Query gi|255764506|ref|YP_003065297.2| GTP cyclohydrolase I [Candidatus Liberibacter asiaticus str. psy62] Match_columns 205 No_of_seqs 115 out of 1575 Neff 5.5 Searched_HMMs 39220 Date Tue May 31 14:43:59 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 255764506.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR00063 folE GTP cyclohydrol 100.0 0 0 552.9 17.2 180 21-203 1-183 (183) 2 PRK09347 folE GTP cyclohydrola 100.0 0 0 522.6 21.2 186 14-203 1-186 (186) 3 COG0302 FolE GTP cyclohydrolas 100.0 0 0 522.9 19.6 187 14-204 8-195 (195) 4 cd00642 GTP_cyclohydro1 GTP cy 100.0 0 0 518.2 21.5 184 17-203 2-185 (185) 5 PRK12606 GTP cyclohydrolase I; 100.0 0 0 517.6 21.6 184 17-203 1-184 (185) 6 KOG2698 consensus 100.0 0 0 468.6 12.6 185 16-204 62-247 (247) 7 pfam01227 GTP_cyclohydroI GTP 100.0 5.1E-34 1.3E-38 231.7 11.7 86 100-185 1-86 (86) 8 PRK13258 7-cyano-7-deazaguanin 98.0 9E-05 2.3E-09 50.7 10.0 99 61-160 9-107 (127) 9 TIGR03139 QueF-II 7-cyano-7-de 97.9 0.00026 6.5E-09 47.9 10.0 93 67-160 5-97 (115) 10 cd00651 TFold Tunnelling fold 97.4 0.0036 9.3E-08 40.7 10.7 105 81-185 2-122 (122) 11 COG0780 Enzyme related to GTP 97.3 0.0031 7.9E-08 41.2 9.7 82 82-163 41-122 (149) 12 TIGR02750 TraN_Ftype type-F co 54.9 5.9 0.00015 20.9 1.2 16 119-134 592-607 (683) 13 PRK11245 folX D-erythro-7,8-di 52.0 21 0.00054 17.4 3.7 84 80-163 5-104 (120) 14 PRK11792 queF 7-cyano-7-deazag 50.9 22 0.00057 17.3 7.4 69 90-160 177-245 (274) 15 KOG3203 consensus 45.0 25 0.00063 17.0 3.1 46 122-167 20-73 (165) 16 PTZ00126 tyrosyl-tRNA syntheta 44.9 16 0.00041 18.2 2.1 71 82-152 303-374 (399) 17 PRK12355 conjugal transfer mat 44.0 12 0.0003 19.0 1.4 16 119-135 532-547 (612) 18 TIGR00313 cobQ cobyric acid sy 42.0 16 0.0004 18.2 1.7 29 176-205 438-466 (502) 19 PRK05337 beta-hexosaminidase; 41.8 31 0.00079 16.4 3.7 125 26-175 107-260 (336) 20 PRK11593 folB bifunctional dih 40.6 32 0.00082 16.3 4.1 80 82-161 3-98 (119) 21 pfam09710 Trep_dent_lipo Trepo 35.8 12 0.0003 19.0 0.3 75 10-84 160-235 (394) 22 pfam05997 Nop52 Nucleolar prot 34.4 29 0.00074 16.6 2.1 16 15-30 14-29 (212) 23 TIGR02393 RpoD_Cterm RNA polym 33.8 33 0.00084 16.2 2.3 38 16-53 84-125 (240) 24 KOG3230 consensus 32.4 21 0.00055 17.4 1.2 31 15-46 153-183 (224) 25 TIGR01754 flav_RNR ribonucleot 30.8 31 0.0008 16.3 1.8 59 139-200 14-78 (145) 26 cd02691 PurM-like2 AIR synthas 30.6 47 0.0012 15.3 3.1 15 142-156 107-121 (346) 27 COG0399 WecE Predicted pyridox 27.6 53 0.0013 15.0 2.8 87 79-170 190-292 (374) 28 COG2345 Predicted transcriptio 27.1 38 0.00097 15.8 1.7 76 25-102 89-168 (218) 29 cd00915 MD-1_MD-2 MD-1 and MD- 26.8 54 0.0014 14.9 2.4 13 102-114 36-48 (130) 30 pfam09626 DHC Dihaem cytochrom 26.4 55 0.0014 14.8 2.6 46 103-153 6-58 (118) 31 PRK10557 hypothetical protein; 25.8 57 0.0014 14.8 3.5 19 174-192 146-164 (178) 32 PRK05568 flavodoxin; Provision 24.9 56 0.0014 14.8 2.2 29 17-45 14-42 (142) 33 pfam06962 rRNA_methylase Putat 24.6 59 0.0015 14.6 3.2 42 104-160 51-92 (140) 34 cd05087 PTKc_Aatyk1_Aatyk3 Cat 24.5 59 0.0015 14.7 2.3 47 107-154 74-120 (269) 35 TIGR02026 BchE magnesium-proto 23.5 63 0.0016 14.5 2.3 47 7-56 346-393 (506) 36 pfam08879 WRC WRC. The WRC dom 23.2 16 0.00041 18.2 -0.8 12 89-100 23-34 (46) 37 TIGR00083 ribF riboflavin bios 22.5 66 0.0017 14.4 2.9 42 70-111 189-232 (296) 38 pfam01340 MetJ Met Apo-repress 22.3 36 0.00092 16.0 0.8 16 21-36 84-99 (104) 39 pfam08921 DUF1904 Domain of un 22.3 53 0.0013 15.0 1.7 37 125-161 59-95 (107) 40 PRK09271 flavodoxin; Provision 22.3 61 0.0016 14.6 2.0 21 17-37 13-33 (160) 41 TIGR00632 vsr DNA mismatch end 21.9 27 0.00068 16.8 0.1 33 20-52 42-81 (143) 42 cd00490 Met_repressor_MetJ Met 21.5 39 0.001 15.7 0.9 16 21-36 84-99 (103) 43 PHA00658 putative lysin 21.1 56 0.0014 14.8 1.6 82 20-102 595-676 (720) 44 COG5441 Uncharacterized conser 20.9 50 0.0013 15.1 1.3 63 82-153 115-178 (401) 45 cd01747 GATase1_Glutamyl_Hydro 20.9 71 0.0018 14.2 2.1 25 86-113 190-214 (273) 46 PRK10416 cell division protein 20.7 46 0.0012 15.3 1.1 22 38-59 202-223 (499) 47 COG1539 FolB Dihydroneopterin 20.5 72 0.0018 14.1 4.0 70 82-151 4-89 (121) 48 pfam03652 UPF0081 Uncharacteri 20.1 52 0.0013 15.0 1.3 32 118-149 67-107 (134) 49 TIGR00250 TIGR00250 conserved 20.1 37 0.00096 15.9 0.5 26 119-144 68-102 (133) 50 pfam07893 DUF1668 Protein of u 20.0 31 0.0008 16.3 0.1 24 97-122 205-229 (330) No 1 >TIGR00063 folE GTP cyclohydrolase I; InterPro: IPR001474 GTP cyclohydrolase I (3.5.4.16 from EC) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects. The comparison of the sequence of the enzyme from bacterial and eukaryotic sources shows that the structure of this enzyme has been extremely well conserved throughout evolution .; GO: 0003934 GTP cyclohydrolase I activity, 0019438 aromatic compound biosynthetic process, 0005737 cytoplasm. Probab=100.00 E-value=0 Score=552.92 Aligned_cols=180 Identities=49% Similarity=0.823 Sum_probs=169.8 Q ss_pred HHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHH-HHHHHCCCCCH-HHHHHHHCCCCCCCCCCEEEECCEEEEEECCCCE Q ss_conf 999999999981478888100112678999999-99976086531-2344320256655667628961805877211002 Q gi|255764506|r 21 AKEAIRVILRWIGDDPDREGLKDTPDRVIKSYK-ELFAGYKQIPT-TQDTSRFHFGEASKYQDMVLIKDISFFSYCEHHI 98 (205) Q Consensus 21 i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~-e~~~Gy~~~~~-~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHl 98 (205) |+.+++++|++|||||+||||.+||+||||||. |+|+||+.++. ...... .+.+++||||+|+||.|||+||||| T Consensus 1 i~~~~~~~l~~iGeD~~regL~~TP~RvAk~~~D~~f~G~~~~~~d~~~~~~---~f~~~~dEMV~V~DI~~~S~CEHHl 77 (183) T TIGR00063 1 IEGAVRQILESIGEDLNREGLLETPKRVAKMYLDELFSGYDEANFDKKIKKA---IFQEKHDEMVLVRDIEFYSTCEHHL 77 (183) T ss_pred CHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHE---ECCCCCCEEEEEECCCEEECCHHHC T ss_conf 9478899999808884667731124899999998864102556332144401---1058852688873241230333330 Q ss_pred EEEEEEEEEEEECCC-CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCCCCE Q ss_conf 346557899996388-5434677999999983154266899999999999732738479999948842522383559985 Q gi|255764506|r 99 LPIWGKIHLAYIPKK-HVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGLT 177 (205) Q Consensus 99 lPf~G~~~IaYiP~~-~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~~s~ 177 (205) +||+|++||||||++ +|+|||||+|||++||||||+|||||.|||.|+++.|+|+||+|+++|+||||.||||++++|. T Consensus 78 vpf~GK~~vaYIPk~GkViGLSKlaR~ve~farRlQvQERLT~QIa~a~~eiL~p~gVaVv~eA~H~Cm~~RGvrk~~s~ 157 (183) T TIGR00063 78 VPFDGKAHVAYIPKDGKVIGLSKLARIVEMFARRLQVQERLTKQIAEALQEILEPRGVAVVVEATHMCMKMRGVRKTGSI 157 (183) T ss_pred CCCCCCEEEEEECCCCEEEEHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEEEEEECEECCCCC T ss_conf 12458258998818964870668889999986265146889999999999873789828998656777653156529981 Q ss_pred EEEEEEEEEECCCHHHHHHHHHHHCC Q ss_conf 99967774430688999999998326 Q gi|255764506|r 178 TVTTAFTGEFSRDKGKTDFFLKMTHN 203 (205) Q Consensus 178 ~~T~~~~G~F~~d~~~r~ef~~li~~ 203 (205) |+||+++|.|++|.++|+|||++|+. T Consensus 158 tvTS~~~G~Fk~~~~TR~EFL~~~~~ 183 (183) T TIGR00063 158 TVTSALRGLFKKDQKTREEFLELIKR 183 (183) T ss_pred EEEEEEECCCHHHHHHHHHHHHHHCC T ss_conf 68865422434246889999997159 No 2 >PRK09347 folE GTP cyclohydrolase I; Provisional Probab=100.00 E-value=0 Score=522.58 Aligned_cols=186 Identities=51% Similarity=0.878 Sum_probs=179.0 Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEE Q ss_conf 52248999999999999814788881001126789999999997608653123443202566556676289618058772 Q gi|255764506|r 14 KKPTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSY 93 (205) Q Consensus 14 ~~~~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~ 93 (205) .+|+.+++++||++||++||+||+|+||.+||+||||||.|+|+||+.+|+..+...|+ +.