Query 024072
Match_columns 273
No_of_seqs 238 out of 1408
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:45:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024072.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024072hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00143 hypF [NiFe] hydrogen 100.0 2.6E-53 5.6E-58 429.5 22.0 231 34-270 132-387 (711)
2 COG0068 HypF Hydrogenase matur 100.0 2.6E-52 5.6E-57 410.3 17.6 235 34-271 165-423 (750)
3 TIGR00057 Sua5/YciO/YrdC/YwlC 100.0 2.3E-51 5E-56 359.7 21.0 190 65-259 8-198 (201)
4 COG0009 SUA5 Putative translat 100.0 5.8E-51 1.3E-55 358.2 22.5 194 65-261 13-207 (211)
5 PRK11630 hypothetical protein; 100.0 1E-50 2.2E-55 356.8 20.6 187 65-256 14-203 (206)
6 PRK10634 tRNA(ANN) t(6)A37 thr 100.0 2E-49 4.3E-54 344.7 19.7 180 65-251 7-190 (190)
7 PF01300 Sua5_yciO_yrdC: Telom 100.0 1.5E-48 3.2E-53 335.9 16.4 176 73-251 1-179 (179)
8 KOG3051 RNA binding/translatio 100.0 2.3E-28 5E-33 215.6 10.5 184 68-254 18-205 (261)
9 PF07503 zf-HYPF: HypF finger; 98.3 1.8E-07 4E-12 59.6 1.0 22 34-55 13-35 (35)
10 COG2192 Predicted carbamoyl tr 96.8 0.019 4.2E-07 57.2 12.2 148 67-225 379-548 (555)
11 TIGR00143 hypF [NiFe] hydrogen 80.2 1.1 2.4E-05 46.7 2.2 24 33-56 81-105 (711)
12 PF02543 CmcH_NodU: Carbamoylt 79.5 4.1 8.9E-05 39.0 5.8 66 67-133 253-327 (360)
13 COG0068 HypF Hydrogenase matur 75.6 1.6 3.4E-05 45.1 1.8 22 34-55 115-137 (750)
14 cd07985 LPLAT_GPAT Lysophospho 58.4 24 0.00051 32.0 5.5 57 63-122 99-170 (235)
15 PRK05406 LamB/YcsF family prot 57.8 49 0.0011 30.2 7.4 76 25-109 160-239 (246)
16 PF03746 LamB_YcsF: LamB/YcsF 48.0 54 0.0012 29.8 6.1 89 8-109 135-237 (242)
17 PLN02349 glycerol-3-phosphate 47.2 22 0.00047 34.7 3.6 46 65-112 280-336 (426)
18 PF09837 DUF2064: Uncharacteri 45.9 34 0.00074 27.4 4.1 31 64-94 74-105 (122)
19 PRK12569 hypothetical protein; 44.7 95 0.0021 28.3 7.1 73 26-109 164-240 (245)
20 PF05785 CNF1: Rho-activating 43.0 11 0.00024 34.8 1.0 35 164-204 102-136 (281)
21 COG0379 NadA Quinolinate synth 37.2 35 0.00076 32.3 3.2 94 66-165 79-175 (324)
22 PRK09375 quinolinate synthetas 31.3 75 0.0016 30.1 4.5 84 68-154 79-165 (319)
23 KOG3475 60S ribosomal protein 28.1 21 0.00046 27.2 0.2 16 35-50 24-40 (92)
24 PF02082 Rrf2: Transcriptional 28.0 86 0.0019 22.9 3.5 34 64-97 38-73 (83)
25 PF00926 DHBP_synthase: 3,4-di 27.2 1.4E+02 0.0031 26.1 5.3 57 68-129 1-63 (194)
26 TIGR00506 ribB 3,4-dihydroxy-2 26.5 1.4E+02 0.0031 26.2 5.1 58 67-129 4-67 (199)
27 PF00639 Rotamase: PPIC-type P 26.0 1.4E+02 0.0031 22.2 4.5 29 65-93 63-92 (95)
28 COG3364 Zn-ribbon containing p 25.1 62 0.0013 25.6 2.3 48 43-91 22-74 (112)
29 KOG2949 Ketopantoate hydroxyme 23.7 67 0.0015 29.3 2.5 40 62-106 113-152 (306)
30 COG5441 Uncharacterized conser 22.2 1.2E+02 0.0026 28.8 4.0 89 9-107 264-361 (401)
31 TIGR02925 cis_trans_EpsD pepti 21.7 1E+02 0.0022 26.9 3.4 28 66-93 194-221 (232)
32 PRK05773 3,4-dihydroxy-2-butan 21.6 2E+02 0.0043 25.8 5.2 57 68-129 3-65 (219)
33 COG0288 CynT Carbonic anhydras 21.5 1.6E+02 0.0035 25.9 4.6 74 18-94 30-108 (207)
34 PRK01130 N-acetylmannosamine-6 21.4 5.3E+02 0.012 22.2 13.3 43 64-120 21-63 (221)
35 TIGR01201 HU_rel DNA-binding p 20.6 1.3E+02 0.0029 24.8 3.6 30 67-96 58-87 (145)
No 1
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=100.00 E-value=2.6e-53 Score=429.50 Aligned_cols=231 Identities=26% Similarity=0.371 Sum_probs=201.1
Q ss_pred cCcCCC-CCCCCCCCCceeEEEcCCCcccCCCHHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCC
Q 024072 34 LNRRFP-KKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKH 112 (273)
Q Consensus 34 ~~RRfh-~~~ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~ 112 (273)
.||||| |+++|+.|||++++.+..|. . ..++.+++|+++|++|+|||+||+|||||+|||+|++||+|||++|+||
T Consensus 132 ~~rr~h~~~~~C~~Cgp~l~l~~~~g~-~-~~~~~i~~aa~~L~~G~IVaipt~ggy~L~cda~n~~AV~rLr~~K~Rp- 208 (711)
T TIGR00143 132 LDRRFHAQPIACPRCGPQLNFVSRGGH-A-EQDDALLEAAKLLKKGKIIAIKGIGGFHLACDARNDEVVERLRLRKNRP- 208 (711)
T ss_pred ccccCCCCCccCCCCCcEEEEEeCCCC-c-cchHHHHHHHHHHhCCCEEEEEcCCcceeecCCCCHHHHHHHHHHhCCC-
Confidence 599999 99999999999999998876 2 2457899999999999999999999999999999999999999999998
Q ss_pred CCCcEEEECCHHHHhhhhccCCchHHHHhccCCCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeE
Q 024072 113 TSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESAL 192 (273)
Q Consensus 113 ~KPfavm~~dl~~l~~~~~v~~~~~~ll~~~~PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PL 192 (273)
