+-+..++++
T Consensus 78 --~~~~s~~~vPl~~~~~~~Gvl~~~~~~~~~~~~~d~~~l~~~a~~~a~alen 129 (129)
T PF13492_consen 78 --LGIRSLLVVPLRSRDRVIGVLCLDSREPEEFSDEDLQLLESLANQLAIALEN 129 (129)
T ss_dssp --TTTCEEEEEEEEETTEEEEEEEEEECTTCG-SHHHHHHHHHHHHHHHHHHH-
T ss_pred --CCCCEEEEEEEeECCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHhCC
Confidence 6679999999954 78999999999999999999999999999988763
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=96.29 E-value=0.013 Score=46.50 Aligned_cols=78 Identities=15% Similarity=0.204 Sum_probs=63.9
Q ss_pred hhHHHHHhhccCceecccccccCCCCCC----CCC------------CCCCCeeEEEecCC----CeEEEEecCCC-ccc
Q 022619 202 GSVYLGVMRSKAQRYLANLLLYPGRSEL----PFL------------PSNTQAVILQPLGD----KGIAIIGGDTI-RGF 260 (294)
Q Consensus 202 G~I~~r~~~~~~~iyL~nl~lyPGr~Ef----~~L------------P~ntqsVlvQPig~----~Gvlvlgs~s~-R~F 260 (294)
.++|..++++++.+.+.|..-.|-..+. ..+ ..+..++++.|+.. -|+|.+....+ |.|
T Consensus 56 ~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~g~~~G~l~l~~~~~~~~~ 135 (154)
T PF01590_consen 56 ESICGQVLQSREPIVISDVAADPRFAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISGGRLIGVLSLYRTRPGRPF 135 (154)
T ss_dssp SSHHHHHHHHTSCEEESSSGGSTTSSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEETTEEEEEEEEEEESSSSS-
T ss_pred ccHHHHHHhCCCeEeeccccccccccccccccccccccccccccccccccCceeeEeeeecccCcEEEEEEEECCCCCCc
Confidence 6779999999999999999877765554 223 56999999999954 47999999999 999
Q ss_pred ChhhHHHHHHHHHHHHHHH
Q 022619 261 TTSDQSWIAFIGEKLDATL 279 (294)
Q Consensus 261 T~kDe~WI~~iA~KL~~tL 279 (294)
|+.|...++.+|+.+..++
T Consensus 136 ~~~d~~ll~~~a~~~a~ai 154 (154)
T PF01590_consen 136 TEEDLALLESFAQQLAIAI 154 (154)
T ss_dssp -HHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhhC
Confidence 9999999999999988754
No 6
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=94.07 E-value=0.84 Score=48.87 Aligned_cols=78 Identities=21% Similarity=0.273 Sum_probs=63.4
Q ss_pred HHHHHhhccCceecccccccCCCCCCC-CCCCCCCeeEEEecCCC----eEEEEecCCCcccChhhHHHHHHHHHHHHHH
Q 022619 204 VYLGVMRSKAQRYLANLLLYPGRSELP-FLPSNTQAVILQPLGDK----GIAIIGGDTIRGFTTSDQSWIAFIGEKLDAT 278 (294)
Q Consensus 204 I~~r~~~~~~~iyL~nl~lyPGr~Ef~-~LP~ntqsVlvQPig~~----Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~t 278 (294)
+|.++.++++++.+.|..--|....++ ..-+++.|+++.|+-.+ |+|-+....+|.||+.|+.++..+|.-+..+
T Consensus 74 i~G~Va~tg~pV~V~Dv~~dprf~~~~~~~~~~~~S~L~VPL~~~geVIGVL~v~~~~~~~Fs~~d~~lL~~LA~~aAiA 153 (748)
T PRK11061 74 IVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPIIYRRQLLGVLVVQQRELRQFDESEESFLVTLATQLAAI 153 (748)
T ss_pred hHHHHhccCceEEECCcccCcccccCccccCccceEEEEEEEeeCCEEEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 588999999999999998655432221 22467899999999653 6888889999999999999999999999888
Q ss_pred Hhh
Q 022619 279 LAK 281 (294)
Q Consensus 279 L~~ 281 (294)
++.