|++||+++||+|+|+ T Consensus 1 ~~~~~~~~e~av~~iL~~lGeD~~r~gL~~TP~Rvak~~~e~~~Gy~~~p~~~~~~~~~----~~~~~mViv~~I~f~S~ 76 (186) T PRK09347 1 NEPDKEKIEEAVREILEALGEDPDREGLLDTPKRVAKMYEELFSGYANDPKEVLNENFE----EVYDEMVLVKDIEFYST 76 (186) T ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCC----CCCCCEEEEECCCEEEE T ss_conf 96389999999999999967899941234579999999999855436896898741444----56884799927513786 Q ss_pred CCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCC Q ss_conf 11002346557899996388543467799999998315426689999999999973273847999994884252238355 Q gi|255764506|r 94 CEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKR 173 (205) Q Consensus 94 CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~ 173 (205) ||||||||+|++||||+|+++|+|||||+|||++||||||+|||||+|||++|++.|+|+||+|+++|+|+||.||||++ T Consensus 77 CEHHllPf~G~~~VaYiP~~~viGLSKl~Riv~~~arRlQvQErlT~qIa~~l~~~l~p~Gv~V~i~A~H~Cm~~RGv~~ 156 (186) T PRK09347 77 CEHHLLPFIGKAHVAYIPNGKVIGLSKIARIVDFFARRPQVQERLTAQIADALQEILGPRGVAVVIEAEHMCMTMRGVRK 156 (186) T ss_pred CCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCCC T ss_conf 42124534016999996488755655799999999738737889999999999983488968999988984152359889 Q ss_pred CCCEEEEEEEEEEECCCHHHHHHHHHHHCC Q ss_conf 998599967774430688999999998326 Q gi|255764506|r 174 DGLTTVTTAFTGEFSRDKGKTDFFLKMTHN 203 (205) Q Consensus 174 ~~s~~~T~~~~G~F~~d~~~r~ef~~li~~ 203 (205) ++|.|+|++++|+|++|+++|+|||++|+. T Consensus 157 ~~s~t~Ts~~~G~F~~d~~~R~Efl~~i~~ 186 (186) T PRK09347 157 PGSKTVTSALRGLFKTDPATRAEFLSLIRH 186 (186) T ss_pred CCCEEEEEEEEEEECCCHHHHHHHHHHHCC T ss_conf 997499978788867898999999998429 No 3 >COG0302 FolE GTP cyclohydrolase I [Coenzyme metabolism] Probab=100.00 E-value=0 Score=522.86 Aligned_cols=187 Identities=49% Similarity=0.884 Sum_probs=174.4 Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHH-HHHHHCCCCCCCCCCEEEECCEEEEE Q ss_conf 52248999999999999814788881001126789999999997608653123-44320256655667628961805877 Q gi|255764506|r 14 KKPTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQ-DTSRFHFGEASKYQDMVLIKDISFFS 92 (205) Q Consensus 14 ~~~~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~-~~~~~~~~~~~~~~~mVvv~~I~f~S 92 (205) +..+.+++++||++||+++||||+||||.+||+||||||.|+|+||+.+|... +...| .+..++||+++||+||| T Consensus 8 ~~~~~e~~e~avr~lL~~~Gedp~reGL~~TP~RVak~~~e~f~G~~~~~~~~~l~~~f----e~~~~emVlvkdI~f~S 83 (195) T COG0302 8 RETDAERIEAAVRELLEALGEDPDREGLLETPKRVAKAYRELFSGYDEDPAEIVLEATF----EEDHDEMVLVKDIEFYS 83 (195) T ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCC----CCCCCCEEEEECCCEEE T ss_conf 33348999999999999827997700334548999999999970007995786640421----23677589995441266 Q ss_pred ECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCC Q ss_conf 21100234655789999638854346779999999831542668999999999997327384799999488425223835 Q gi|255764506|r 93 YCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIK 172 (205) Q Consensus 93 ~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~ 172 (205) +||||||||+|++||||||+|+|+|||||+|+|++||||||+|||||.|||++|++.|+|+||+|+|+|+||||.||||+ T Consensus 84 ~CEHHllPf~GkahVAYiP~gkV~GlSKiaRiV~~~arR~QvQErlT~qIA~al~~~L~p~GVaVvieA~HmCm~mRGv~ 163 (195) T COG0302 84 LCEHHLLPFFGKAHVAYIPDGKVIGLSKIARIVDIFARRLQVQERLTEQIADALQEILKPRGVAVVIEAEHMCMSMRGVR 163 (195) T ss_pred ECCCCCCCCCCEEEEEECCCCCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEHHCCCC T ss_conf 23544243246589998269805207999999999961368999999999999998608685499997777120222746 Q ss_pred CCCCEEEEEEEEEEECCCHHHHHHHHHHHCCC Q ss_conf 59985999677744306889999999983268 Q gi|255764506|r 173 RDGLTTVTTAFTGEFSRDKGKTDFFLKMTHNQ 204 (205) Q Consensus 173 ~~~s~~~T~~~~G~F~~d~~~r~ef~~li~~~ 204 (205) +++|.|+|++++|.|++|+++|.|||++|+.+ T Consensus 164 k~~s~t~Ts~~~G~F~~~~~~R~efl~li~~~ 195 (195) T COG0302 164 KPGSSTVTSALRGLFKEDAKTRAEFLRLIKGH 195 (195) T ss_pred CCCCEEEEEEEEEEECCCHHHHHHHHHHHHCC T ss_conf 89965888765435536888899999987359 No 4 >cd00642 GTP_cyclohydro1 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In vertebrates and insects it is the biosynthtic precursor of tetrahydrobiopterin (BH4) which is involved in the formation of catacholamines, nitric oxide, and the stimulation of T lymphocytes. The biosynthetic reaction of BH4 is controlled by a regulatory protein GFRP which mediates feedback inhibition of GTP-CH-I by BH4. This inhibition is reversed by phenylalanine. The decameric GTP-CH-I forms a complex with two pentameric GFRP in the presence of phenylalanine or a combination of GTP and BH4, respectively. Probab=100.00 E-value=0 Score=518.21 Aligned_cols=184 Identities=49% Similarity=0.864 Sum_probs=174.3 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 48999999999999814788881001126789999999997608653123443202566556676289618058772110 Q gi|255764506|r 17 TVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEH 96 (205) Q Consensus 17 ~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEH 96 (205) .++++++||++||++||+||+|+||.+||+||||||.|+|+||+.++.......++ +++|++||+++||+|+|+||| T Consensus 2 ~i~~ie~av~~iL~~lGeD~~r~gL~~TP~Rvak~~~e~~~G~~~~~~~~~~~~~~---~~~~~~~V~~~~I~f~S~CEH 78 (185) T cd00642 2 RLEKIAAAVREILELLGEDPNREGLLETPERVAKAYQEITSGYDQALNDPKNTAIF---DEDHDEMVIVKDITLFSMCEH 78 (185) T ss_pred HHHHHHHHHHHHHHHHCCCCCCCHHHHCHHHHHHHHHHHHHCCCCCCHHHHCCCCC---CCCCCEEEEEECCCEEEECCC T ss_conf 58999999999999967999950013579999999999973717892055316676---778871799918247884255 Q ss_pred CEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCCCC Q ss_conf 02346557899996388543467799999998315426689999999999973273847999994884252238355998 Q gi|255764506|r 97 HILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGL 176 (205) Q Consensus 97 HllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~~s 176 (205) |||||+|++||||+|+++|+|||||+|||++||||||+|||||+|||++|++.|+|+||+|+++|+|+||.||||++++| T Consensus 79 HllPf~G~~~VaYiP~~~viGLSKl~RiV~~~arRlQvQErlT~qIa~~l~~~l~~~gV~V~ieA~H~Cm~~RGv~~~~s 158 (185) T cd00642 79 HLVPFYGKVHIAYIPKDKVIGLSKLARIVEFFSRRLQVQERLTKQIAVAIQEILGPQGVAVVIEATHMCMVMRGVRKPGS 158 (185) T ss_pred CCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCCCCCC T ss_conf 66616668999997688504389999999999648689989999999999984098978999998983176618889997 Q ss_pred EEEEEEEEEEECCCHHHHHHHHHHHCC Q ss_conf 599967774430688999999998326 Q gi|255764506|r 177 TTVTTAFTGEFSRDKGKTDFFLKMTHN 203 (205) Q Consensus 177 ~~~T~~~~G~F~~d~~~r~ef~~li~~ 203 (205) .|+|++++|+|++|+++|+|||++|+. T Consensus 159 ~t~T~~~~G~F~~d~~~R~Efl~~i~~ 185 (185) T cd00642 159 KTVTSAMLGVFKEDPKTREEFLRLIRK 185 (185) T ss_pred EEEEEEEEEEECCCHHHHHHHHHHHCC T ss_conf 399988788947898999999997459 No 5 >PRK12606 GTP cyclohydrolase I; Reviewed Probab=100.00 E-value=0 Score=517.62 Aligned_cols=184 Identities=43% Similarity=0.753 Sum_probs=174.9 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 48999999999999814788881001126789999999997608653123443202566556676289618058772110 Q gi|255764506|r 17 TVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEH 96 (205) Q Consensus 17 ~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEH 96 (205) |.+++++||++||++||+||+|+||.+||+||||||.|+|+||..+|+..+...+ ..+++++||+++||+|+|+||| T Consensus 1 D~~~ie~av~~lL~~lGeD~~regL~~TP~Rvak~~~e~~~G~~~~p~~~~~~~~---~~~~~~~mVvv~~I~f~S~CEH 77 (185) T PRK12606 1 DPPALEAAYREILEALGEDPDREGLLDTPQRAAKAMQYLCDGYEQDPAEAVNGAL---FDSDNDEMVIVRDIELYSLCEH 77 (185) T ss_pred CHHHHHHHHHHHHHHHCCCCCCCCHHHCHHHHHHHHHHHHCCCCCCHHHHCCCCC---CCCCCCCEEEEECCCEEEECCC T ss_conf 9789999999999996799996310358999999999995686789578504667---7788884699818526785343 Q ss_pred CEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCCCC Q ss_conf 02346557899996388543467799999998315426689999999999973273847999994884252238355998 Q gi|255764506|r 97 HILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGL 176 (205) Q Consensus 97 HllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~~s 176 (205) |||||+|++||||||+++|+|||||+|||++||||||+|||||+|||++|++.|+|+||+|+++|+|+||.