+|||+||++|++++++|+++++.++++|.+ |++|++ |+++++...+++.++++.+|||||+||||+|++|++.+|.||
T Consensus 209 ~KPlavmv~d~~~~~~~~~~~~~e~~lL~~-~~~Piv-ll~~~~~~~l~~~v~~~~~tiGvrlP~~pl~~~Ll~~~g~PL 286 (711)
T TIGR00143 209 LKPFAVMSPDLESAEQHAELNNLECELLTS-PAAPIV-LLRKKPDIKLAPNIAPNLPTIGVMLPYTPLHHLLLQLLAFPL 286 (711)
T ss_pred CCCEEEEECCHHHHHHHhcCCHHHHHHHHc-CCCCEE-EEECCCCCCCChhhcCCCCEEEEEcCCCHHHHHHHHHcCCcE
Confidence 699999999999999999998888888876 688875 588764324788999999999999999999999999999999
Q ss_pred EEecCCCCCCCCCCCHHHH-HhhhhcccEEEcCcccCCCCCCCeeEEcccCCcc-----------------------EEE
Q 024072 193 ALTSANLTGQPSSVSVKDF-ENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKF-----------------------KIL 248 (273)
Q Consensus 193 v~TSAN~SGep~~~~~~~~-~~~~~~vd~ivd~g~~~~~~~~STVVdl~~~~~~-----------------------~Il 248 (273)
||||||+||+|++++.+++ +++.+.+|+++++++...++.+||||+++. +++ .||
T Consensus 287 v~TSAN~SGep~~~~~~e~~~~l~~~~D~~L~~~r~i~~~~dsSVV~~~~-~~~~ilR~~RG~aP~~~~l~~~~~~~~vl 365 (711)
T TIGR00143 287 VMTSANLPGLPMAIDNAEILDKLQGIADGFLVHNRRIVNRVDDSVVQHVA-GEILFLRRSRGFAPQPLTLPPNGNPKKIL 365 (711)
T ss_pred EECccCCCCCCCCCCHHHHHHHhcCCccEEEeCCCCcCCCCCCceEEEEC-CeeEEEeccCCCCCcccccCCcCCCCcEE
Confidence 9999999999999999885 567788999998887666778999999874 222 377
Q ss_pred ecCCChHHHHHHHhcCCccccC
Q 024072 249 RPGSAKEETIAILEKHSLVEEP 270 (273)
Q Consensus 249 R~G~~~k~~~~l~~~~~~~~~~ 270 (273)
+.|+.+|||+|+.+++..+-.|
T Consensus 366 a~G~~lknt~~l~~~~~~~~S~ 387 (711)
T TIGR00143 366 ALGAELKNTFSLLKGGQAYLSQ 387 (711)
T ss_pred EechhhcceEEEEeCCEEEEcC
Confidence 7777788888887776655444
No 2
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.6e-52 Score=410.30 Aligned_cols=235 Identities=27% Similarity=0.375 Sum_probs=201.1
Q ss_pred cCcCCC-CCCCCCCCCceeEEEcCCCcccCCCHHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCC
Q 024072 34 LNRRFP-KKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKH 112 (273)
Q Consensus 34 ~~RRfh-~~~ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~ 112 (273)
+||||| ||+||+.|||++++.+.+|+.+.....++.++++.|+.|+|||+||.|||||+||++|++||++||++|+||
T Consensus 165 ~nRRfHAQp~aCp~CGP~~~l~~~~g~~~~~~~~ai~~a~klL~~G~IvAIKGiGGFhLaCda~~~eaV~~LR~rk~Rp- 243 (750)
T COG0068 165 LNRRFHAQPIACPKCGPHLFLVNHDGEAIAEANEAIRKAAKLLKVGKIVAIKGIGGFHLACDARNEEAVAKLRKRKNRP- 243 (750)
T ss_pred cccccccccccCcccCCCeEEEcCCCcchhhhhHHHHHHHHHHhhCCEEEEeecCceeeeecCCchHHHHHHHHhcCCC-
Confidence 499999 999999999999999988876655555899999999999999999999999999999999999999999999
Q ss_pred CCCcEEEECCHHHHhhhhccCCchHHHHhccCCCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHH-hCCCe
Q 024072 113 TSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIAR-GLESA 191 (273)
Q Consensus 113 ~KPfavm~~dl~~l~~~~~v~~~~~~ll~~~~PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~-~~g~P 191 (273)
.||||||++|++++++||.++..++++|.+.. +|+ |++++++...+++.++|++++||||+||+|+|++|++ ....|
T Consensus 244 ~KPFAvM~kdl~~i~~~a~~~~~E~~lL~S~~-rPI-Vll~Kk~~~~~~~~iAP~l~~iGVMLPYtpLhhLLl~~~~~~~ 321 (750)
T COG0068 244 LKPFAVMAKDLETIEEFAEVNDEEEELLTSPS-RPI-VLLKKKKVFLLESNIAPGLHTIGVMLPYTPLHHLLLQESLDIP 321 (750)
T ss_pred CCCceeeeccHHHHHHhhccCHHHHHHhcCcc-Cce-EEeccccccccccccCCCCCCcceeecCCchhhhhhhhccCce
Confidence 69999999999999999999999999999863 666 6788876545677799999999999999999999999 78889
Q ss_pred EEEecCCCCCCCCCCCHHH-HHhhhhcccEEEcCcccCCCCCCCeeEEccc---------------------CCccEEEe
Q 024072 192 LALTSANLTGQPSSVSVKD-FENLWERCACVYDGGVLPSGRAGSTVVDLTR---------------------LGKFKILR 249 (273)
Q Consensus 192 Lv~TSAN~SGep~~~~~~~-~~~~~~~vd~ivd~g~~~~~~~~STVVdl~~---------------------~~~~~IlR 249 (273)
+||||||+||+|+..+.++ ++++.+.+|+++.+++.+.+|.+.+||.+.. ++..+||+
T Consensus 322 ~VmTSaNl~g~Pm~~dN~eal~kL~~IADyfL~HNR~I~~r~DDSVVrvV~g~~~~iRrSRGy~P~pi~lp~~~~~~ila 401 (750)
T COG0068 322 YVMTSANLPGEPMAIDNEEALEKLKGIADYFLLHNREIVNRCDDSVVRVVAGRIAFIRRSRGYAPKPIELPFNNVKKILA 401 (750)
T ss_pred EEEecCCCCCCCcccCCHHHHHHhhhhhheeeecccccccccCCcceeEeCCceeeeehhcCCCCcceecCCCCccceee
Confidence 9999999999999988877 5667667777766665555555555554332 12336899
Q ss_pred cCCChHHHHHHHhcCCccccCC
Q 024072 250 PGSAKEETIAILEKHSLVEEPA 271 (273)
Q Consensus 250 ~G~~~k~~~~l~~~~~~~~~~~ 271 (273)
.|+.+|+|+|+++++..+-.|-
T Consensus 402 ~GaelknTf~l~k~~~~~lSQ~ 423 (750)
T COG0068 402 LGAELKNTFCLLKGGKAYLSQH 423 (750)
T ss_pred ecccccceEEEEECCeEeeccc
Confidence 9999999999999887765553
No 3
>TIGR00057 Sua5/YciO/YrdC/YwlC family protein. partial match to sua5, which is involved in regulation of translation initiation. 3' end of sua5 has matches to sua5, BS3690, and weakly to AF0781 and BB0734.