T Consensus 154 L~n 156 (748)
T PRK11061 154 LSQ 156 (748)
T ss_pred HHH
Confidence 865
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=93.43 E-value=0.98 Score=45.69 Aligned_cols=79 Identities=10% Similarity=0.143 Sum_probs=60.4
Q ss_pred hhHHHHHhhccCceecccccccCCCCC-CCCCCCCCCeeEEEecCCC----eEEEEecCC-CcccChhhHHHHHHHHHHH
Q 022619 202 GSVYLGVMRSKAQRYLANLLLYPGRSE-LPFLPSNTQAVILQPLGDK----GIAIIGGDT-IRGFTTSDQSWIAFIGEKL 275 (294)
Q Consensus 202 G~I~~r~~~~~~~iyL~nl~lyPGr~E-f~~LP~ntqsVlvQPig~~----Gvlvlgs~s-~R~FT~kDe~WI~~iA~KL 275 (294)
-.+|.++.++++++.+.|...-|-... ......+++++||.||..+ |+|.+.+.. ++.||+.|...+..+|+.+
T Consensus 73 ~gi~g~v~~~~~pvii~Dv~~d~~~~~~~~~~~~~~~S~l~VPL~~~g~viGvL~v~s~~~~~~ft~~d~~lL~~lA~~i 152 (534)
T TIGR01817 73 EGAIGQIVATGNSLVVPDVAAEPLFLDRLSLYDPGPVPFIGVPIKADSETIGVLAADRDFRSRERLEEEVRFLEMVANLI 152 (534)
T ss_pred ccHHHHHHhcCCeEEecccccCchhhhccccccCCcceEEEEEEcCCCEEEEEEEEEeccccccccHHHHHHHHHHHHHH
Confidence 467889999999999999865443211 1233567899999999654 577777764 5788999999999999998
Q ss_pred HHHHh
Q 022619 276 DATLA 280 (294)
Q Consensus 276 ~~tL~ 280 (294)
...+.
T Consensus 153 a~aI~ 157 (534)
T TIGR01817 153 GQTVR 157 (534)
T ss_pred HHHHH
Confidence 87763
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=92.37 E-value=2.4 Score=38.00 Aligned_cols=116 Identities=10% Similarity=-0.016 Sum_probs=78.5
Q ss_pred HHHhHHHHHHHHhhhccccEEEEEECCeEEEEEeeccCCCCCccchhhcccccchhhHHHHHhhccCceeccccc--ccC
Q 022619 147 VVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVMRSKAQRYLANLL--LYP 224 (294)
Q Consensus 147 ~k~ELAWas~~LLtnT~a~svlV~~~G~vllrRG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~~~~~~iyL~nl~--lyP 224 (294)
..+...=.-+.|...|.+ +|.|..+.+++...|.-...-..+ . --+..+++|++++.....+.. +|+
T Consensus 54 ~~~~A~~~aeII~~~t~~-aVaITDr~~ILA~~G~g~d~~~~~--------~--is~~t~~~i~~gk~~~~~~~~~~~i~ 122 (180)
T TIGR02851 54 LGDFAKEYAESLYQSLGH-IVLITDRDTVIAVAGVSKKEYLNK--------P--ISDELEDTMEERKTVILSDTKDGPIE 122 (180)
T ss_pred hHHHHHHHHHHHHHHhCC-EEEEECCCcEEEEECCChhhcCCC--------c--cCHHHHHHHHcCCEEEecCCccceec
Confidence 444445567899999999 999999999998888664421111 1 123467889988877666532 122
Q ss_pred CCCCCCCCCCC--CCeeEEEecCCC----eEEEEecCCCc--ccChhhHHHHHHHHHHHHHHH
Q 022619 225 GRSELPFLPSN--TQAVILQPLGDK----GIAIIGGDTIR--GFTTSDQSWIAFIGEKLDATL 279 (294)
Q Consensus 225 Gr~Ef~~LP~n--tqsVlvQPig~~----Gvlvlgs~s~R--~FT~kDe~WI~~iA~KL~~tL 279 (294)
=. . -++ ..+.++.||-.+ |.|.+- ...+ .||+.++.+..++|+=|..-|
T Consensus 123 c~---~--~~~~~l~s~ii~Pl~~~g~viGtLkly-~k~~~~~~~~~e~~la~glA~lLS~QL 179 (180)
T TIGR02851 123 II---D--GQEFEYTSQVIAPIIAEGDPIGAVIIF-SKEPGEKLGEVEQKAAETAAAFLGKQM 179 (180)
T ss_pred cc---c--CCCCCcceEEEEEEEECCeEEEEEEEE-ECCccCCCCHHHHHHHHHHHHHHHHhh
Confidence 11 0 122 568999999543 445555 5666 999999999999998877644
No 9