||||++++| T Consensus 78 HllPf~G~ahVaYiP~~~viGLSKl~Riv~~~arRlQ~QErlT~qIa~~l~~~l~~~gVaV~i~A~H~Cm~~RGv~~~~s 157 (185) T PRK12606 78 HLLPFIGKAHVAYLPGGRVLGLSKIARIVDMFARRLQIQENLTRQIATAVVTVTQARGVAVVIEAEHMCMMMRGVEKQNS 157 (185) T ss_pred CCEEEEEEEEEEEECCCCEECHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCCCCCC T ss_conf 42047768999996898013568999999999728548989999999999984198978999998982074459889997 Q ss_pred EEEEEEEEEEECCCHHHHHHHHHHHCC Q ss_conf 599967774430688999999998326 Q gi|255764506|r 177 TTVTTAFTGEFSRDKGKTDFFLKMTHN 203 (205) Q Consensus 177 ~~~T~~~~G~F~~d~~~r~ef~~li~~ 203 (205) .|+|++++|+|++|+++|+|||++|+. T Consensus 158 ~t~T~~~~G~F~~d~~~R~Efl~~i~~ 184 (185) T PRK12606 158 RMITSVMLGAFRDSAQTRNEFLRLIGR 184 (185) T ss_pred EEEEEEEEEEECCCHHHHHHHHHHHCC T ss_conf 499988788957898999999997566 No 6 >KOG2698 consensus Probab=100.00 E-value=0 Score=468.59 Aligned_cols=185 Identities=44% Similarity=0.787 Sum_probs=172.7 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHH-HHHHHCCCCCCCCCCEEEECCEEEEEEC Q ss_conf 248999999999999814788881001126789999999997608653123-4432025665566762896180587721 Q gi|255764506|r 16 PTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQ-DTSRFHFGEASKYQDMVLIKDISFFSYC 94 (205) Q Consensus 16 ~~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~-~~~~~~~~~~~~~~~mVvv~~I~f~S~C 94 (205) ....++..|+++||..|||||+|.||.+||.|+|||+..|+.||++.-... +...| .++++|||+|+||+.|||| T Consensus 62 ~~lp~m~~a~~siL~~LGEdp~RqgLl~TP~R~aKaMl~Ftkgy~~~l~dvlN~Avf----dedhdEmvivkdiemfSmC 137 (247) T KOG2698 62 EVLPEMANAYSSILKSLGEDPNRQGLLKTPERAAKAMLYFTKGYEQNLNDVLNEAVF----DEDHDEMVIVKDIEMFSMC 137 (247) T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCCEEEEEECCHHHHHH T ss_conf 673999999999998736892220222187999999999986288789998521203----6666525888500687776 Q ss_pred CCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCC Q ss_conf 10023465578999963885434677999999983154266899999999999732738479999948842522383559 Q gi|255764506|r 95 EHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRD 174 (205) Q Consensus 95 EHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~ 174 (205) ||||+||+|++||||||+++|+||||++|||++|+||||+|||||+|||.+|.+.++|.||+|++||.||||.||||++. T Consensus 138 EHHLvPF~GkVhIGY~pnkkvlGlSklarIve~ysrrLQVQERlTkQIA~a~s~~v~p~gVaVV~Ea~HmCMVmRGvqK~ 217 (247) T KOG2698 138 EHHLVPFYGKVHIGYIPNKKVLGLSKLARIVEMYSRRLQVQERLTKQIAVALSQAVQPAGVAVVVEATHMCMVMRGVQKI 217 (247) T ss_pred HHCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCEEEEEEECCCCC T ss_conf 64356501257774226874104799999999998999999999999999999861866649998505454321033315 Q ss_pred CCEEEEEEEEEEECCCHHHHHHHHHHHCCC Q ss_conf 985999677744306889999999983268 Q gi|255764506|r 175 GLTTVTTAFTGEFSRDKGKTDFFLKMTHNQ 204 (205) Q Consensus 175 ~s~~~T~~~~G~F~~d~~~r~ef~~li~~~ 204 (205) +|+|+|++++|+|.+|+.+|+|||++|+.+ T Consensus 218 ~SsTvTs~mlGvFr~d~ktReeFl~li~~~ 247 (247) T KOG2698 218 GSSTVTSTMLGVFRDDPKTREEFLNLINSR 247 (247) T ss_pred CCCHHHHHHHHHHCCCCHHHHHHHHHHCCC T ss_conf 762222543210156833699999984269 No 7 >pfam01227 GTP_cyclohydroI GTP cyclohydrolase I. This family includes GTP cyclohydrolase enzymes and a family of related bacterial proteins. Probab=100.00 E-value=5.1e-34 Score=231.73 Aligned_cols=86 Identities=56% Similarity=0.956 Sum_probs=85.2 Q ss_pred EEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEECCCCCCCCEEE Q ss_conf 46557899996388543467799999998315426689999999999973273847999994884252238355998599 Q gi|255764506|r 100 PIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEGQHMCMSMRGIKRDGLTTV 179 (205) Q Consensus 100 Pf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A~H~Cm~~RGv~~~~s~~~ 179 (205) ||+|++||||+|+++|+|||||+|+|++||+|||+|||||+|||++|++.|+|+||+|.++|+|+||.+||++++++.|+ T Consensus 1 P~~G~~~IaYiP~~~viGlskl~riv~~fa~R~q~QErlt~~Ia~~l~~~l~p~gv~V~~~a~H~C~~~RGv~~~~~~~~ 80 (86) T pfam01227 1 PFFGKAHIAYIPNGKVIGLSKLARYVDSFARRLQVQERLTNQIADALVEALKPKGVAVVIEAEHLCMTMRGVRKPGSKTV 80 (86) T ss_pred CEEEEEEEEEECCCEEEEHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEECCCCCCCCCCEEE T ss_conf 94789999995599266078999999999747646899999999999984098979999999997676538889997699 Q ss_pred EEEEEE Q ss_conf 967774 Q gi|255764506|r 180 TTAFTG 185 (205) Q Consensus 180 T~~~~G 185 (205) |++++| T Consensus 81 T~~~~G 86 (86) T pfam01227 81 TSALRG 86 (86) T ss_pred EEEEEC T ss_conf 966379 No 8 >PRK13258 7-cyano-7-deazaguanine reductase; Provisional Probab=98.01 E-value=9e-05 Score=50.68 Aligned_cols=99 Identities=19% Similarity=0.177 Sum_probs=78.4 Q ss_pred CCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHH Q ss_conf 65312344320256655667628961805877211002346557899996388543467799999998315426689999 Q gi|255764506|r 61 QIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTM 140 (205) Q Consensus 61 ~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~ 140 (205) ..|...+..+|+++... .+-.|-..-=.|+|+|.=.=+|=+|++.|-|+|+++++-+-.|-...--|-..---.|..++ T Consensus 9 ~~p~~~~Le~f~n~~~~-~~y~i~~~~~EFtslCPvTgQPDfa~i~I~Y~p~~~~vE~KSLk~Yl~sfRn~~~FHE~~~~ 87 (127) T PRK13258 9 FSPEPEVLETFPNPHPG-RDYTIRFTCPEFTSLCPKTGQPDFATIVIDYIPDKKCVESKSLKLYLFSFRNHGIFHEDCTN 87 (127) T ss_pred CCCCHHHHCCCCCCCCC-CCEEEEEECCCEEECCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHCCHHHHHHHH T ss_conf 99798991036899999-77899994575375277879995599999980798634789999999999861447999999 Q ss_pred HHHHHHHHHCCCCCEEEEEE Q ss_conf 99999997327384799999 Q gi|255764506|r 141 QIAHAIESSTDSKGVAVLIE 160 (205) Q Consensus 141 qIa~~l~~~l~~~gv~V~i~ 160 (205) +|.+.|.+.++|+-..|... T Consensus 88 ~I~~dl~~~~~P~~l~V~~~ 107 (127) T PRK13258 88 RILDDLVALLDPKWLRVGGD 107 (127) T ss_pred HHHHHHHHHCCCCEEEEEEE T ss_conf 99999997559739999999 No 9 >TIGR03139 QueF-II 7-cyano-7-deazaguanine reductase. The enzymatic step represents the first point at which the biosynthesis of queuosine in bacteria and eukaryotes is distinguished from the biosynthesis of archaeosine in archaea. Probab=97.85 E-value=0.00026 Score=47.86 Aligned_cols=93 Identities=17% Similarity=0.182 Sum_probs=76.1 Q ss_pred HHHHHCCCCCCCCCCEEEECCEEEEEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 44320256655667628961805877211002346557899996388543467799999998315426689999999999 Q gi|255764506|r 67 DTSRFHFGEASKYQDMVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAI 146 (205) Q Consensus 67 ~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l 146 (205) +..+|+++... .+-.|-..-=+|+|+|.=-=+|=+|++.|-|+|+++++-+..|-....-|-..---.|..+.+|.+.| T Consensus 5 ~Le~f~N~~~~-~~y~i~~~~pEFtslCPvTgQPDfati~I~Y~p~~~~vE~kSLk~Yl~SfRn~~~FHE~~~~~I~~dl 83 (115) T TIGR03139 5 LLEAFPNPYPD-RDYTIEFVCPEFTSLCPKTGQPDFATIVISYIPDQRCVELKSLKLYLFSFRNHGIFHENVTNTILDDL 83 (115) T ss_pred HCCCCCCCCCC-CCEEEEEECCCEEECCCCCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 71004999999-87799994575377388889996389999984897733889999999997545750899999999999 Q ss_pred HHHCCCCCEEEEEE Q ss_conf 97327384799999 Q gi|255764506|r 147 ESSTDSKGVAVLIE 160 (205) Q Consensus 147 ~~~l~~~gv~V~i~ 160 (205) .+.++|+-+.|... T Consensus 84 ~~~~~P~~l~V~g~ 97 (115) T TIGR03139 84 VKLLQPRYLRVIGD 97 (115) T ss_pred HHHCCCCEEEEEEE T ss_conf 97569629999999 No 10 >cd00651 TFold Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase). They bind to substrates belonging to the purine or pterin families, and share a fold-related binding site with a glutamate or glutamine residue anchoring the substrate and a lot of conserved interactions. They also share a similar oligomerization mode: several T-folds join together to form a beta(2n)alpha(n) barrel, then two barrels join together in a head-to-head fashion to made up the native enzymes. The functional enzyme is a tetramer for UO, a hexamer for PTPS, an octamer for DHNA/DHNTPE and a decamer for GTPCH-1. The substrate is located in a deep and narrow pocket at the interface between monomers. In PTPS, the active site is located at the interface of thr Probab=97.41 E-value=0.0036 Score=40.72 Aligned_cols=105 Identities=19% Similarity=0.124 Sum_probs=83.1 Q ss_pred CEEEECCEEEEEECC----CCEEEEEEEEEEEEECCCCC----------CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHH Q ss_conf 628961805877211----00234655789999638854----------3467799999998315426689999999999 Q gi|255764506|r 81 DMVLIKDISFFSYCE----HHILPIWGKIHLAYIPKKHV----------IGLSKLVRILEVYSRRLQIQERLTMQIAHAI 146 (205) Q Consensus 81 ~mVvv~~I~f~S~CE----HHllPf~G~~~IaYiP~~~v----------iGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l 146 (205) +.