Probab=100.00 E-value=2.3e-51 Score=359.66 Aligned_cols=190 Identities=34% Similarity=0.593 Sum_probs=173.7
Q ss_pred HHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhccCCchHHHHhccC
Q 024072 65 EAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLL 144 (273)
Q Consensus 65 ~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~v~~~~~~ll~~~~ 144 (273)
.+.++++++.|++||||++||||+|||+||++|++||+|||++|+|+.+|||++|++|++++.+|+.+++.++++++.+|
T Consensus 8 ~~~i~~a~~~L~~G~ii~~PTdTvYgL~~~~~~~~av~ri~~iK~R~~~Kpl~~l~~~~~~l~~~~~~~~~~~~l~~~~~ 87 (201)
T TIGR00057 8 QRGIEQAVKILRKGGIVVYPTDTVYGIGADALDEDAVRRLYRIKGRPSNKPLTVLVSDLSEIEKYAYVPDDAKRLMKKFW 87 (201)
T ss_pred HHHHHHHHHHHHCCCEEEEeCCCHHHhhcCCCCHHHHHHHHHHhCCCCCCCeEEEECCHHHHHHHhcCCHHHHHHHHhcC
Confidence 45689999999999999999999999999999999999999999999999999999999999999998887889999999
Q ss_pred CCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeEEEecCCCCCCCCCCCHHHHHh-hhhcccEEEc
Q 024072 145 PGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFEN-LWERCACVYD 223 (273)
Q Consensus 145 PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PLv~TSAN~SGep~~~~~~~~~~-~~~~vd~ivd 223 (273)
|||+|+|+++++ .+++.+.++.+|||||+|+||++++|++.+|.||++||||+||+|++++.+++.+ +.+.+|+|+|
T Consensus 88 Pgp~T~Il~~~~--~~~~~l~~~~~tigiRvP~~~~~~~L~~~~g~PL~~TSAN~sG~~~~~~~~~i~~~~~~~vd~ild 165 (201)
T TIGR00057 88 PGPLTLVLKKTP--EIPRRVSGKRKTIGIRVPDNPIALELLEELGKPIVATSANLSGKPSATDVEEAVDELGKLVDLIID 165 (201)
T ss_pred CCCeEEEEECCC--CCCHhHcCCCCeEEEECCCCHHHHHHHHHhCCCEEECCCCCCCCCCCCCHHHHHHHhCCCccEEEc
Confidence 999999999865 4788888889999999999999999999999999999999999999999999754 5567999999
Q ss_pred CcccCCCCCCCeeEEcccCCccEEEecCCChHHHHH
Q 024072 224 GGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEETIA 259 (273)
Q Consensus 224 ~g~~~~~~~~STVVdl~~~~~~~IlR~G~~~k~~~~ 259 (273)
+|++. .+.+|||||++. ++++|+|+|++. +.+.
T Consensus 166 ~g~~~-~~~~STVid~~~-~~~~ilR~G~~~-~~i~ 198 (201)
T TIGR00057 166 AGPCL-GGEPSTIIDLTD-DTPKVLREGVGS-EPIE 198 (201)
T ss_pred CCCCC-CCCCCcEEEccC-CceEEEecCCCH-HHHH
Confidence 99764 447999999986 578999999998 5543
No 4
>COG0009 SUA5 Putative translation factor (SUA5) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.8e-51 Score=358.18 Aligned_cols=194 Identities=37% Similarity=0.607 Sum_probs=176.6
Q ss_pred HHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhccCCchHHHHhccC
Q 024072 65 EAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLL 144 (273)
Q Consensus 65 ~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~v~~~~~~ll~~~~ 144 (273)
+..+++|++.|++|++|+|||||+|||+||++|++||+|||++|+||.+|||+++++|+++++.|+.+++..+++++.||
T Consensus 13 ~~~~~~a~~~l~~G~vVa~PTeTVYGLg~~~~~~~Av~~i~~~K~Rp~~kpLil~~~~~~~l~~~~~~~~~~~~l~~~fw 92 (211)
T COG0009 13 PRAIEKAVEALRKGGVVAYPTDTVYGLGADATNEEAVERLYEIKQRPSDKPLILHVASLEQLKEYADVPDVARKLLKAFW 92 (211)
T ss_pred hHHHHHHHHHHHcCCEEEEEccchheeecCCCCHHHHHHHHHHhCCCCCCCEEEEeCCHHHHHHHhcCCHHHHHHHHHhC
Confidence 45799999999999999999999999999999999999999999999999999999999999999998888999999999
Q ss_pred CCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeEEEecCCCCCCCCCCCHHHHH-hhhhcccEEEc
Q 024072 145 PGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFE-NLWERCACVYD 223 (273)
Q Consensus 145 PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PLv~TSAN~SGep~~~~~~~~~-~~~~~vd~ivd 223 (273)
|||+|+|+++++.... +.+.++.+|||||+|+||+.++|++++|.||++||||+||+|++++.+++. ++.+.+|+|+|
T Consensus 93 PGPlT~Il~~~~~~~~-~~~~~~~~TiavRvP~hpi~~~Li~~~G~Pl~stSANlsG~ps~tt~~ev~~~~~~~v~~iid 171 (211)
T COG0009 93 PGPLTFILPATKEVPR-RLVTAGLSTIAVRVPDHPIALALIEALGEPLASTSANLSGQPSPTTAEEVRADFGGQVDLIID 171 (211)
T ss_pred CCCeEEEEeCCCCCCh-hhhcCCCCeEEEECCCCHHHHHHHHHhCCceEEcCcCcCCCCCCCCHHHHHHHhcccCeEEEe
Confidence 9999999998554333 678888899999999999999999999999999999999999999999975 45567999999
Q ss_pred CcccCCCCCCCeeEEcccCCccEEEecCCChHHHHHHH
Q 024072 224 GGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEETIAIL 261 (273)
Q Consensus 224 ~g~~~~~~~~STVVdl~~~~~~~IlR~G~~~k~~~~l~ 261 (273)
+|.+..+ .+|||||++. +++.|+|+|++..+.+..+
T Consensus 172 gg~~~~g-~pSTIiDlt~-~~~~ilR~G~i~~~~i~~~ 207 (211)
T COG0009 172 GGPCRGG-LPSTIIDLTD-DPPRILRPGAISLEEIEKL 207 (211)
T ss_pred CCccCCC-CCceEEECCC-CCcEEEeCCCCCHHHHHHH
Confidence 9988655 7999999995 5679999999998777554
No 5
>PRK11630 hypothetical protein; Provisional
Probab=100.00 E-value=1e-50 Score=356.79 Aligned_cols=187 Identities=23% Similarity=0.405 Sum_probs=169.1
Q ss_pred HHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhccCCchHHHHhccC
Q 024072 65 EAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLL 144 (273)
Q Consensus 65 ~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~v~~~~~~ll~~~~ 144 (273)
.+.+++|+++|++|++|++||||+|||+||++|++||+|||++|+|+.+|||++|++|++++.+|+.+++.++++++++|
T Consensus 14 ~~~i~~a~~~L~~G~vi~~PTdTvYgL~~d~~n~~Av~~l~~lK~R~~~Kpl~ll~~~~~~~~~~~~~~~~~~~l~~~~w 93 (206)
T PRK11630 14 QRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELSTYSFVDNVAFRLMKNNT 93 (206)