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=90.27 E-value=3.3 Score=43.38 Aligned_cols=82 Identities=21% Similarity=0.243 Sum_probs=62.9
Q ss_pred chhhHHHHHhhccCceeccccc---ccC-CCCCCCCCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHH
Q 022619 200 KQGSVYLGVMRSKAQRYLANLL---LYP-GRSELPFLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFI 271 (294)
Q Consensus 200 ~pG~I~~r~~~~~~~iyL~nl~---lyP-Gr~Ef~~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~i 271 (294)
..|.+..+++++++++.+.+.. +.+ ++..++....++.++|+.|+.. -|+|.+++...+.||++|..-++.+
T Consensus 254 ~~~~l~g~V~~~~~p~lv~~~~~d~~~~~~~~~~~~~~~~~~s~l~vPL~~~~~v~GvL~l~~~~~~~F~~~dl~lL~~i 333 (686)
T PRK15429 254 EAGTLTERVFKSKEMLLINLHERDDLAPYERMLFDTWGNQIQTLCLLPLMSGDTMLGVLKLAQCEEKVFTTTNLKLLRQI 333 (686)
T ss_pred cccchHHHHHhcCceEEEECccCcccchhhhhhhhcccccceEEEEEeEEECCEEEEEEEEeeCCCCcCCHHHHHHHHHH
Confidence 3457888999999988775432 111 2233455567899999999843 5899998888899999999999999
Q ss_pred HHHHHHHHhh
Q 022619 272 GEKLDATLAK 281 (294)
Q Consensus 272 A~KL~~tL~~ 281 (294)
|+....+++.
T Consensus 334 A~~~A~Aie~ 343 (686)
T PRK15429 334 AERVAIAVDN 343 (686)
T ss_pred HHHHHHHHHH
Confidence 9999988854
No 10
>COG1956 GAF domain-containing protein [Signal transduction mechanisms]
Probab=89.78 E-value=1.5 Score=39.27 Aligned_cols=74 Identities=16% Similarity=0.244 Sum_probs=62.5
Q ss_pred hHHHHHhhccCceecccccccCCCCCCCCCCCCCCeeEEEecCCCe----EEEEecCCCcccChhhHHHHHHHHHHHHHH
Q 022619 203 SVYLGVMRSKAQRYLANLLLYPGRSELPFLPSNTQAVILQPLGDKG----IAIIGGDTIRGFTTSDQSWIAFIGEKLDAT 278 (294)
Q Consensus 203 ~I~~r~~~~~~~iyL~nl~lyPGr~Ef~~LP~ntqsVlvQPig~~G----vlvlgs~s~R~FT~kDe~WI~~iA~KL~~t 278 (294)
-+|..+-++++.+=.-|..-|||-++=| +.++|=||.|+-.+| +|=+=|.++=.||+.||.|++.+|+-|...
T Consensus 83 GVCg~A~~~~~t~~V~DV~~~~ghiaCD---~as~SEIVvPi~~~g~~iGvlDiDS~~~~~Fd~~D~~~Le~~~~~l~~~ 159 (163)
T COG1956 83 GVCGTAAATGETVRVDDVHAFPGHIACD---AASNSEIVVPIFKDGKLIGVLDIDSPTPGRFDEEDEAGLEKLAALLEKS 159 (163)
T ss_pred chhHHHHhcCCeEEecccccCCCccccc---cccCceEEEEEEECCEEEEEEecCCCCcccCCHHHHHHHHHHHHHHHHH
Confidence 3688888999999999999999988776 468899999996654 555678888899999999999999888765
Q ss_pred H
Q 022619 279 L 279 (294)
Q Consensus 279 L 279 (294)
+
T Consensus 160 ~ 160 (163)
T COG1956 160 L 160 (163)
T ss_pred h
Confidence 4
No 11
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=75.14 E-value=43 Score=34.04 Aligned_cols=131 Identities=14% Similarity=-0.019 Sum_probs=77.6
Q ss_pred CCCCHHHHHhHHHHHHHHhhhccccEEEEEECCeEEEEEeeccCCCCCccchhhcccccc--hhhHHHHHhhccCceecc
Q 022619 141 SYLPDSVVSELLWAWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLK--QGSVYLGVMRSKAQRYLA 218 (294)
Q Consensus 141 ~~Lsd~~k~ELAWas~~LLtnT~a~svlV~~~G~vllrRG~~~~~~~~g~a~~~d~~~~~--pG~I~~r~~~~~~~iyL~ 218 (294)
.|+.+.+..=+..+.+.+- ..+.++.++ +++.+ ..-.... .....+...+. .|+++..++++++.+-..