+.++|+.+++.+. .+.++-...++|..-.+... +.-..+.+++..+..+.+++|+++.+||..| T Consensus 2 d~i~l~~l~~~~~~G~~~~e~~~~q~~~vdV~~~~d~~~a~~~d~l~~t~~y~~v~~~v~~~~~~~~liE~lae~ia~~i 81 (122) T cd00651 2 DGVRVKDLLKVTRLGFVTLERTVGQIFEVDVTLSWDGKKAAASDDVATDTVYNTIYRLAKEYVEGSQLIERLAEEIAYLI 81 (122) T ss_pred CEEEEECCEEEEEEECCHHHHHCCCEEEEEEEEEECCCCCCCCCCHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHH T ss_conf 88999587999997088899830987999999996373001558888738999999999999736326999999999999 Q ss_pred HHHCC--CCCEEEEEEEEEEEEEECCCCCCCCEEEEEEEEE Q ss_conf 97327--3847999994884252238355998599967774 Q gi|255764506|r 147 ESSTD--SKGVAVLIEGQHMCMSMRGIKRDGLTTVTTAFTG 185 (205) Q Consensus 147 ~~~l~--~~gv~V~i~A~H~Cm~~RGv~~~~s~~~T~~~~G 185 (205) .+... ...|.|.+...|.|+..|+|..+......+..+| T Consensus 82 ~~~f~~~~~~v~v~v~kp~a~~~~~~v~~~~~~~~~~i~r~ 122 (122) T cd00651 82 AEHFLSSVAEVKVEEKKPHAVIPDRGVFKPTDSPGVTIERG 122 (122) T ss_pred HHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEEEECC T ss_conf 98513545389999969999987556533346427999629 No 11 >COG0780 Enzyme related to GTP cyclohydrolase I [General function prediction only] Probab=97.34 E-value=0.0031 Score=41.16 Aligned_cols=82 Identities=18% Similarity=0.199 Sum_probs=74.1 Q ss_pred EEEECCEEEEEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEE Q ss_conf 28961805877211002346557899996388543467799999998315426689999999999973273847999994 Q gi|255764506|r 82 MVLIKDISFFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEG 161 (205) Q Consensus 82 mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A 161 (205) .+.+--=.|.|.|.=-=+|=+|.+.|-|+|++.++-+-.|-+...-|-.+--.+|..+++|++.|.+.++|+-+.|...- T Consensus 41 ~~~l~~~ef~S~CpiTgqPD~~ti~I~Y~p~~~~ve~ksLk~yl~SFR~h~~fHE~c~~~I~~dl~~~l~P~~l~V~~~~ 120 (149) T COG0780 41 LVKLVSPEFKSLCPITGQPDFATIYIEYIPDKACVESKSLKLYLFSFRNHGIFHEQCANRIFNDLKALLKPEYLEVYGKF 120 (149) T ss_pred EEEEECCCCEECCCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEEE T ss_conf 89994162012587769997379999982751434168899999987431148999999999999987398789999998 Q ss_pred EE Q ss_conf 88 Q gi|255764506|r 162 QH 163 (205) Q Consensus 162 ~H 163 (205) .+ T Consensus 121 ~p 122 (149) T COG0780 121 TP 122 (149) T ss_pred EC T ss_conf 53 No 12 >TIGR02750 TraN_Ftype type-F conjugative transfer system mating-pair stabilization protein TraN; InterPro: IPR014121 TraN is a large cysteine-rich outer membrane protein involved in the mating-pair stabilisation (adhesin) component of the F-type conjugative plasmid transfer system. TraN is believed to interact with the core type IV secretion system apparatus through the TraV protein , , .. Probab=54.91 E-value=5.9 Score=20.86 Aligned_cols=16 Identities=44% Similarity=0.563 Sum_probs=15.3 Q ss_pred HHHHHHHHHHHCCCCC Q ss_conf 7799999998315426 Q gi|255764506|r 119 SKLVRILEVYSRRLQI 134 (205) Q Consensus 119 SKl~Riv~~~a~RlQ~ 134 (205) |||||||..-+++.|| T Consensus 592 SKLArIVQ~QG~~gQL 607 (683) T TIGR02750 592 SKLARIVQEQGRKGQL 607 (683) T ss_pred HHHHHHHHHHCCCCCC T ss_conf 0554576741788717 No 13 >PRK11245 folX D-erythro-7,8-dihydroneopterin triphosphate 2'-epimerase; Provisional Probab=52.04 E-value=21 Score=17.43 Aligned_cols=84 Identities=13% Similarity=0.223 Sum_probs=55.8 Q ss_pred CCEEEECCEEEEEEC---CC---CEEEEEEEEEEEEECC--------CCCCCHHHHHHHHHHH--HCCCCCHHHHHHHHH Q ss_conf 762896180587721---10---0234655789999638--------8543467799999998--315426689999999 Q gi|255764506|r 80 QDMVLIKDISFFSYC---EH---HILPIWGKIHLAYIPK--------KHVIGLSKLVRILEVY--SRRLQIQERLTMQIA 143 (205) Q Consensus 80 ~~mVvv~~I~f~S~C---EH---HllPf~G~~~IaYiP~--------~~viGlSKl~Riv~~~--a~RlQ~QErlT~qIa 143 (205) .+.|.++|+.++..= +| +-+|+.=.+.+.|=.+ ...+--+++...+.-+ +++.++.|+|+.+|| T Consensus 5 ~d~I~I~~L~v~~~IGV~~~Er~~~Q~v~idl~i~~d~~~a~~sDdi~dtvdY~~i~~~i~~~v~~~~f~LlE~LA~~ia 84 (120) T PRK11245 5 AAIIRIKNLRLRTFIGIKEEEINNRQDVVINVTIHYPADKARTSDDIDDALNYRTITKNIIQHVENNRFSLLEKLTQDVL 84 (120) T ss_pred CCEEEECCCEEEEEECCCHHHHCCCCEEEEEEEEECCCHHHCCCCCHHHHEEHHHHHHHHHHHHHCCCHHHHHHHHHHHH T ss_conf 55899938799999778989975698899999992374131035778880479999999999996497123999999999 Q ss_pred HHHHHHCCCCCEEEEEEEEE Q ss_conf 99997327384799999488 Q gi|255764506|r 144 HAIESSTDSKGVAVLIEGQH 163 (205) Q Consensus 144 ~~l~~~l~~~gv~V~i~A~H 163 (205) +.+.+.-....|-|.++=-| T Consensus 85 ~~ll~~~~v~~v~v~v~KP~ 104 (120) T PRK11245 85 DIAREHPWVTYAEVEIDKPH 104 (120) T ss_pred HHHHCCCCCCEEEEEEECCH T ss_conf 99964689868999998953 No 14 >PRK11792 queF 7-cyano-7-deazaguanine reductase; Provisional Probab=50.88 E-value=22 Score=17.27 Aligned_cols=69 Identities=23% Similarity=0.338 Sum_probs=57.3 Q ss_pred EEEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEE Q ss_conf 87721100234655789999638854346779999999831542668999999999997327384799999 Q gi|255764506|r 90 FFSYCEHHILPIWGKIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIE 160 (205) Q Consensus 90 f~S~CEHHllPf~G~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~ 160 (205) |.|.|..-=+|=+|.+.|-|-..+ +--..|-+.+--|-.-----|.-..+|...|++.+.|.-..|... T Consensus 177 lRSnCPVT~QPDWatI~I~y~G~~--Id~~~Ll~YliSfR~h~~FHE~CvE~If~dl~~~~~p~~L~V~~~ 245 (274) T PRK11792 177 LKSNCLVTGQPDWGSVQIRYRGKK--IDREGLLRYLISFRQHNEFHEQCVERIFTDIMRFCQPEKLTVYAR 245 (274) T ss_pred HHHCCCCCCCCCCEEEEEEEECCC--CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEE T ss_conf 530687779998189999996874--699999999998721464089999999999997569877999999 No 15 >KOG3203 consensus Probab=44.96 E-value=25 Score=16.99 Aligned_cols=46 Identities=24% Similarity=0.327 Sum_probs=20.3 Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHC--------CCCCEEEEEEEEEEEEE Q ss_conf 99999983154266899999999999732--------73847999994884252 Q gi|255764506|r 122 VRILEVYSRRLQIQERLTMQIAHAIESST--------DSKGVAVLIEGQHMCMS 167 (205) Q Consensus 122 ~Riv~~~a~RlQ~QErlT~qIa~~l~~~l--------~~~gv~V~i~A~H~Cm~ 167 (205) +|+=.++..+-|.-+||+.+||..|...- +..+..|+++|++.-|+ T Consensus 20 aRvW~vvDa~~q~lGrLAs~ia~~L~GkhKPiYhP~~DcGD~VVV~N~~~Ia~s 73 (165) T KOG3203 20 ARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFS 73 (165) T ss_pred HHHHEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCHHHEEC T ss_conf 665125334567568999999999860467764876677887999545564412 No 16 >PTZ00126 tyrosyl-tRNA synthetase; Provisional Probab=44.86 E-value=16 Score=18.17 Aligned_cols=71 Identities=10% Similarity=0.107 Sum_probs=55.2 Q ss_pred EEEECCEEEEEECCCCEEEEEEEEEEEEECC-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCC Q ss_conf 2896180587721100234655789999638-8543467799999998315426689999999999973273 Q gi|255764506|r 82 MVLIKDISFFSYCEHHILPIWGKIHLAYIPK-KHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDS 152 (205) Q Consensus 82 mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~-~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~ 152 (205) +-.+.+-|+..+++|+++|.+|...|-=-++ |--+-.+.+..+..-|...---.-.|-.-+|++|.+.