T ss_pred HHHHHHHHHHHHCCCEEEEeCCChHhhhcCCCCHHHHHHHHHHcCCCCCCCeEEEECCHHHHHHHhcCCHHHHHHHHhcC
Confidence 44689999999999999999999999999999999999999999999999999999999999999988877889999999
Q ss_pred CCCeEEEEccCCCCcccc-ccCCCCCeEEEEcCCcHHHHHHHHhCCCeEEEecCCCCCCCC-CCCHHHHH-hhhhcccEE
Q 024072 145 PGPVTVVLSRGESSNLEK-SLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPS-SVSVKDFE-NLWERCACV 221 (273)
Q Consensus 145 PgpiTvIl~~~~~~~l~~-~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PLv~TSAN~SGep~-~~~~~~~~-~~~~~vd~i 221 (273)
|||+|+|+++++ .+++ +++++.++||||+|+||++++|++.+|.||++||||+||+++ .++.+++. ++.+.+|+|
T Consensus 94 PGplT~Il~a~~--~~p~~~~~~~~~tigiRip~~~~~~~L~~~~g~PL~~TSAN~sG~~~~~~~~~~i~~~~~~~vd~i 171 (206)
T PRK11630 94 PGNYTFILKGTK--EVPRRLLQEKRKTIGLRVPSNPIALALLEALGEPMLSTSLMLPGSDFTESDPEEIKDRLEKQVDLI 171 (206)
T ss_pred CCCeEEEEECCC--CCCHHHcCCCCCeEEEECCCCHHHHHHHHHhCCcEEECCcCcCCCCCCCCCHHHHHHHhcCCceEE
Confidence 999999999865 3665 777888999999999999999999999999999999999876 47888865 455679999
Q ss_pred EcCcccCCCCCCCeeEEcccCCccEEEecCCChHH
Q 024072 222 YDGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKEE 256 (273)
Q Consensus 222 vd~g~~~~~~~~STVVdl~~~~~~~IlR~G~~~k~ 256 (273)
+|++... + .+|||||++. ++++|+|+|++..+
T Consensus 172 ldg~~~~-~-~pSTIvd~~~-~~~~ilR~G~~~~~ 203 (206)
T PRK11630 172 IHGGYLG-Q-QPTTVIDLTD-DTPVVVREGVGDVK 203 (206)
T ss_pred EeCCCCC-C-CCCEEEEccC-CceEEEecCCCchh
Confidence 9998763 3 7999999986 57899999998754
No 6
>PRK10634 tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; Provisional
Probab=100.00 E-value=2e-49 Score=344.65 Aligned_cols=180 Identities=27% Similarity=0.400 Sum_probs=162.8
Q ss_pred HHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhc---cCCchHHHHh
Q 024072 65 EAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAV---TDHLPHGLLD 141 (273)
Q Consensus 65 ~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~---v~~~~~~ll~ 141 (273)
.+.++++++.|++|+||++||||+|||+||+.|++||+|||++|+|+.+|||++|++|++++.+|+. +++.++++++
T Consensus 7 ~~~i~~a~~~L~~G~vv~~PTdTvYgL~~~~~n~~Av~ri~~iK~R~~~Kpl~ll~~~~~~l~~~~~~~~~~~~~~~l~~ 86 (190)
T PRK10634 7 GDAIAAAVDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLKPYIDDSMLTDAQRETIF 86 (190)
T ss_pred HHHHHHHHHHHHCCCEEEEeCCchhhhhcCCCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHHHHHHhcCCCHHHHHHHH
Confidence 4678999999999999999999999999999999999999999999999999999999999999997 4566778999
Q ss_pred ccCCCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeEEEecCCCCCCCCCCCHHHHHh-hhhcccE
Q 024072 142 SLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFEN-LWERCAC 220 (273)
Q Consensus 142 ~~~PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PLv~TSAN~SGep~~~~~~~~~~-~~~~vd~ 220 (273)
++||||+|+||++++ .+++++.++.++||||+|+|+++++|++.+|.||++||||+||+|++++.+++.+ +.+.+|
T Consensus 87 ~~wPGPlTlil~~~~--~~p~~l~~~~~tigvRiP~~~~~~~ll~~~g~Pl~~TSAN~sG~~~~~~~~~i~~~~~~~v~- 163 (190)
T PRK10634 87 SCWPGPVTFVFPAPA--TTPRWLTGRFDSLAVRVTDHPLVVALCQAYGKPLVSTSANLSGLPPCRTVEEVRAQFGAAFP- 163 (190)
T ss_pred HhCCCCEEEEEECCC--CCCHHHcCCCCeEEEECCCCHHHHHHHHHhCCcEEECCcccCCCCCCCCHHHHHHHhCCCcE-
Confidence 999999999999864 4788999999999999999999999999999999999999999999999999765 445688
Q ss_pred EEcCcccCCCCCCCeeEEcccCCccEEEecC
Q 024072 221 VYDGGVLPSGRAGSTVVDLTRLGKFKILRPG 251 (273)
Q Consensus 221 ivd~g~~~~~~~~STVVdl~~~~~~~IlR~G 251 (273)
++|++.... ..+|||||+++ + +|+|+|
T Consensus 164 i~dg~~~~~-~~pSTIvd~~~-~--~ilR~G 190 (190)
T PRK10634 164 VVPGETGGR-LNPSEIRDALT-G--ELFRQG 190 (190)
T ss_pred EEcCCCCCC-CCCCeEEECCC-C--eEEeCC
Confidence 578876543 36999999984 2 899998
No 7
>PF01300 Sua5_yciO_yrdC: Telomere recombination; InterPro: IPR006070 The YrdC family of hypothetical proteins are widely distributed in eukaryotes and prokaryotes and occur as: (i) independent proteins, (ii) with C-terminal extensions, and (iii) as domains in larger proteins, some of which are implicated in regulation []. The YrdC protein, which consists solely of this domain, forms an alpha/beta twisted open-sheet structure composed of seven alpha helices and seven beta strands []. YrdC from Escherichia coli preferentially binds to double-stranded RNA and DNA. YrdC is predicted to be an rRNA maturation factor, as deletions in its gene lead to immature ribosomal 30S subunits and, consequently, fewer translating ribosomes []. Therefore, YrdC may function by keeping an rRNA structure needed for proper processing of 16S rRNA, especially at lower temperatures. Sua5 is an example of a multi-domain protein that contains an N-terminal YrdC-like domain and a C-terminal Sua5 domain. Sua5 was identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a translation initiation defect in the cytochrome c gene and is required for normal growth in yeast; however its exact function remains unknown []. HypF is involved in the synthesis of the active site of [NiFe]-hydrogenases [].; PDB: 3L7V_A 1KK9_A 1K7J_A 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A 2EQA_A ....