T Consensus 17 ~d~~e~L~~vl~~l~~~l~--~~~~~l~l~-~~~~l-~~~as~g-----l~~~~~~~~~~~geGP~l~av~~~g~~v~v~ 87 (509)
T PRK05022 17 LPHQDRFQRLLTTLRQVLP--CDASALLRL-DGDQL-VPLAIDG-----LSPDVLGRRFALEEHPRLEAILRAGDPVRFP 87 (509)
T ss_pred CCHHHHHHHHHHHHHHHcC--CCEEEEEec-CCCcE-EEEEEcC-----CChHhhCCccCCCcchHHHHHHhcCCeEEEe
Confidence 4566777777888888883 234444444 44432 2211111 00111222344 456778888878777555
Q ss_pred cccc----cCCCCCCCCCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHHHHh
Q 022619 219 NLLL----YPGRSELPFLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLA 280 (294)
Q Consensus 219 nl~l----yPGr~Ef~~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~ 280 (294)
+..- |++...-.-.-.+..|+|+.|+-- -|+|=+-+..+..|++.|..-+..+|+-+..++.
T Consensus 88 ~~~~~p~~~~~~~~~~~~~~gi~S~l~vPL~~~~~~~GvL~l~~~~~~~f~~~~~~~l~~~a~~~a~Al~ 157 (509)
T PRK05022 88 ADSELPDPYDGLIPGVQESLPVHDCMGLPLFVDGRLIGALTLDALDPGQFDAFSDEELRALAALAAATLR 157 (509)
T ss_pred cCCCCCcccccccccccccCCcceEEEEEEEECCEEEEEEEEeeCCCCcCCHHHHHHHHHHHHHHHHHHH
Confidence 5432 222111012234677999999832 4677787877889999999999999987666554
No 12
>PRK13558 bacterio-opsin activator; Provisional
Probab=60.13 E-value=15 Score=37.48 Aligned_cols=45 Identities=16% Similarity=0.222 Sum_probs=40.3
Q ss_pred CeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHHHHhh
Q 022619 237 QAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDATLAK 281 (294)
Q Consensus 237 qsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~tL~~ 281 (294)
+|+++-||-. =|+|.+.+..++.|+..|+.-++.+|+.+...+..
T Consensus 389 ~s~~~vPL~~~g~~~GvL~v~~~~~~~f~~~e~~ll~~la~~ia~aI~~ 437 (665)
T PRK13558 389 SAVAAVPLVYRETTYGVLVVYTAEPDEIDDRERVVLEALGRAVGAAINA 437 (665)
T ss_pred ceEEEEeEEECCEEEEEEEEeeCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3999999933 47999999999999999999999999999988854
No 13
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=54.89 E-value=18 Score=32.88 Aligned_cols=31 Identities=26% Similarity=0.477 Sum_probs=23.1
Q ss_pred hhhhhhcc-cccccCcccCCCCCccchh---hhhc
Q 022619 27 PRFIRASA-SSQSQGGYRGPKPSQDLVA---DWVM 57 (294)
Q Consensus 27 ~~~~~~~~-~~~~~~~~~~~~p~~~~~~---~wv~ 57 (294)
=+|||||+ |++.+..+..++|..+.+. +|..
T Consensus 20 ~ffiraS~KdRt~~~~~~s~~p~~~~~~~l~~yf~ 54 (173)
T PF12046_consen 20 FFFIRASVKDRTEQVTFESPQPPDEVLEQLKAYFE 54 (173)
T ss_pred HHHHHHhccccEEEEEEEcCCCHHHHHHHHHHHHH
Confidence 47898875 7888889999998766554 5655
No 14