|+| T Consensus 303 p~~ve~NPvLe~~kyvIfP~~~~f~V~R~ek~GG~~ty~s~eeLe~dy~~g~LHP~DLK~ava~~Ln~iL~P 374 (399) T PTZ00126 303 PGVIEGNPIIAYFKSIVFPKFNSFTIERKEKNGGDVTYNTYEELEADYLSGALHPADLKPALAKYLNLMLQP 374 (399) T ss_pred CCCCCCCCHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 988687839999887320457835885675558877155899999999759989899999999999999999 No 17 >PRK12355 conjugal transfer mating pair stabilization protein TraN; Reviewed Probab=43.99 E-value=12 Score=18.95 Aligned_cols=16 Identities=44% Similarity=0.580 Sum_probs=10.4 Q ss_pred HHHHHHHHHHHCCCCCH Q ss_conf 77999999983154266 Q gi|255764506|r 119 SKLVRILEVYSRRLQIQ 135 (205) Q Consensus 119 SKl~Riv~~~a~RlQ~Q 135 (205) |||+|||+--+|. ||. T Consensus 532 SkLArIiqeQgr~-QLg 547 (612) T PRK12355 532 SKLARIIQEQGRP-QLG 547 (612) T ss_pred CHHHHHHHHHHHH-HHC T ss_conf 6999999998599-748 No 18 >TIGR00313 cobQ cobyric acid synthase CobQ; InterPro: IPR004459 Cobyric acid synthase (CobQ) catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolysed for each amidation .; GO: 0003824 catalytic activity, 0009236 cobalamin biosynthetic process. Probab=41.99 E-value=16 Score=18.23 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=13.8 Q ss_pred CEEEEEEEEEEECCCHHHHHHHHHHHCCCC Q ss_conf 859996777443068899999999832688 Q gi|255764506|r 176 LTTVTTAFTGEFSRDKGKTDFFLKMTHNQR 205 (205) Q Consensus 176 s~~~T~~~~G~F~~d~~~r~ef~~li~~~r 205 (205) -...-+++.|.| +|-..|+.|.+++|+|| T Consensus 438 g~~~GtYlHGlF-~N~~fRry~~N~LR~Rk 466 (502) T TIGR00313 438 GNVWGTYLHGLF-ENYEFRRYFLNLLRKRK 466 (502) T ss_pred CEEEECHHCCCH-HHHHHHHHHHHHHCCCC T ss_conf 103121003300-11236667763100026 No 19 >PRK05337 beta-hexosaminidase; Provisional Probab=41.77 E-value=31 Score=16.40 Aligned_cols=125 Identities=17% Similarity=0.167 Sum_probs=69.2 Q ss_pred HHHHHHHCCCCC--------C-------HHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCC---CCCCCCCCEEEECC Q ss_conf 999998147888--------8-------10011267899999999976086531234432025---66556676289618 Q gi|255764506|r 26 RVILRWIGDDPD--------R-------EGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHF---GEASKYQDMVLIKD 87 (205) Q Consensus 26 ~~lL~~LGeDp~--------r-------egL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~---~~~~~~~~mVvv~~ 87 (205) ..-|+++|.|.+ . =...+.|+.|+++=..+.+|+...--....+-|+- ...+.|-++.++ + T Consensus 107 a~eL~a~Gin~nfAPVlDl~~~~~vIg~RsFg~dp~~V~~la~a~i~G~~~~Gv~~~~KHFPGHG~~~~DSH~~lp~~-~ 185 (336) T PRK05337 107 AAELRACGIDLSFAPVLDLDGISAVIGDRAFHRDPQVVAALASAFIDGMHAAGMAATGKHFPGHGAVEADSHVETPVD-E 185 (336) T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEHHCCCCCCCCCCCCCCCCCCCC-C T ss_conf 999998098844065504789986657888889999999999999998885693022121788888778887677777-7 Q ss_pred EEEEEECCCCEEEE----------EEEEEEEEEC-CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEE Q ss_conf 05877211002346----------5578999963-885434677999999983154266899999999999732738479 Q gi|255764506|r 88 ISFFSYCEHHILPI----------WGKIHLAYIP-KKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVA 156 (205) Q Consensus 88 I~f~S~CEHHllPf----------~G~~~IaYiP-~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~ 156 (205) -+.-.+.++.|+|| .-.+||.|-- +....++|+.. |-+-|-+.++=+||. T Consensus 186 ~s~~~l~~~Dl~PF~~li~~~~~~vM~aHv~yp~iD~~PAs~S~~~-------------------i~~iLR~~lgF~Gvi 246 (336) T PRK05337 186 RPLEEIRAEDMAPFRALIDGGLDAVMPAHVIYPQVDPQPAGFSRYW-------------------LQDILRQELGFDGVI 246 (336) T ss_pred CCHHHHHHCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCHHH-------------------HHHHHHHHCCCCCEE T ss_conf 7899998436478999986698616762433466689877379999-------------------999999755998489 Q ss_pred EEEEEEEEEEEECCCCCCC Q ss_conf 9999488425223835599 Q gi|255764506|r 157 VLIEGQHMCMSMRGIKRDG 175 (205) Q Consensus 157 V~i~A~H~Cm~~RGv~~~~ 175 (205) +. -|+.|.|+.... T Consensus 247 iS-----DDL~M~a~~~~~ 260 (336) T PRK05337 247 FS-----DDLSMEGAAVAG 260 (336) T ss_pred EC-----CCCCCCCHHHCC T ss_conf 76-----275861113249 No 20 >PRK11593 folB bifunctional dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase; Provisional Probab=40.60 E-value=32 Score=16.28 Aligned_cols=80 Identities=14% Similarity=0.203 Sum_probs=50.2 Q ss_pred EEEECCEEEEEEC------CCCEEEEEEEEEEEEEC------C--CCCCCHHHHHHHHHHH--HCCCCCHHHHHHHHHHH Q ss_conf 2896180587721------10023465578999963------8--8543467799999998--31542668999999999 Q gi|255764506|r 82 MVLIKDISFFSYC------EHHILPIWGKIHLAYIP------K--KHVIGLSKLVRILEVY--SRRLQIQERLTMQIAHA 145 (205) Q Consensus 82 mVvv~~I~f~S~C------EHHllPf~G~~~IaYiP------~--~~viGlSKl~Riv~~~--a~RlQ~QErlT~qIa~~ 145 (205) .|.++|+.++... -..-+||.=.+.+.+-. + ...+--+.+...+..+ +++..+.|.|+.+||+. T Consensus 3 ~I~I~~L~v~~~iGv~~~Er~~~Q~~~idl~l~~d~~~a~~sDdl~~tvdY~~v~~~i~~~~~~~~~~LiEtLAe~ia~~ 82 (119) T PRK11593 3 IVFIEQLSVITTIGVYDWEQTIEQKLVFDIEMAWDNRKAAKSDDVADCLSYADIAETVISHVEGARFALVERVAEEVAEL 82 (119) T ss_pred EEEECCCEEEEEECCCHHHHCCCCEEEEEEEEEECCHHHCCCCCHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH T ss_conf 99997879999978898996799779999999417246256875443248999999999999679914199999999999 Q ss_pred HHHHCCCCCEEEEEEE Q ss_conf 9973273847999994 Q gi|255764506|r 146 IESSTDSKGVAVLIEG 161 (205) Q Consensus 146 l~~~l~~~gv~V~i~A 161 (205) |.+.-+...|-|.++- T Consensus 83 ll~~f~v~~v~v~v~K 98 (119) T PRK11593 83 LLARFNSPWVRIKLSK 98 (119) T ss_pred HHHHCCCCEEEEEEEC T ss_conf 9965897679999989 No 21 >pfam09710 Trep_dent_lipo Treponema clustered lipoprotein (Trep_dent_lipo). This entry represents a family of six predicted lipoproteins from a region of about 20 tandemly arranged genes in the Treponema denticola genome. Two other neighbouring genes share the lipoprotein signal peptide region but do not show more extensive homology. The function of this locus is unknown. Probab=35.76 E-value=12 Score=19.00 Aligned_cols=75 Identities=13% Similarity=0.104 Sum_probs=52.4 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHH-HHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEE Q ss_conf 3666522489999999999998147888810011267899999-99997608653123443202566556676289 Q gi|255764506|r 10 NMKLKKPTVEEAKEAIRVILRWIGDDPDREGLKDTPDRVIKSY-KELFAGYKQIPTTQDTSRFHFGEASKYQDMVL 84 (205) Q Consensus 10 ~~~~~~~~~~~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~-~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVv 84 (205) +.++-....+.++.-|-..+...-.||+++.+..-=+|+..-| .+-+.+|.+.|...+.-..-++.+.|||+-+| T Consensus 160 E~ni~~i~~~~i~~qvHG~i~e~e~d~~kd~~IklFE~Y~n~~Tk~~~~~~~~y~y~vlDYVkGNFTnSGyDEYiV 235 (394) T pfam09710 160 ELNIGVINEELIENQVHGSVYEMENDPKKDEMIKLFEDYENTYTKVKTNKYKQYDYRVLDYVKGNFTNSGYDEYIV 235 (394) T ss_pred CCCEEEECHHHHHHHHCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEE T ss_conf 4870365035554320326765134857455568899875420231005656675587675324666788643899 No 22 >pfam05997 Nop52 Nucleolar protein,Nop52. Nop52 believed to be involved in the generation of 28S rRNA. Probab=34.39 E-value=29 Score=16.55 Aligned_cols=16 Identities=31% Similarity=0.372 Sum_probs=6.0 Q ss_pred CCCHHHHHHHHHHHHH Q ss_conf 2248999999999999 Q gi|255764506|r 15 KPTVEEAKEAIRVILR 30 (205) Q Consensus 15 ~~~~~~i~~av~~lL~ 30 (205) +..++++-+.++..|. T Consensus 14 k~~Rd~al~~L~~~L~ 29 (212) T pfam05997 14 KETRDKALRSLRKYLS 29 (212) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 1079999999999998 No 23 >TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=33.82 E-value=33 Score=16.23 Aligned_cols=38 Identities=26% Similarity=0.398 Sum_probs=29.4 Q ss_pred CCHHHHHHHHHHHHHHHCCCCCCHHHCC----CHHHHHHHHH Q ss_conf 2489999999999998147888810011----2678999999 Q gi|255764506|r 16 PTVEEAKEAIRVILRWIGDDPDREGLKD----TPDRVIKSYK 53 (205) Q Consensus 16 ~~~~~i~~av~~lL~~LGeDp~regL~~----TP~Rvak~~~ 53 (205) .+++++...-+.|+..+|.||+.|.|.+ ++++|..-.. T Consensus 84 ETINk~~~~~R~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~ 125 (240) T TIGR02393 84 ETINKLIKAERKLLQELGREPTDEELAERMGLPVEKVREIKK 125 (240) T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 788899999899998728899877899870899899999998 No 24 >KOG3230 consensus Probab=32.40 E-value=21 Score=17.38 Aligned_cols=31 Identities=26% Similarity=0.378 Sum_probs=19.2 Q ss_pred CCCHHHHHHHHHHHHHHHCCCCCCHHHCCCHH Q ss_conf 22489999999999998147888810011267 Q gi|255764506|r 15 KPTVEEAKEAIRVILRWIGDDPDREGLKDTPD 46 (205) Q Consensus 15 ~~~~~~i~~av~~lL~~LGeDp~regL~~TP~ 46 (205) ..