Probab=100.00 E-value=1.5e-48 Score=335.87 Aligned_cols=176 Identities=40% Similarity=0.680 Sum_probs=151.6
Q ss_pred HHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhc--cCCchHHHHhccCCCCeEE
Q 024072 73 QALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAV--TDHLPHGLLDSLLPGPVTV 150 (273)
Q Consensus 73 ~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~--v~~~~~~ll~~~~PgpiTv 150 (273)
++|++||+|++||||+|||+|+++|++|++|||++|+|+.+|||++|++|++++++|++ +++...++++.+||||+|+
T Consensus 1 e~Lk~G~vvi~PTdT~ygl~~~~~n~~av~ri~~iK~R~~~Kpl~ll~~~~~~l~~~~~~~~~~~~~~l~~~~wPgp~t~ 80 (179)
T PF01300_consen 1 EILKAGGVVIYPTDTVYGLGCDAFNPEAVERIYKIKQRPKNKPLILLVSSIEQLEEYVDSPVSPKARRLLEKFWPGPLTL 80 (179)
T ss_dssp -HHHTT-EEEEEESSSEEEEEETTSHHHHHHHHHHHTSSTTS--EEEESSHHHHHHHEETT--HHHHHHHHHCHSSSEEE
T ss_pred CccccCCEEEEECCCEEEEEEecCCHHHHHHHHHhhcccCCCCEEEEECCHHHHHHHhhccccHHHHHHHHhccccCeeE
Confidence 57999999999999999999999999999999999999999999999999999999998 5566778999999999999
Q ss_pred EEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeEEEecCCCCCCCCCCCHHHHH-hhhhcccEEEcCcccCC
Q 024072 151 VLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFE-NLWERCACVYDGGVLPS 229 (273)
Q Consensus 151 Il~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PLv~TSAN~SGep~~~~~~~~~-~~~~~vd~ivd~g~~~~ 229 (273)
|+++++. .+++.+.++.+|||||+|++|++++|++.+|.||++||||+||+++.++.+++. ++.+.+|+|+|++....
T Consensus 81 I~~~~~~-~l~~~~~~~~~ti~vRip~~~~~~~l~~~~g~Pl~~TSAN~sg~~~~~~~~~i~~~~~~~vd~iv~~~~~~~ 159 (179)
T PF01300_consen 81 ILPAKKE-NLPKYLTSKRGTIGVRIPDHPILRELLEALGGPLISTSANLSGEPPATDFEEIIERFGDKVDLIVDGGEIPS 159 (179)
T ss_dssp EEEEGTT-CSHHHHHTTTSEEEEECHCSHHHHHHHHHHTS-EEEEESSSTTSSCTTSHHHHHHHHTTTSSEEEECCHHSS
T ss_pred eeccccc-cCChhhcCCCCeEEEEecChHHHHHHHHhcCCceEecccccccCCCCCCHHHHHHHhccCceEEEECCCCCC
Confidence 9997432 488899999999999999999999999999999999999999999999999974 56678999999996543
Q ss_pred CCCCCeeEEcccCCccEEEecC
Q 024072 230 GRAGSTVVDLTRLGKFKILRPG 251 (273)
Q Consensus 230 ~~~~STVVdl~~~~~~~IlR~G 251 (273)
..+|||||++. ++++|||+|
T Consensus 160 -~~~STIvd~~~-~~~~ilR~G 179 (179)
T PF01300_consen 160 -GQPSTIVDLTN-GKPKILREG 179 (179)
T ss_dssp -SS--EEEETTS-SSSEEEE--
T ss_pred -CCCCeEEEeeC-CceEEEeeC
Confidence 47999999996 688999998
No 8
>KOG3051 consensus RNA binding/translational regulation protein of the SUA5 family [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=2.3e-28 Score=215.65 Aligned_cols=184 Identities=36% Similarity=0.569 Sum_probs=158.9
Q ss_pred HHHHHH-HHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhcc--CCchHHHHhccC
Q 024072 68 AEEAIQ-ALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVT--DHLPHGLLDSLL 144 (273)
Q Consensus 68 i~~a~~-~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~v--~~~~~~ll~~~~ 144 (273)
...++. +-+.++.+++||+|+||+++++.|+.|+.+|++.|+||.++|+.+.+.+..+++..... ......|++.+|
T Consensus 18 ~~~aa~~~r~~~~~va~pT~t~yg~g~~~~~~~av~~v~~~K~rP~~~pL~~~~~s~~~~~~v~~~~i~~~~~~L~~~l~ 97 (261)
T KOG3051|consen 18 LYDAALIVRRTDKRVAFPTETVYGLGASAYNEVAVLRLYKLKNRPADNPLIVHVSSVDQLKRVVAINIPSLYLPLASYLW 97 (261)
T ss_pred hhhhhhheeccCCceecCchhhhhhhhhhhccccchhhhhhhcCccccchhhccccHHHHHHHHhhcchhhhhHHHhhcC
Confidence 334444 44569999999999999999999999999999999999999999999999999987643 334567899999
Q ss_pred CCCeEEEEccCCCCccccccCCCCCeEEEEcCCcHHHHHHHHhCCCeEEEecCCCCCCCCC-CCHHHHHhhhhcccEEEc
Q 024072 145 PGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSS-VSVKDFENLWERCACVYD 223 (273)
Q Consensus 145 PgpiTvIl~~~~~~~l~~~l~~~~~tiGvrlP~~p~~~~Ll~~~g~PLv~TSAN~SGep~~-~~~~~~~~~~~~vd~ivd 223 (273)
|||+|+++++.+. .+++.++++..++|+|+|++|++..|++.++.|++.||||.|+.|.. ...+++++++.++++|+|
T Consensus 98 PGPltlll~~~~~-~l~~~~~~~~~svAvRiP~~~~a~~li~~~~~Pla~tSAN~Ssr~s~tlai~~~~Dl~~~i~lilD 176 (261)
T KOG3051|consen 98 PGPLTLLLERADE-CLSKLTNPGLPSVAVRIPDHPVASALIPKLGVPLALTSANASSRPSPTLAIHVFADLQPKIPLILD 176 (261)
T ss_pred CCceEEEeecchh-hccccccCCCcceeEEccCCHHHHHHHHHhCCCccccccccccCCCCcchhhhhhhhccchhheec
Confidence 9999999998653 58899999999999999999999999999999999999999999984 456778889999999999
Q ss_pred CcccCCCCCCCeeEEcccCCccEEEecCCCh
Q 024072 224 GGVLPSGRAGSTVVDLTRLGKFKILRPGSAK 254 (273)
Q Consensus 224 ~g~~~~~~~~STVVdl~~~~~~~IlR~G~~~ 254 (273)
+|.|..+ ..||+++... ++..|+|.|.+.