>PRK10963 hypothetical protein; Provisional
Probab=49.06 E-value=46 Score=30.47 Aligned_cols=48 Identities=13% Similarity=0.304 Sum_probs=40.5
Q ss_pred CCCeeEEEecCC---CeEEEEecCCCcccCh-hhHHHHHHHHHHHHHHHhhc
Q 022619 235 NTQAVILQPLGD---KGIAIIGGDTIRGFTT-SDQSWIAFIGEKLDATLAKY 282 (294)
Q Consensus 235 ntqsVlvQPig~---~Gvlvlgs~s~R~FT~-kDe~WI~~iA~KL~~tL~~~ 282 (294)
..+|+.+-|++. -|+|++||.-+.-|++ .|--.++-+|+=+...|.+-
T Consensus 168 ~v~S~AllpL~~~~~~GlLalGS~D~~rF~~~mgT~fL~~la~vvs~~L~~~ 219 (223)
T PRK10963 168 AVGSVAMSLLGSDGDLGVLLFSSRDAQHYQQGQGTQLLQHLALMLPELLERW 219 (223)
T ss_pred cCceeEEEeccCCCceEEEEEeCCChhhcCCCccHHHHHHHHHHHHHHHHHH
Confidence 578999999976 5999999988888875 67789999999988888764
No 15
>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=48.01 E-value=2.2e+02 Score=29.66 Aligned_cols=81 Identities=17% Similarity=0.149 Sum_probs=50.3
Q ss_pred hhhHHHHHhhccCceecccccccCCC---CCC-CCCCCCCCeeEEEecCC----CeEEEEecC-CCcccChhhHHHHHHH
Q 022619 201 QGSVYLGVMRSKAQRYLANLLLYPGR---SEL-PFLPSNTQAVILQPLGD----KGIAIIGGD-TIRGFTTSDQSWIAFI 271 (294)
Q Consensus 201 pG~I~~r~~~~~~~iyL~nl~lyPGr---~Ef-~~LP~ntqsVlvQPig~----~Gvlvlgs~-s~R~FT~kDe~WI~~i 271 (294)
..++|+...+.+.-+-+.+....|-. .+. +.+.....+.+|.|+.. -|+++++.+ +++.|+..|..+++.+
T Consensus 370 ~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~vPL~~~~~~~G~l~l~~~~~~~~~~~e~~~lL~~l 449 (679)
T TIGR02916 370 DSAFCQFLQESGWIINLEEARSEPDHYSGLVLPEWLREIPNAWLIVPLISGEELVGFVVLARPRTAGEFNWEVRDLLKTA 449 (679)
T ss_pred CCHHHHHHHhCCCcccchhhcCCcccccccccchhhhcCCCceEEEEeccCCEEEEEEEEecCCCCCCCCHHHHHHHHHH
Confidence 34567665555444433333322221 112 22223345689999954 467888765 5668999999999999
Q ss_pred HHHHHHHHhh
Q 022619 272 GEKLDATLAK 281 (294)
Q Consensus 272 A~KL~~tL~~ 281 (294)
++.+...+++
T Consensus 450 ~~q~a~~l~~ 459 (679)
T TIGR02916 450 GRQAASYLAQ 459 (679)
T ss_pred HHHHHHHHHH
Confidence 9988777654
No 16
>COG2203 FhlA FOG: GAF domain [Signal transduction mechanisms]
Probab=42.12 E-value=38 Score=25.84 Aligned_cols=77 Identities=12% Similarity=0.169 Sum_probs=53.6
Q ss_pred HHHHhhccCceecccccccCCCCCC--CCCCCCCCeeEEEecCC----CeEEEEecCCCc-ccChhhHHHHHHHHHHHHH
Q 022619 205 YLGVMRSKAQRYLANLLLYPGRSEL--PFLPSNTQAVILQPLGD----KGIAIIGGDTIR-GFTTSDQSWIAFIGEKLDA 277 (294)
Q Consensus 205 ~~r~~~~~~~iyL~nl~lyPGr~Ef--~~LP~ntqsVlvQPig~----~Gvlvlgs~s~R-~FT~kDe~WI~~iA~KL~~ 277 (294)
+..+...++.+-..|...=|...+. ....++..+.++.||-. =|.+.+....++ -|++.|+.-+..+|+.+..