+.++.++-|...|..||.|.+.+ |..+|. T Consensus 153 ~edEEEtd~lvnqVLDEiGvdl~~q-L~~~P~ 183 (224) T KOG3230 153 DEDEEETDDLVNQVLDEIGVDLASQ-LSSLPS 183 (224) T ss_pred CCHHHHHHHHHHHHHHHHCCCHHHH-HCCCCC T ss_conf 3206779999999999974118888-603763 No 25 >TIGR01754 flav_RNR ribonucleotide reductase-associated flavodoxin, putative; InterPro: IPR010088 This entry represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulphate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation.. Probab=30.76 E-value=31 Score=16.34 Aligned_cols=59 Identities=15% Similarity=0.175 Sum_probs=34.5 Q ss_pred HHHHHHHHHHHCCCCCEEEE-EEEEEEEEEECCCCCCCCEEEEEEEEEEECCC-----HHHHHHHHHH Q ss_conf 99999999973273847999-99488425223835599859996777443068-----8999999998 Q gi|255764506|r 139 TMQIAHAIESSTDSKGVAVL-IEGQHMCMSMRGIKRDGLTTVTTAFTGEFSRD-----KGKTDFFLKM 200 (205) Q Consensus 139 T~qIa~~l~~~l~~~gv~V~-i~A~H~Cm~~RGv~~~~s~~~T~~~~G~F~~d-----~~~r~ef~~l 200 (205) |++||+.|.+.|..+|+-|= |+-.=.-.. -..-+-..-+-.++|.|-.| ...+.+...| T Consensus 14 T~eVA~~I~~~l~~~G~eVDW~~~r~~~La---~~pldPe~ydL~~LGtwT~~~GrTP~e~KdFiaEl 78 (145) T TIGR01754 14 TKEVADIIRDILEKDGHEVDWVEFRISTLA---DAPLDPEDYDLYLLGTWTVERGRTPDEMKDFIAEL 78 (145) T ss_pred HHHHHHHHHHHHHHCCCEEEEEEECCHHHH---CCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHH T ss_conf 789999999999847977676640004642---46789986315774312235789966689999999 No 26 >cd02691 PurM-like2 AIR synthase (PurM) related protein, archaeal subgroup 2 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain. Probab=30.61 E-value=47 Score=15.29 Aligned_cols=15 Identities=13% Similarity=0.448 Sum_probs=5.2 Q ss_pred HHHHHHHHCCCCCEE Q ss_conf 999999732738479 Q gi|255764506|r 142 IAHAIESSTDSKGVA 156 (205) Q Consensus 142 Ia~~l~~~l~~~gv~ 156 (205) |...+....+.-||. T Consensus 107 i~~~m~~aa~~~gV~ 121 (346) T cd02691 107 FTAGVTAVSEATGVP 121 (346) T ss_pred HHHHHHHHHHHCCCC T ss_conf 999999999985998 No 27 >COG0399 WecE Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane] Probab=27.57 E-value=53 Score=14.96 Aligned_cols=87 Identities=21% Similarity=0.277 Sum_probs=53.2 Q ss_pred CCCEEEECCEEEEEECCCCEEEEEEEE----------EEEEECC----CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHH Q ss_conf 676289618058772110023465578----------9999638----85434677999999983154266899999999 Q gi|255764506|r 79 YQDMVLIKDISFFSYCEHHILPIWGKI----------HLAYIPK----KHVIGLSKLVRILEVYSRRLQIQERLTMQIAH 144 (205) Q Consensus 79 ~~~mVvv~~I~f~S~CEHHllPf~G~~----------~IaYiP~----~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~ 144 (205) .++||+-.|=.++.-|. .+.++|.. .+||=-+ ---+|+.+|.|+-++..+|-.+-++..+..++ T Consensus 190 EGGav~tnd~ela~k~~--~lr~hG~~~~~~~~y~~~~~G~N~rm~~iqAAigl~QL~~l~~~~~~R~~~a~~Y~~~l~~ 267 (374) T COG0399 190 EGGAVVTNDEELAEKAR--SLRNHGLSRDAVFKYLHEELGYNYRLTEIQAAIGLAQLERLDEINERRREIAQIYAEALKG 267 (374) T ss_pred CCEEEEECCHHHHHHHH--HHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 75079838899999999--9998376778665643521330038779999999999988899999999999999998610 Q ss_pred H--HHHHCCCCCEEEEEEEEEEEEEECC Q ss_conf 9--9973273847999994884252238 Q gi|255764506|r 145 A--IESSTDSKGVAVLIEGQHMCMSMRG 170 (205) Q Consensus 145 ~--l~~~l~~~gv~V~i~A~H~Cm~~RG 170 (205) . +.-...+.+. ..+.|++....- T Consensus 268 ~~~~~~p~~~~~~---~~~~~~~~i~~~ 292 (374) T COG0399 268 LPGITLPPEPDGA---VHAWHLYTILVD 292 (374) T ss_pred CCCCCCCCCCCCC---EEEEEEEEEEEC T ss_conf 7874335789876---123036689826 No 28 >COG2345 Predicted transcriptional regulator [Transcription] Probab=27.08 E-value=38 Score=15.84 Aligned_cols=76 Identities=14% Similarity=0.119 Sum_probs=32.7 Q ss_pred HHHHHHHHCCCCCCHHHCCC----HHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCCCEEE Q ss_conf 99999981478888100112----67899999999976086531234432025665566762896180587721100234 Q gi|255764506|r 25 IRVILRWIGDDPDREGLKDT----PDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEHHILP 100 (205) Q Consensus 25 v~~lL~~LGeDp~regL~~T----P~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHllP 100 (205) ...+|+.|.++..++.+..- .+|....|.....| +.+....+....+.-+..+|-.-.-.-+..-+++|||| .| T Consensus 89 ~~~~l~~l~~~~G~~~l~~~l~~r~~~~~~~~~~~~~~-~~~~ee~~e~Lv~l~~~~gy~~e~~~~~~~~~~l~e~n-CP 166 (218) T COG2345 89 ALALLDALEETGGEEALNAFLEKRAQAIGAQYRPAMGG-DADLEEKVERLVELLSDLGYMPELRPVDNGRVQLIEHN-CP 166 (218) T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECC-CC T ss_conf 99999999985459999999999999999997624788-89999999999999985786654523589863887418-82 Q ss_pred EE Q ss_conf 65 Q gi|255764506|r 101 IW 102 (205) Q Consensus 101 f~ 102 (205) |+ T Consensus 167 i~ 168 (218) T COG2345 167 IS 168 (218) T ss_pred HH T ss_conf 38 No 29 >cd00915 MD-1_MD-2 MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 directly binds the lipid A moiety of LPS. The TLR4-like receptor, RP105, which mediates LPS-induced lymphocyte proliferation, interacts with MD-1; MD-1 enhances RP105-mediated LPS-induced growth of B cells. These proteins belong to the ML domain family. Probab=26.79 E-value=54 Score=14.90 Aligned_cols=13 Identities=23% Similarity=0.496 Sum_probs=9.3 Q ss_pred EEEEEEEEECCCC Q ss_conf 5578999963885 Q gi|255764506|r 102 WGKIHLAYIPKKH 114 (205) Q Consensus 102 ~G~~~IaYiP~~~ 114 (205) .|.+|++|||..- T Consensus 36 ~~~l~~~~I~R~d 48 (130) T cd00915 36 NGFIRIKFILRRD 48 (130) T ss_pred CEEEEEEEEEHHH T ss_conf 4699999988323 No 30 >pfam09626 DHC Dihaem cytochrome c. Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway. DHC acts as the physiological electron donor for SHP during phototrophic growth. In certain species DHC is found upstream of pfam01292. Probab=26.43 E-value=55 Score=14.84 Aligned_cols=46 Identities=13% Similarity=0.312 Sum_probs=27.7 Q ss_pred EEEEEEEECC-------CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCC Q ss_conf 5789999638-------85434677999999983154266899999999999732738 Q gi|255764506|r 103 GKIHLAYIPK-------KHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSK 153 (205) Q Consensus 103 G~~~IaYiP~-------~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~ 153 (205) |.||+||=|+ .+|+ ..+-++|+....+-+.-..+|-+.|.....+. T Consensus 6 gsCH~AyPP~lLP~~SW~~im-----~~l~~HFG~~asld~~~~~~I~~yL~~naa~~ 58 (118) T pfam09626 6 GSCHMAYPPELLPAASWRKIM-----ADLDDHFGTDASLDPPTRALIWAYLRANAADL 58 (118) T ss_pred CCCCCCCCCCCCCHHHHHHHH-----HHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCC T ss_conf 027740694528999999999-----73775258686878789999999999825334 No 31 >PRK10557 hypothetical protein; Provisional Probab=25.81 E-value=57 Score=14.77 Aligned_cols=19 Identities=5% Similarity=-0.080 Sum_probs=9.3 Q ss_pred CCCEEEEEEEEEEECCCHH Q ss_conf 9985999677744306889 Q gi|255764506|r 174 DGLTTVTTAFTGEFSRDKG 192 (205) Q Consensus 174 ~~s~~~T~~~~G~F~~d~~ 192 (205) ..+...|..+.|.-+.+|. T Consensus 146 ~~~~~~~v~L~~~~~~~P~ 164 (178) T PRK10557 146 GFSPVLTLNLRAASKGEPQ 164 (178) T ss_pred CCCEEEEEEEEEECCCCCC T ss_conf 8843799998552034998 No 32 >PRK05568 flavodoxin; Provisional Probab=24.90 E-value=56 Score=14.79 Aligned_cols=29 Identities=10% Similarity=-0.008 Sum_probs=19.7 Q ss_pred CHHHHHHHHHHHHHHHCCCCCCHHHCCCH Q ss_conf 48999999999999814788881001126 Q gi|255764506|r 17 TVEEAKEAIRVILRWIGDDPDREGLKDTP 45 (205) Q Consensus 17 ~~~~i~~av~~lL~~LGeDp~regL~~TP 45 (205) +.+++.+++.+=|+.-|.+..--.+.++. T Consensus 14 nTe~mA~~Iaegl~~~Gv~V~~~~~~~~~ 42 (142) T PRK05568 14 NTEAMANLIAEGAKENGLEVKLLNVSEAS 42 (142) T ss_pred HHHHHHHHHHHHHHHCCCEEEEEEECCCC T ss_conf 49999999999998669839999800499 No 33 >pfam06962 rRNA_methylase Putative rRNA methylase. This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins. Probab=24.62 E-value=59 Score=14.63 Aligned_cols=42 Identities=14% Similarity=0.338 Sum_probs=26.4 Q ss_pred EEEEEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEE Q ss_conf 789999638854346779999999831542668999999999997327384799999 Q gi|255764506|r 104 KIHLAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIE 160 (205) Q Consensus 104 ~~~IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~ 160 (205) .