T Consensus 177 gG~c~~g-~~~~~~~g~~-~p~~i~~pgG~~ 205 (261)
T KOG3051|consen 177 GGACGSG-VESTVVEGST-DPVDILRPGGIT 205 (261)
T ss_pred CcccccC-cCceeecccc-CcceeeccCCcc
Confidence 9999876 6788888765 356777777643
No 9
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=98.31 E-value=1.8e-07 Score=59.56 Aligned_cols=22 Identities=23% Similarity=0.267 Sum_probs=16.7
Q ss_pred cCcCCC-CCCCCCCCCceeEEEc
Q 024072 34 LNRRFP-KKMAFSLENGQVSVEN 55 (273)
Q Consensus 34 ~~RRfh-~~~ac~~cgp~~~~~~ 55 (273)
.||||| |+++|+.|||++++.+
T Consensus 13 ~~RR~~~~~isC~~CGPr~~i~~ 35 (35)
T PF07503_consen 13 SNRRFHYQFISCTNCGPRYSIID 35 (35)
T ss_dssp TSTTTT-TT--BTTCC-SCCCES
T ss_pred CCCcccCcCccCCCCCCCEEEeC
Confidence 489999 9999999999998753
No 10
>COG2192 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]
Probab=96.77 E-value=0.019 Score=57.16 Aligned_cols=148 Identities=19% Similarity=0.161 Sum_probs=100.4
Q ss_pred HHHHHHHHHhcCceEEEe---------cCceEEEEeecCCHHHHHHHHHHhC-CCCCCCcEEEECCHHHHhhhhccCCch
Q 024072 67 HAEEAIQALKTGKVIAVP---------TDTLYGFACDACSSEAVNRIYEIKG-RKHTSPLAICVGDVSDINRFAVTDHLP 136 (273)
Q Consensus 67 ~i~~a~~~L~~G~Ivaip---------tdtgYgL~cda~n~~AV~rLr~~K~-R~~~KPfavm~~dl~~l~~~~~v~~~~ 136 (273)
..+.+++.|.+|++|+.= ..|+=.+.+||.++...++|....+ |+.-+||+--+- -+.+.+|.+.+
T Consensus 379 l~~~va~~LadgkvVgwfqGRmEfGPRALGnRSILadPr~~~~kd~iN~~vK~Re~FrPFAPsiL-~E~~~~~fe~~--- 454 (555)
T COG2192 379 LPDRVAELLADGKVVGWFQGRMEFGPRALGNRSILADPRDPGMKDKINLKVKFREGFRPFAPSIL-EEDVERYFELP--- 454 (555)
T ss_pred HHHHHHHHHhCCCeEEEEeeccccCccccCCceeecCCCChHHHHHHHHHhcccCccCCcCcchh-hhhhhHHhhCC---
Confidence 478899999999999862 3566679999999999999998777 998899987654 34444544322
Q ss_pred HHHHhccCCCC-eEEEEccCCCCc--ccc--ccCCCCCeEEEEcCCcHHHHHHHHhC----CCe-EEEecCCCCCCCCCC
Q 024072 137 HGLLDSLLPGP-VTVVLSRGESSN--LEK--SLNPGLESIGVRVPDSNFVRVIARGL----ESA-LALTSANLTGQPSSV 206 (273)
Q Consensus 137 ~~ll~~~~Pgp-iTvIl~~~~~~~--l~~--~l~~~~~tiGvrlP~~p~~~~Ll~~~----g~P-Lv~TSAN~SGep~~~ 206 (273)
.|-| .|++++.++... +|. .+.......-|+=-.+|..+.|++++ |.| |+-||=|+.|||+.-
T Consensus 455 -------~~sPyM~~~~~~~~~~r~~lpaV~HvDgTaR~QtV~r~~nP~y~~ll~aF~~~TG~gvllNTSFN~~GEPIVc 527 (555)
T COG2192 455 -------SPSPYMTLVFRVREEFRERLPAVTHVDGTARPQTVRRDANPRYYGLLRAFKERTGVGVLLNTSFNVHGEPIVC 527 (555)
T ss_pred -------CCCCceeeeehhhHHHHhhCCceEeecCCccceeeccccChhHHHHHHHHHHhcCCcEEEecccccCCCceec
Confidence 2445 355555543211 332 23333344566666778888888754 544 889999999999988
Q ss_pred CHHHHH-hhh-hcccEEEcCc
Q 024072 207 SVKDFE-NLW-ERCACVYDGG 225 (273)
Q Consensus 207 ~~~~~~-~~~-~~vd~ivd~g 225 (273)
+.+|.- .+. ..+|+.+-++
T Consensus 528 sp~DA~~~f~~t~~d~Lvi~~ 548 (555)
T COG2192 528 SPADAIRTFLSTGLDALVLED 548 (555)
T ss_pred CHHHHHHHHHhCCCcEEEEcC
Confidence 888843 332 3466555443
No 11
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=80.25 E-value=1.1 Score=46.72 Aligned_cols=24 Identities=8% Similarity=0.162 Sum_probs=19.8
Q ss_pred ccCcCCCCC-CCCCCCCceeEEEcC
Q 024072 33 HLNRRFPKK-MAFSLENGQVSVENK 56 (273)
Q Consensus 33 ~~~RRfh~~-~ac~~cgp~~~~~~~ 56 (273)
-.|||||.| ++|..|||+++....
T Consensus 81 p~~Rry~YpF~nCt~CGPr~~i~~~ 105 (711)
T TIGR00143 81 KNDRRYLYPFISCTHCGPRFTIIEA 105 (711)
T ss_pred CCcccccCCcccccCCCCCeEEeec
Confidence 368999965 789999999888654
No 12
>PF02543 CmcH_NodU: Carbamoyltransferase; InterPro: IPR003696 The putative O-carbamoyltransferases (O-Cases) encoded by the nodU genes of Rhizobium fredii and Bradyrhizobium japonicum are involved in the synthesis of nodulation factors []. The cmcH genes of Nocardia lactamdurans and Streptomyces clavuligerus encode a functional 3'-hydroxymethylcephem O-carbamoyltransferase 2.1.3.7 from EC for cephamycin biosynthesis that shows significant similarity to the O-carbamoyltransferases [].; GO: 0003824 catalytic activity, 0009058 biosynthetic process; PDB: 3VES_A 3VER_A 3VEN_A 3VF2_A 3VEX_A 3VEW_A 3VET_A 3VEO_A 3VEZ_A 3VF4_A.
Probab=79.52 E-value=4.1 Score=38.96 Aligned_cols=66 Identities=23% Similarity=0.202 Sum_probs=48.0
Q ss_pred HHHHHHHHHhcCceEEEe---------cCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhccC
Q 024072 67 HAEEAIQALKTGKVIAVP---------TDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVTD 133 (273)
Q Consensus 67 ~i~~a~~~L~~G~Ivaip---------tdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~v~ 133 (273)
..++++++|.+|+||+.= ..|.=-|.+||.+.+..++|-++|+|..-.||+=++- .|.+.+|.+..
T Consensus 253 ~~~~~A~lLa~gkiVgwfqGr~EfGPRALGnRSILAdP~~~~~~d~iN~~iKRE~fRPfAPsvl-~E~a~~~f~~~ 327 (360)
T PF02543_consen 253 LAEQVAELLADGKIVGWFQGRMEFGPRALGNRSILADPRSPDMKDRINRRIKREWFRPFAPSVL-EEDAEEYFELD 327 (360)
T ss_dssp HHHHHHHHHHTT--EEEE-SS-B-SSS--SSEEEEEESS-SSHHHHHHHTTS--TT---EEEEE-HHHHHHHBSS-
T ss_pred HHHHHHHHHHcCCEEEEEecCccccCccccccccccCCCChHHHHHHhhhcCccccCCcCcchh-HHHHHHhccCC
Confidence 568899999999999874 3566679999999999999999999999999999887 78888887654
No 13
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=75.63 E-value=1.6 Score=45.14 Aligned_cols=22 Identities=9% Similarity=0.116 Sum_probs=18.7
Q ss_pred cCcCCCCC-CCCCCCCceeEEEc
Q 024072 34 LNRRFPKK-MAFSLENGQVSVEN 55 (273)
Q Consensus 34 ~~RRfh~~-~ac~~cgp~~~~~~ 55 (273)
.|||||.| ++|..|||+.+...