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~vPl~~~~~~~G~l~~~~~~~~~~~~~~e~~ll~~la~~~a~ 160 (175)
T COG2203 81 IGIALREGRPVVVEDILQDPRFRDNPLVLLEPPIRSYLGVPLIAQGELLGLLCVHDSEPRRQWSEEELELLEELAEQVAI 160 (175)
T ss_pred hhhhhcCCceEEeeccccCcccccCHHHHHHHHHHHheeeeeeECCEeeEEeeeeccCCCCCCCHHHHHHHHHHHHHHHH
Confidence 3444555666666666554433322 33444478999999854 467777777766 5999999999999999998
Q ss_pred HHhh
Q 022619 278 TLAK 281 (294)
Q Consensus 278 tL~~ 281 (294)
.+.+
T Consensus 161 ai~~ 164 (175)
T COG2203 161 AIER 164 (175)
T ss_pred HHHH
Confidence 8765
No 17
>COG3159 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.90 E-value=75 Score=29.97 Aligned_cols=51 Identities=24% Similarity=0.382 Sum_probs=43.1
Q ss_pred CCCCC--CCeeEEEecC---CCeEEEEecCCCcccCh-hhHHHHHHHHHHHHHHHhh
Q 022619 231 FLPSN--TQAVILQPLG---DKGIAIIGGDTIRGFTT-SDQSWIAFIGEKLDATLAK 281 (294)
Q Consensus 231 ~LP~n--tqsVlvQPig---~~Gvlvlgs~s~R~FT~-kDe~WI~~iA~KL~~tL~~ 281 (294)
++|+. .+||.|.|++ .-|+|++||--+|.|++ .|--.+..+|+-+..+|++
T Consensus 159 ~~~ea~~vgSvAi~~L~~~~~~gllafgS~D~~hf~~gmGT~fL~~la~vl~~~L~R 215 (218)
T COG3159 159 GLPEAKAVGSVAIVPLGSQAPLGLLAFGSRDPRHFQPGMGTLFLRHLALVLARLLER 215 (218)
T ss_pred cCCcccccceeEEEEccCCCCceEEEecCCCccccCCCcchHHHHHHHHHHHHHHhh
Confidence 44543 6799999998 68999999999999987 4778999999999998875
No 18
>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=37.07 E-value=1.1e+02 Score=27.03 Aligned_cols=76 Identities=16% Similarity=0.239 Sum_probs=47.8
Q ss_pred HHHHHhhhccccEEEEEECCeEEEEEeeccCCCCCccchhhcccccchhhHHHHHh-hccCceeccccc--ccCCCCCCC
Q 022619 154 AWESLSAVTCCRSLVVVYDGIYLLQIGMAAESGNSGEAVIVDASKLKQGSVYLGVM-RSKAQRYLANLL--LYPGRSELP 230 (294)
Q Consensus 154 as~~LLtnT~a~svlV~~~G~vllrRG~~~~~~~~g~a~~~d~~~~~pG~I~~r~~-~~~~~iyL~nl~--lyPGr~Ef~ 230 (294)
....|++-..|.+++|+++|++. ..|-..+.. .--.|+++.. ...+.+|-.+-. .||+-.+
T Consensus 25 ~~~~ll~l~~AdG~al~~~g~~~-~~G~~P~~~-------------~i~~L~~wl~~~~~~~v~~T~~L~~~~p~~~~-- 88 (182)
T PF00360_consen 25 QAPDLLDLVDADGVALVIDGEVY-TFGETPPEE-------------QIRALAEWLREQADGEVFATDSLSEDYPDAAA-- 88 (182)
T ss_dssp TCCCHHHCTT-SEEEEEETTEEE-EEESS--HH-------------HHHHHHHHCCCTTT-SEEEESBGGGTSGGGGG--
T ss_pred ccHHHHhhccCCEEEEEECCEEE-EecCCcCHH-------------HHHHHHHHHHhhCCCccchhhhHhHhChhhhh--
Confidence 45568899999999999999865 568655410 1123445443 355556544433 3886655
Q ss_pred CCCCCCCeeEEEecCC
Q 022619 231 FLPSNTQAVILQPLGD 246 (294)
Q Consensus 231 ~LP~ntqsVlvQPig~ 246 (294)
+.+..-+||+.||..
T Consensus 89 -~~~~aaGvLai~l~~ 103 (182)
T PF00360_consen 89 -LAERAAGVLAIPLSS 103 (182)
T ss_dssp -GCCCHSEEEEEEECT
T ss_pred -hcccCCCcEEEECCC
Confidence 457788999999965
No 19
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=35.19 E-value=56 Score=34.40 Aligned_cols=74 Identities=9% Similarity=0.040 Sum_probs=52.6
Q ss_pred HHHhhccCceecccccc---cCCCCCCCCCCCCCCeeEEEecCC----CeEEEEecCCCcccChhhHHHHHHHHHHHHHH
Q 022619 206 LGVMRSKAQRYLANLLL---YPGRSELPFLPSNTQAVILQPLGD----KGIAIIGGDTIRGFTTSDQSWIAFIGEKLDAT 278 (294)
Q Consensus 206 ~r~~~~~~~iyL~nl~l---yPGr~Ef~~LP~ntqsVlvQPig~----~Gvlvlgs~s~R~FT~kDe~WI~~iA~KL~~t 278 (294)
..+++++++.++.+..+ ||...+....| ...+.+-.||-. =|+|.+-+...+.||..|+.=+..+|.-....