-+.||+|++- +....+-.-|-.=-++..+.|.|.|+.+++- T Consensus 51 ~FNLGYLPggD---------------k~i~T~~~tTi~Al~~al~lL~~gG~i~i~~ 92 (140) T pfam06962 51 IFNLGYLPGGD---------------KSITTKPDTTLEAIKKLLELLKPGGLIILVI 92 (140) T ss_pred EEECCCCCCCC---------------CCCEECCHHHHHHHHHHHHHHCCCCEEEEEE T ss_conf 99667688999---------------8758777209999999999636698999999 No 34 >cd05087 PTKc_Aatyk1_Aatyk3 Catalytic Domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinases 1 and 3. Protein Tyrosine Kinase (PTK) family; Apoptosis-associated tyrosine kinase 1 (Aatyk1) and Aatyk3; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk1 and Aatyk3 are members of the Aatyk subfamily of proteins. Aatyk3 is a receptor kinase containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk1 has a similar domain arrangement but without the transmembrane segment and is thus, a cytoplasmic (or nonreceptor) kinase. The expression of Aatyk1 (also referred simply as Aatyk) is upregulated during growth arrest and apoptosis in myeloid cells Probab=24.46 E-value=59 Score=14.66 Aligned_cols=47 Identities=15% Similarity=0.277 Sum_probs=23.2 Q ss_pred EEEECCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCC Q ss_conf 999638854346779999999831542668999999999997327384 Q gi|255764506|r 107 LAYIPKKHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSKG 154 (205) Q Consensus 107 IaYiP~~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~g 154 (205) .-|.|+|.+-.+=+-.|..+....-+....++..|||.++.- |+.++ T Consensus 74 ~Ey~~~GsL~~~l~~~~~~~~~~~~~~~~~~~~~qia~gl~y-LH~~~ 120 (269) T cd05087 74 MEFCPLGDLKGYLRSCRAAELMTPDPRTLQRMACEIASGLLH-LHKHN 120 (269) T ss_pred EECCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHH-HHHCC T ss_conf 981689869999874454455783899999999999999999-95299 No 35 >TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase; InterPro: IPR011772 This entry respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions . This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This entry identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologues of this gene are not found in plants which rely solely on the aerobic cyclase.; GO: 0016709 oxidoreductase activity acting on paired donors with incorporation or reduction of molecular oxygen NADH or NADPH as one donor and incorporation of one atom of oxygen, 0050661 NADP binding, 0015995 chlorophyll biosynthetic process. Probab=23.46 E-value=63 Score=14.49 Aligned_cols=47 Identities=34% Similarity=0.478 Sum_probs=38.0 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHH-HCCCHHHHHHHHHHHH Q ss_conf 1013666522489999999999998147888810-0112678999999999 Q gi|255764506|r 7 GVFNMKLKKPTVEEAKEAIRVILRWIGDDPDREG-LKDTPDRVIKSYKELF 56 (205) Q Consensus 7 ~~~~~~~~~~~~~~i~~av~~lL~~LGeDp~reg-L~~TP~Rvak~~~e~~ 56 (205) +-|=++++....+.++++.+.+|.+ |||--. +.=||-|.+..|.++- T Consensus 346 A~fi~g~e~~~~~~~~etyr~~ldw---~PD~~~w~~yTPwpft~lf~~l~ 393 (506) T TIGR02026 346 AQFIVGLENETDETLEETYRQLLDW---DPDLANWLMYTPWPFTSLFEELS 393 (506) T ss_pred EEEEECCCCCCHHHHHHHHHHHHCC---CCCHHHHCCCCCCCCHHHHHHHC T ss_conf 0024254358756899999997337---83324214558987636788630 No 36 >pfam08879 WRC WRC. The WRC domain, named after the conserved Trp-Arg-Cys motif, contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that the WRC domain functions in DNA binding. Probab=23.19 E-value=16 Score=18.17 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=9.4 Q ss_pred EEEEECCCCEEE Q ss_conf 587721100234 Q gi|255764506|r 89 SFFSYCEHHILP 100 (205) Q Consensus 89 ~f~S~CEHHllP 100 (205) +-.++||+||.- T Consensus 23 ~~~~~Ce~H~~~ 34 (46) T pfam08879 23 PGKKLCERHLHR 34 (46) T ss_pred CCCCHHHHHHHH T ss_conf 870188998860 No 37 >TIGR00083 ribF riboflavin biosynthesis protein RibF; InterPro: IPR002606 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme , the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family . The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases . This entry represents the bifunctional enzyme, FAD synthetase / riboflavin kinase.; GO: 0003919 FMN adenylyltransferase activity, 0008531 riboflavin kinase activity, 0009231 riboflavin biosynthetic process. Probab=22.46 E-value=66 Score=14.37 Aligned_cols=42 Identities=12% Similarity=0.033 Sum_probs=31.6 Q ss_pred HHCCCCCCCCCCEEEECCEEEEEECCCCEE--EEEEEEEEEEEC Q ss_conf 202566556676289618058772110023--465578999963 Q gi|255764506|r 70 RFHFGEASKYQDMVLIKDISFFSYCEHHIL--PIWGKIHLAYIP 111 (205) Q Consensus 70 ~~~~~~~~~~~~mVvv~~I~f~S~CEHHll--Pf~G~~~IaYiP 111 (205) .|+.-|-.=.+.++.++.-...-.-.-|=. ||.|+++|||.| T Consensus 189 GFPTANi~L~~~~~~~~~g~y~~~~~~~~~dv~~~GV~NiG~RP 232 (296) T TIGR00083 189 GFPTANIKLKNQVLPLKGGYYVVVVLLNGEDVPYPGVGNIGKRP 232 (296) T ss_pred CCCCCCCCCCCCEEECCCEEEEEEEEECCCEEEEEEEEECCCCC T ss_conf 47525645677543047158999985176000330134508876 No 38 >pfam01340 MetJ Met Apo-repressor, MetJ. Probab=22.34 E-value=36 Score=15.99 Aligned_cols=16 Identities=44% Similarity=0.619 Sum_probs=5.6 Q ss_pred HHHHHHHHHHHHCCCC Q ss_conf 9999999999814788 Q gi|255764506|r 21 AKEAIRVILRWIGDDP 36 (205) Q Consensus 21 i~~av~~lL~~LGeDp 36 (205) +-+.++.+++++|.|| T Consensus 84 iP~~ak~~m~~~Gi~~ 99 (104) T pfam01340 84 IPEAAKEIMRELGIDP 99 (104) T ss_pred CCHHHHHHHHHHCCCH T ss_conf 6099999999919983 No 39 >pfam08921 DUF1904 Domain of unknown function (DUF1904). This domain is found in a set of hypothetical bacterial proteins. Probab=22.34 E-value=53 Score=14.95 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=29.7 Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEE Q ss_conf 9998315426689999999999973273847999994 Q gi|255764506|r 125 LEVYSRRLQIQERLTMQIAHAIESSTDSKGVAVLIEG 161 (205) Q Consensus 125 v~~~a~RlQ~QErlT~qIa~~l~~~l~~~gv~V~i~A 161 (205) |-||.|-.++|.++.+-|-+++.+..+-..|+|.-.+ T Consensus 59 VlWF~R~qe~~d~vA~~It~~v~~~~~~~~V~V~F~~ 95 (107) T pfam08921 59 VLWFPRDQETQDLVAQIITEAVRAVNGLQDVAVIFTA 95 (107) T ss_pred EEEECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEE T ss_conf 9980389899999999999999843899739999996 No 40 >PRK09271 flavodoxin; Provisional Probab=22.32 E-value=61 Score=14.56 Aligned_cols=21 Identities=14% Similarity=0.061 Sum_probs=15.7 Q ss_pred CHHHHHHHHHHHHHHHCCCCC Q ss_conf 489999999999998147888 Q gi|255764506|r 17 TVEEAKEAIRVILRWIGDDPD 37 (205) Q Consensus 17 ~~~~i~~av~~lL~~LGeDp~ 37 (205) +.+++++.|.+-|+..|-+++ T Consensus 13 NTE~vA~~I~~~l~~~G~eV~ 33 (160) T PRK09271 13 NTREVARMIAARCEEAGHAVT 33 (160) T ss_pred CHHHHHHHHHHHHHHCCCEEE T ss_conf 689999999999997698237 No 41 >TIGR00632 vsr DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine . GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine . The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology . ; GO: 0004519 endonuclease activity, 0006298 mismatch repair. Probab=21.88 E-value=27 Score=16.80 Aligned_cols=33 Identities=39% Similarity=0.656 Sum_probs=24.5 Q ss_pred HHHHHHHHHHHHHCC----C---CCCHHHCCCHHHHHHHH Q ss_conf 999999999998147----8---88810011267899999 Q gi|255764506|r 20 EAKEAIRVILRWIGD----D---PDREGLKDTPDRVIKSY 52 (205) Q Consensus 20 ~i~~av~~lL~~LGe----D---p~regL~~TP~Rvak~~ 52 (205) ++|.+++++|-+||. | -+++||.+||.=|.+.| T Consensus 42 ~pE~~l~s~L~~lGlryRkdfl~~~~~G~~g~PD~vf~~~ 81 (143) T TIGR00632 42 KPEKALASLLFALGLRYRKDFLLRDKDGLPGTPDIVFKEY 81 (143) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCC T ss_conf 1789999999998899888987523689854675443473 No 42 >cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer. Probab=21.45 E-value=39 Score=15.75 Aligned_cols=16 Identities=31% Similarity=0.547 Sum_probs=5.4 Q ss_pred HHHHHHHHHHHHCCCC Q ss_conf 9999999999814788 Q gi|255764506|r 21 AKEAIRVILRWIGDDP 36 (205) Q Consensus 21 i~~av~~lL~~LGeDp 36 (205) +-+.