T Consensus 115 ~~rrY~YPF~~CT~CGPRfTIi~ 137 (750)
T COG0068 115 NSRRYLYPFINCTNCGPRFTIIE 137 (750)
T ss_pred CCcceeccccccCCCCcceeeec
Confidence 58999965 89999999988763
No 14
>cd07985 LPLAT_GPAT Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT. Lysophospholipid acyltransferase (LPLAT) superfamily member: glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB). LPLATs are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. This subgroup includes glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB).
Probab=58.38 E-value=24 Score=31.97 Aligned_cols=57 Identities=23% Similarity=0.237 Sum_probs=40.5
Q ss_pred CCHHHHHHHHHHHhcCce--EEEecC--------ceEEEEeecCCHHHHHHHHHHhCCCCCCC-----cEEEECC
Q 024072 63 ATEAHAEEAIQALKTGKV--IAVPTD--------TLYGFACDACSSEAVNRIYEIKGRKHTSP-----LAICVGD 122 (273)
Q Consensus 63 ~~~~~i~~a~~~L~~G~I--vaiptd--------tgYgL~cda~n~~AV~rLr~~K~R~~~KP-----favm~~d 122 (273)
.+..+++.+.++|++|+. .++|-- +-+.- .+++.++++-.+.+=++.. .| +++.+.|
T Consensus 99 ~~~~alk~~~~lLk~G~~~i~IfPEGtR~r~~~~g~~~p--~~Fd~~~~~~~~~La~~s~-~p~hi~Plai~~yd 170 (235)
T cd07985 99 ANLATLKEMQQLLNEGGQLIWVAPSGGRDRPDANGEWYP--DPFDPSAVEMMRLLAQKSR-VPTHLYPMALLTYD 170 (235)
T ss_pred ccHHHHHHHHHHHHcCCeEEEEcCCCCCCCCCCCCCccC--CccchHHHHHHHHHHHhcC-CCceEEeeEEEeec
Confidence 345689999999999975 466753 33333 4688889998888888874 54 7776543
No 15
>PRK05406 LamB/YcsF family protein; Provisional
Probab=57.83 E-value=49 Score=30.18 Aligned_cols=76 Identities=17% Similarity=0.216 Sum_probs=48.2
Q ss_pred eEEEEeecccCcCCCCCCCCCCCCceeEEEcCCCcccCCCHHHHHHHHHHHhcCceEEEecCceE----EEEeecCCHHH
Q 024072 25 KLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLY----GFACDACSSEA 100 (273)
Q Consensus 25 ~~~~~~~~~~~RRfh~~~ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~~~L~~G~IvaiptdtgY----gL~cda~n~~A 100 (273)
++|+=.|. ||+|+....- ......|-++...++.++++.+++++|.|..+-+...- -|++...|+.|
T Consensus 160 ~~~~E~FA--DR~Y~~dG~L-------v~R~~~gAvi~d~~~v~~~~~~~~~~g~v~t~~G~~i~~~adTiCvHgD~p~A 230 (246)
T PRK05406 160 RTASEVFA--DRAYTADGTL-------VPRSQPGAVIHDEEEAAAQVLQMVQEGRVTAIDGEWIPVEADTICVHGDGPGA 230 (246)
T ss_pred cEEEEEEe--cCCcCCCCCC-------cCCCCCCCccCCHHHHHHHHHHHHHcCCEEecCCCEEeecCCeeEeCCCCHHH
Confidence 35666666 9999942211 11122344443334567899999998877665543221 36777889999
Q ss_pred HHHHHHHhC
Q 024072 101 VNRIYEIKG 109 (273)
Q Consensus 101 V~rLr~~K~ 109 (273)
|+-++++++
T Consensus 231 v~~a~~ir~ 239 (246)
T PRK05406 231 VAFARRIRA 239 (246)
T ss_pred HHHHHHHHH
Confidence 998888775
No 16
>PF03746 LamB_YcsF: LamB/YcsF family; InterPro: IPR005501 This entry represents the uncharacterised protein family UPF0271, including LamB. The lam locus of Emericella nidulans (Aspergillus nidulans) consists of two divergently transcribed genes, lamA and lamB, involved in the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression []. The exact molecular function of the proteins in this family is unknown.; PDB: 1V6T_A 1XW8_A 2XU2_A 2DFA_A.
Probab=48.03 E-value=54 Score=29.79 Aligned_cols=89 Identities=24% Similarity=0.350 Sum_probs=49.3
Q ss_pred hhhccCcccccc-------ccCCCeEEEEeecccCcCCCCCCCCCCCCceeEEEcCCCcccCCCHHHHHHHHHHHhcCce
Q 024072 8 AEKLPLLSSRVS-------LIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKV 80 (273)
Q Consensus 8 ~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~RRfh~~~ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~~~L~~G~I 80 (273)
...|||++.+-+ +-|. ++|+=.|. ||+|+.--. |.-....|-++...++.++++.+++++|.+
T Consensus 135 ~~~l~l~~~ags~~~~~A~~~Gl-~~~~E~FA--DR~Y~~dG~-------Lv~R~~~gAvi~d~~~~~~q~~~~~~~g~v 204 (242)
T PF03746_consen 135 DPDLPLYGLAGSELEKAAKELGL-PVVFEAFA--DRAYDDDGS-------LVPRSQPGAVIHDPEEAAEQVLQMVKEGSV 204 (242)
T ss_dssp -TT-EEEEETTSHHHHHHHHCT---EEEEEET--TBEB-TTSS-------BEETTSTTCB---HHHHHHHHHHHHHCSEE
T ss_pred CCCcEEEEcCCcHHHHHHHHCCC-cEEEEEEE--cccCcCCCC-------EeecCCCCCccCCHHHHHHHHHHHHhCCcE
Confidence 345777665433 2333 45555566 999994321 222334444543345678999999997765
Q ss_pred E-------EEecCceEEEEeecCCHHHHHHHHHHhC
Q 024072 81 I-------AVPTDTLYGFACDACSSEAVNRIYEIKG 109 (273)
Q Consensus 81 v-------aiptdtgYgL~cda~n~~AV~rLr~~K~ 109 (273)
. -++-| -|+....++.|++-++.+++
T Consensus 205 ~t~~G~~i~~~ad---TiCvHgD~p~Av~~a~~ir~ 237 (242)
T PF03746_consen 205 TTIDGKKIPIKAD---TICVHGDTPGAVEIAKAIRA 237 (242)
T ss_dssp EBTTSSEEE---S---EEEE-SSSHHHHHHHHHHHH
T ss_pred EecCCCEEEecCC---EEEeCCCChHHHHHHHHHHH
Confidence 4 44555 35677889999998888764
No 17
>PLN02349 glycerol-3-phosphate acyltransferase
Probab=47.22 E-value=22 Score=34.72 Aligned_cols=46 Identities=13% Similarity=0.189 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHhcCceEEE-----------ecCceEEEEeecCCHHHHHHHHHHhCCCC
Q 024072 65 EAHAEEAIQALKTGKVIAV-----------PTDTLYGFACDACSSEAVNRIYEIKGRKH 112 (273)
Q Consensus 65 ~~~i~~a~~~L~~G~Ivai-----------ptdtgYgL~cda~n~~AV~rLr~~K~R~~ 112 (273)
..++++....|++||.++. |-++-|. -+++|.++|+..|++=++..