T Consensus 82 g~vl~~~~~l~~~~~~~~~~~~~l~~~~~~~-~~~~~lgvPl~~~~~v~G~l~l~~~~~~~Ft~~d~~ll~~la~~a~~a 160 (686)
T PRK15429 82 RRILSRPDTLHCSYEEFCETWPQLAAGGLYP-KFGHYCLMPLAAEGHIFGGCEFIRYDDRPWSEKEFNRLQTFTQIVSVV 160 (686)
T ss_pred eEEeecCceEEEchHHhhhccHHHhhccccc-CccceEEeceeeCCeeEEEEEEEEcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 34677788888777665 66666664443 233466679844 46888888889999999999998877766655
Q ss_pred Hh
Q 022619 279 LA 280 (294)
Q Consensus 279 L~ 280 (294)
++
T Consensus 161 ie 162 (686)
T PRK15429 161 TE 162 (686)
T ss_pred HH
Confidence 53
No 20
>PF00481 PP2C: Protein phosphatase 2C; InterPro: IPR001932 This domain is found in protein phosphatase 2C, as well as other proteins eg. pyruvate dehydrogenase (lipoamide)-phosphatase (3.1.3.43 from EC), adenylate cyclase (4.6.1.1 from EC) and some bacterial stage II sporulation E proteins (3.1.3.16 from EC). Protein phosphatase 2C (PP2C) is one of the four major classes of mammalian serine/threonine specific protein phosphatases (3.1.3.16 from EC). PP2C [] is a monomeric enzyme of about 42 Kd which shows broad substrate specificity and is dependent on divalent cations (mainly manganese and magnesium) for its activity. Its exact physiological role is still unclear. Three isozymes are currently known in mammals: PP2C-alpha, -beta and -gamma. In yeast, there are at least four PP2C homologs: phosphatase PTC1 [], which has weak tyrosine phosphatase activity in addition to its activity on serines, phosphatases PTC2 and PTC3, and hypothetical protein YBR125c. Isozymes of PP2C are also known from Arabidopsis thaliana (ABI1, PPH1), Caenorhabditis elegans (FEM-2, F42G9.1, T23F11.1), Leishmania chagasi and Paramecium tetraurelia. In A. thaliana, the kinase associated protein phosphatase (KAPP) [] is an enzyme that dephosphorylates the Ser/Thr receptor-like kinase RLK5 and which contains a C-terminal PP2C domain. PP2C does not seem to be evolutionary related to the main family of serine/ threonine phosphatases: PP1, PP2A and PP2B. However, it is significantly similar to the catalytic subunit of pyruvate dehydrogenase phosphatase 3.1.3.43 from EC (PDPC) [], which catalyzes dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex. PDPC is a mitochondrial enzyme and, like PP2C, is magnesium-dependent.; GO: 0003824 catalytic activity; PDB: 2I0O_A 2POP_C 2POM_A 2J4O_A 2I44_B 3MQ3_A 3N3C_A 2PNQ_B 2P8E_A 2IQ1_A ....
Probab=34.43 E-value=1.4e+02 Score=27.00 Aligned_cols=65 Identities=11% Similarity=0.026 Sum_probs=34.4
Q ss_pred chhhcccccchhhHHHHHhhccCcee--------cccccccCCCCCCCC----CCCCCCeeEEEecCCC-eEEEEecCCC
Q 022619 191 AVIVDASKLKQGSVYLGVMRSKAQRY--------LANLLLYPGRSELPF----LPSNTQAVILQPLGDK-GIAIIGGDTI 257 (294)
Q Consensus 191 a~~~d~~~~~pG~I~~r~~~~~~~iy--------L~nl~lyPGr~Ef~~----LP~ntqsVlvQPig~~-Gvlvlgs~s~ 257 (294)
.+..|.....+.+ .+|..+.+..+. |..++-| |..++.. .--..|-|...++.++ .+|||+||--
T Consensus 134 ~Lt~dH~~~~~~E-~~RI~~~gg~v~~~~rv~g~l~~sRal-Gd~~~k~~~~~~v~~~P~i~~~~l~~~d~flvlaSDGl 211 (254)
T PF00481_consen 134 QLTRDHKPSNPDE-RERIRKAGGRVSENGRVNGVLAVSRAL-GDFDLKPPGKPGVIAEPDISEVDLTPDDEFLVLASDGL 211 (254)
T ss_dssp ESS---STTSHHH-HHHHHHTT-GEEETEEETTTBSSSB-E-E-GGGTTCTSSSSB---EEEEEEEBTTEEEEEEE-HHH
T ss_pred ccccccccchhhc-cceeeccccccccchhhhhcccccccc-ccccccccccceeeeecccccccccccceEEEEEcccc
Confidence 5666665555666 577777777666 2333333 5444432 4455667777788665 6999999864
No 21
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=34.28 E-value=96 Score=28.04 Aligned_cols=49 Identities=22% Similarity=0.461 Sum_probs=40.9
Q ss_pred CCCCeeEEEecCC---CeEEEEecCCCcccCh-hhHHHHHHHHHHHHHHHhhc
Q 022619 234 SNTQAVILQPLGD---KGIAIIGGDTIRGFTT-SDQSWIAFIGEKLDATLAKY 282 (294)
Q Consensus 234 ~ntqsVlvQPig~---~Gvlvlgs~s~R~FT~-kDe~WI~~iA~KL~~tL~~~ 282 (294)
+..+|+.+-|+++ -|+|.+||..+--|++ .+--+++-+|+-+...|.+.