++.+++++|.|| T Consensus 84 iP~~ak~~m~~~Gi~~ 99 (103) T cd00490 84 IPEAAKELMREMGIEP 99 (103) T ss_pred CCHHHHHHHHHCCCCH T ss_conf 6099999999909981 No 43 >PHA00658 putative lysin Probab=21.11 E-value=56 Score=14.77 Aligned_cols=82 Identities=21% Similarity=0.371 Sum_probs=36.9 Q ss_pred HHHHHHHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCEEEECCEEEEEECCCCEE Q ss_conf 99999999999814788881001126789999999997608653123443202566556676289618058772110023 Q gi|255764506|r 20 EAKEAIRVILRWIGDDPDREGLKDTPDRVIKSYKELFAGYKQIPTTQDTSRFHFGEASKYQDMVLIKDISFFSYCEHHIL 99 (205) Q Consensus 20 ~i~~av~~lL~~LGeDp~regL~~TP~Rvak~~~e~~~Gy~~~~~~~~~~~~~~~~~~~~~~mVvv~~I~f~S~CEHHll 99 (205) .|...+..-|+-+|+||+-..-.-..+||-. +..|..||-........+.|+..+.+.+-+-...++-.+.......-+ T Consensus 595 aikagldtrlrmmgddptpkdgssdaervga-mrkfidgyfiaaqreagkkftdaeveqhldalfmknatvrgwfsnssv 673 (720) T PHA00658 595 AIKAGLDTRLRMMGDDPTPKDGSSDAERVGA-MRKFIDGYFIAAQREAGKKFTDAEVEQHLDALFMKNATVRGWFSNSSV 673 (720) T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHH-HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCC T ss_conf 8861135667760799999888643888888-987621344466576444454588999999998515402221047876 Q ss_pred EEE Q ss_conf 465 Q gi|255764506|r 100 PIW 102 (205) Q Consensus 100 Pf~ 102 (205) |+. T Consensus 674 pil 676 (720) T PHA00658 674 PIL 676 (720) T ss_pred CEE T ss_conf 136 No 44 >COG5441 Uncharacterized conserved protein [Function unknown] Probab=20.92 E-value=50 Score=15.12 Aligned_cols=63 Identities=11% Similarity=0.212 Sum_probs=48.3 Q ss_pred EEEECCEEEEEECCCCEEEEEEEEEEEEECC-CCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCC Q ss_conf 2896180587721100234655789999638-85434677999999983154266899999999999732738 Q gi|255764506|r 82 MVLIKDISFFSYCEHHILPIWGKIHLAYIPK-KHVIGLSKLVRILEVYSRRLQIQERLTMQIAHAIESSTDSK 153 (205) Q Consensus 82 mVvv~~I~f~S~CEHHllPf~G~~~IaYiP~-~~viGlSKl~Riv~~~a~RlQ~QErlT~qIa~~l~~~l~~~ 153 (205) ++.+-.+-++.+-.-|++|..|...|.-+|. .-+-||-.+.|+|-.-| ..+|+-+.....+|. T Consensus 115 PlgvPK~mVST~Asgdv~pyv~~sDi~Mm~svtd~aGLNrisR~VLsnA---------a~aiag~a~~~~~~s 178 (401) T COG5441 115 PLGVPKVMVSTLASGDVAPYVGVSDIIMMYSVTDMAGLNRISRVVLSNA---------AHAIAGMAKRPAEPS 178 (401) T ss_pred CCCCCCEEEEEEECCCCCCCCCHHHEEEEEECCCCCCCCHHHHHHHHHH---------HHHHHHHHHCCCCCC T ss_conf 7677610256410267578777657253100143112348889999878---------899888873567898 No 45 >cd01747 GATase1_Glutamyl_Hydrolase Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. gamma-Glutamyl Hydrolase catalyzes the cleavage of the gamma-glutamyl chain of folylpoly-gamma-glutamyl substrates and is a central enzyme in folyl and antifolyl poly-gamma-glutamate metabolism. GATase activity involves the removal of the ammonia group from a glutamate molecule and its subsequent transfer to a specific substrate, thus creating a new carbon-nitrogen group on the substrate. gamma-Glutamyl hydrolases belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site. Probab=20.87 E-value=71 Score=14.17 Aligned_cols=25 Identities=32% Similarity=0.517 Sum_probs=20.1 Q ss_pred CCEEEEEECCCCEEEEEEEEEEEEECCC Q ss_conf 1805877211002346557899996388 Q gi|255764506|r 86 KDISFFSYCEHHILPIWGKIHLAYIPKK 113 (205) Q Consensus 86 ~~I~f~S~CEHHllPf~G~~~IaYiP~~ 113 (205) .+..|.|..||.--||+|+-+ -|-+ T Consensus 190 ~g~eFVStiE~k~YP~yg~Qf---HPEK 214 (273) T cd01747 190 NGVEFISTVEAYKYPIYGVQW---HPEK 214 (273) T ss_pred CCCEEEEEEECCCCCEEEEEE---CCCC T ss_conf 998898863032476466740---6875 No 46 >PRK10416 cell division protein FtsY; Provisional Probab=20.73 E-value=46 Score=15.32 Aligned_cols=22 Identities=23% Similarity=0.406 Sum_probs=14.4 Q ss_pred CHHHCCCHHHHHHHHHHHHHHC Q ss_conf 8100112678999999999760 Q gi|255764506|r 38 REGLKDTPDRVIKSYKELFAGY 59 (205) Q Consensus 38 regL~~TP~Rvak~~~e~~~Gy 59 (205) +.||.+|-..+...+..+|+|- T Consensus 202 k~gL~kt~~~l~~~~~~lf~~k 223 (499) T PRK10416 202 KRSLLKTKENLGSGFISLFRGK 223 (499) T ss_pred HHHHHHHHHHHHHHHHHHHCCC T ss_conf 9899999999999999986689 No 47 >COG1539 FolB Dihydroneopterin aldolase [Coenzyme metabolism] Probab=20.47 E-value=72 Score=14.11 Aligned_cols=70 Identities=21% Similarity=0.363 Sum_probs=41.7 Q ss_pred EEEECCEEEEEE-----CCCCE-EEEEEEEEEEEECC-----CC---CCCHHH-HHHHHHHH-HCCCCCHHHHHHHHHHH Q ss_conf 289618058772-----11002-34655789999638-----85---434677-99999998-31542668999999999 Q gi|255764506|r 82 MVLIKDISFFSY-----CEHHI-LPIWGKIHLAYIPK-----KH---VIGLSK-LVRILEVY-SRRLQIQERLTMQIAHA 145 (205) Q Consensus 82 mVvv~~I~f~S~-----CEHHl-lPf~G~~~IaYiP~-----~~---viGlSK-l~Riv~~~-a~RlQ~QErlT~qIa~~ 145 (205) -|.++++.|+.. .|+++ +||.=.+.++|=.. +. -+--.- ..++.+++ .++..+.|+|+.+||+. T Consensus 4 ~v~i~~l~~~~~iGv~~~E~~~~Q~~~Vdl~l~~d~~~A~~~Ddl~dtl~Y~~v~~~i~~~v~~~~~~LiE~lA~~ia~~ 83 (121) T COG1539 4 RVFIENLEFFAYIGVLDEERKLGQKFVVDLTLGYDLRKAAESDDLADTLNYAEVSELIKEIVEGKRFALIETLAEEIADL 83 (121) T ss_pred EEEECCEEEEEEECCCHHHHCCCCEEEEEEEEECCCHHHCCCCCHHHEECHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH T ss_conf 89983469999973778996069719999999526045147663222536999999999998579534499999999999 Q ss_pred HHHHCC Q ss_conf 997327 Q gi|255764506|r 146 IESSTD 151 (205) Q Consensus 146 l~~~l~ 151 (205) +...-. T Consensus 84 l~~~~~ 89 (121) T COG1539 84 LLARFP 89 (121) T ss_pred HHHHCC T ss_conf 986388 No 48 >pfam03652 UPF0081 Uncharacterized protein family (UPF0081). Probab=20.12 E-value=52 Score=14.97 Aligned_cols=32 Identities=28% Similarity=0.327 Sum_probs=22.4 Q ss_pred HHHHHHHHHHHHCCCCC---------HHHHHHHHHHHHHHH Q ss_conf 67799999998315426---------689999999999973 Q gi|255764506|r 118 LSKLVRILEVYSRRLQI---------QERLTMQIAHAIESS 149 (205) Q Consensus 118 lSKl~Riv~~~a~RlQ~---------QErlT~qIa~~l~~~ 149 (205) .|..++.+..|+++|+- -||+|...|..+... T Consensus 67 ~~~~~~~v~~f~~~L~~~~~i~v~~~DEr~TS~~A~~~l~~ 107 (134) T pfam03652 67 EGEQTKRVRKFARRLKKRFGLPVELVDERLTTVEAERILRE 107 (134) T ss_pred CCHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHH T ss_conf 08899999999999998619986886343279999999997 No 49 >TIGR00250 TIGR00250 conserved hypothetical protein TIGR00250; InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VIIcolicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma urealyticum (Q9PQY7 from SWISSPROT, ). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase . This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC . ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0004518 nuclease activity, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus. Probab=20.10 E-value=37 Score=15.87 Aligned_cols=26 Identities=27% Similarity=0.399 Sum_probs=15.5 Q ss_pred HHHHHHHHHHHCCCCCH---------HHHHHHHHH Q ss_conf 77999999983154266---------899999999 Q gi|255764506|r 119 SKLVRILEVYSRRLQIQ---------ERLTMQIAH 144 (205) Q Consensus 119 SKl~Riv~~~a~RlQ~Q---------ErlT~qIa~ 144 (205) +..+.=+..||+|++-| ||||.-=|+ T Consensus 68 g~~~~~~~kFA~r~~~~~~v~v~l~DERL~t~~A~ 102 (133) T TIGR00250 68 GPLTKRAQKFAKRLEGRFGVPVELMDERLSTVEAE 102 (133) T ss_pred CHHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHH T ss_conf 50268889999886554066437861761378999 No 50 >pfam07893 DUF1668 Protein of unknown function (DUF1668). The hypothetical proteins found in this family are expressed by Oryza sativa and are of unknown function. Probab=20.02 E-value=31 Score=16.34 Aligned_cols=24 Identities=33% Similarity=0.537 Sum_probs=18.4 Q ss_pred CEEEEEEEEEEEEECC-CCCCCHHHHH Q ss_conf 0234655789999638-8543467799 Q gi|255764506|r 97 HILPIWGKIHLAYIPK-KHVIGLSKLV 122 (205) Q Consensus 97 HllPf~G~~~IaYiP~-~~viGlSKl~ 122 (205) -.|||.|+++ |.|. +--+|||.-. T Consensus 205 w~LPF~G~a~--yv~el~lw~Gls~~~ 229 (330) T pfam07893 205 WTLPFDGQAE--YVPELDLWFGLSRGD 229 (330) T ss_pred CCCCCCCCEE--ECCCCCCEEEEECCC T ss_conf 5067377278--741108079770379 Done!