T Consensus 171 ~~v~S~AlipL~~~~~~G~LalGS~D~~rF~p~mgT~fL~~La~vv~~~L~r~ 223 (225)
T PF04340_consen 171 AQVGSVALIPLGSGRPIGLLALGSRDPDRFQPDMGTDFLEQLAEVVSAALERW 223 (225)
T ss_dssp CC-SEEEEEEEESSSEEEEEEEEESSTTCCCSTTTTHHHHHHHHHHHHHGGG-
T ss_pred ccccchheeeccCCCceEEEEecCCChhhCCCCccHHHHHHHHHHHHHHHhcc
Confidence 6789999999985 5899999998888876 57789999999999988763
No 22
>PF05309 TraE: TraE protein; InterPro: IPR007973 This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilisation of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression []. The exact function of the TraE protein is unknown.; GO: 0000746 conjugation
Probab=22.08 E-value=2.5e+02 Score=24.81 Aligned_cols=61 Identities=13% Similarity=0.053 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHhhhhcccCCCcccCCCCccceeecCC-CCHHHHHhHHHH-HHHHhhhccc
Q 022619 104 AISLAVTSILTGLVWLSIRPKSITVVNPKGVECQMICSY-LPDSVVSELLWA-WESLSAVTCC 164 (294)
Q Consensus 104 gl~Lsa~liL~Gllw~~~~P~~~~~V~L~G~e~f~l~~~-Lsd~~k~ELAWa-s~~LLtnT~a 164 (294)
++++.+.+++.+.+|..++-...--+++.-.+.|.++.+ .|++-.++++.- .+++++.|+.
T Consensus 25 ~~l~~~~v~l~~~~~~~~~~~~~vivPp~~~~~~~vs~~~as~~Yl~~m~~~~~~L~lNvtP~ 87 (187)
T PF05309_consen 25 LVLLIANVVLGYLLYAASTNQRTVIVPPTLNKPFWVSGNSASAEYLEQMGRYVAQLLLNVTPE 87 (187)
T ss_pred HHHHHHHHHHHHHHHHHhcCCeEEEECCcccccEEEECCcCCHHHHHHHHHHHHHHhcCCChh
Confidence 333444566666677777744444455555788999875 899999999854 4444444443
No 23
>TIGR02761 TraE_TIGR type IV conjugative transfer system protein TraE. TraE is a component of type IV secretion systems involved in conjugative transfer of plasmid DNA. The function of the TraE protein is unknown.
Probab=21.18 E-value=2.9e+02 Score=24.53 Aligned_cols=62 Identities=15% Similarity=0.095 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHhhhhcccCCCcccCCCCccceeecCC-CCHHHHHhHH-HHHHHHhhhcccc
Q 022619 104 AISLAVTSILTGLVWLSIRPKSITVVNPKGVECQMICSY-LPDSVVSELL-WAWESLSAVTCCR 165 (294)
Q Consensus 104 gl~Lsa~liL~Gllw~~~~P~~~~~V~L~G~e~f~l~~~-Lsd~~k~ELA-Was~~LLtnT~a~ 165 (294)
.+.|+++.++...++...+-....-+++...+.|.++.+ .+++=.++++ ...+++|+-|+..
T Consensus 25 ~~~l~~~~ll~~~~~~~~~~~~~iivPp~i~~~~~vs~~~as~~YLe~ma~~~~~L~lNvTP~~ 88 (181)
T TIGR02761 25 SGVLAVNVLLSIVLIVALKKTRTVVVPPTISQAFTVSAASADATYLELMGLYFIQLRLNVTPES 88 (181)
T ss_pred HHHHHHHHHHHHHHHHHcCCceEEEECCCCCccEEEeCCcCCHHHHHHHHHHHHHHhccCChhh
Confidence 445555666666666665533334444566788999875 8888888877 5666666666643
Done!