T Consensus 280 ~kslk~~~~lL~~Gg~~iwIaPsGgRdR~d~~~g~~~--papFD~~svd~mR~l~~~s~ 336 (426)
T PLN02349 280 TRTLKEMALLLREGGQLIWIAPSGGRDRPDPLTGEWT--PAPFDPSAVDNMRRLTEKSK 336 (426)
T ss_pred HHHHHHHHHHHhcCCeEEEEeCCCCCCCCCccCCCcc--CCCCChHHHHHHHHHHHhcC
Confidence 4578888999999887776 3233333 47899999999999988773
No 18
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=45.88 E-value=34 Score=27.45 Aligned_cols=31 Identities=29% Similarity=0.287 Sum_probs=25.2
Q ss_pred CHHHHHHHHHHHhcCceEEEec-CceEEEEee
Q 024072 64 TEAHAEEAIQALKTGKVIAVPT-DTLYGFACD 94 (273)
Q Consensus 64 ~~~~i~~a~~~L~~G~Ivaipt-dtgYgL~cd 94 (273)
+.+.+++|.+.|++..+|+-|+ ||||-|.+-
T Consensus 74 ~~~~l~~A~~~L~~~d~VlgPa~DGGy~LiG~ 105 (122)
T PF09837_consen 74 TPDDLEQAFEALQRHDVVLGPAEDGGYYLIGL 105 (122)
T ss_dssp -HHHHHHHHHHTTT-SEEEEEBTTSSEEEEEE
T ss_pred CHHHHHHHHHHhccCCEEEeeccCCCEEEEec
Confidence 4577999999999999999996 788888774
No 19
>PRK12569 hypothetical protein; Provisional
Probab=44.71 E-value=95 Score=28.32 Aligned_cols=73 Identities=12% Similarity=0.195 Sum_probs=46.4
Q ss_pred EEEEeecccCcCCCCCCCCCCCCceeEEEcCCCcccCCCHHHHHHHHHHHhcCceEEEecCc----eEEEEeecCCHHHH
Q 024072 26 LWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDT----LYGFACDACSSEAV 101 (273)
Q Consensus 26 ~~~~~~~~~~RRfh~~~ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~~~L~~G~Ivaiptdt----gYgL~cda~n~~AV 101 (273)
+|+=.|. ||+|+.-.+ |......|-+ ..++.++++.+++++|.|..+-+.. .=-|+....|+.||
T Consensus 164 ~~~E~FA--DR~Y~~dG~-------Lv~R~~~gAv--d~~~~~~~~~~m~~~g~v~t~~G~~i~~~adTiCvHGD~p~Av 232 (245)
T PRK12569 164 VVREFYA--DRDYDDSGS-------IVFTRRVGAL--DPQQVAAKVLRACREGKVRTVDGKDIDIDFDSICIHSDTPGAL 232 (245)
T ss_pred eEEEEEe--cCccCCCCC-------EecCCCCCCC--CHHHHHHHHHHHHHcCCEEecCCCEEEecCCEEEECCCCHHHH
Confidence 4555566 999994321 1111223323 3346789999999998875554411 11367788899999
Q ss_pred HHHHHHhC
Q 024072 102 NRIYEIKG 109 (273)
Q Consensus 102 ~rLr~~K~ 109 (273)
+-++++++
T Consensus 233 ~~a~~ir~ 240 (245)
T PRK12569 233 ALARATRA 240 (245)
T ss_pred HHHHHHHH
Confidence 99988875
No 20
>PF05785 CNF1: Rho-activating domain of cytotoxic necrotizing factor; InterPro: IPR008430 This entry represents several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) is a toxin whose structure from Escherichia coli revealed a 4-layer alpha/beta/beta/alpha structure containing mixed beta-sheets []. CNF1 is expressed in strains of E. coli causing uropathogenic and neonatal meningitis. CNF1 alters host cell actin cytoskeleton and promotes bacterial invasion of the blood-brain barrier endothelial cells []. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton []. Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain [].; PDB: 1HZG_A 1HQ0_A.
Probab=43.02 E-value=11 Score=34.84 Aligned_cols=35 Identities=20% Similarity=0.252 Sum_probs=21.3
Q ss_pred cCCCCCeEEEEcCCcHHHHHHHHhCCCeEEEecCCCCCCCC
Q 024072 164 LNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPS 204 (273)
Q Consensus 164 l~~~~~tiGvrlP~~p~~~~Ll~~~g~PLv~TSAN~SGep~ 204 (273)
-++..+++|+|++=..+ .-|.|++.||+++||--+
T Consensus 102 ~NG~rGt~GikI~L~~i------~~g~pviitsG~LSGCT~ 136 (281)
T PF05785_consen 102 SNGARGTNGIKIALSDI------KEGKPVIITSGALSGCTM 136 (281)
T ss_dssp --BTEEEEEEEEEGGG-------BTTB-EEEE---BSS-EE
T ss_pred cCCCCcceeEEEEHHHc------CCCCeEEEeCCccCCCEE
Confidence 34567899999985543 457899999999999743
No 21
>COG0379 NadA Quinolinate synthase [Coenzyme metabolism]
Probab=37.19 E-value=35 Score=32.26 Aligned_cols=94 Identities=16% Similarity=0.252 Sum_probs=68.7
Q ss_pred HHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhcc---CCchHHHHhc
Q 024072 66 AHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVT---DHLPHGLLDS 142 (273)
Q Consensus 66 ~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~v---~~~~~~ll~~ 142 (273)
....+.+++|.-.+-|.+|+..- +|.-.+--.++.+++.|.+-.+-|..+.+.+-..++-++.+ |....+++++
T Consensus 79 ~FMaETAkiLnPeK~VL~Pd~~A---gCsmA~~~~~~~~~~~~~~~P~~~vV~YvNtsA~vKA~~Di~cTSsNAvkvVe~ 155 (324)
T COG0379 79 HFMAETAKILNPEKTVLLPDLEA---GCSMADMITAEEVRAFKEKHPDAPVVTYVNTSAEVKAEADICCTSSNAVKVVES 155 (324)
T ss_pred eehHhhHhhcCCCCeEecCCCCC---CCCcccCCCHHHHHHHHHHCCCCceEEEeeChHHHHhhcCeEEecchHHHHHHh
Confidence 34567889999999999998643 46655555668888888887789999999999999988763 5566778776
Q ss_pred cCCCCeEEEEccCCCCccccccC
Q 024072 143 LLPGPVTVVLSRGESSNLEKSLN 165 (273)
Q Consensus 143 ~~PgpiTvIl~~~~~~~l~~~l~ 165 (273)
.+.+.-++.+|.+ +|..+++
T Consensus 156 ~~~~~~Iif~PD~---~Lg~yva 175 (324)
T COG0379 156 ALDGDKILFLPDK---NLGRYVA 175 (324)
T ss_pred ccCCCcEEEcCcH---HHHHHHH
Confidence 4556665556643 3555554
No 22
>PRK09375 quinolinate synthetase; Provisional
Probab=31.34 E-value=75 Score=30.06 Aligned_cols=84 Identities=13% Similarity=0.184 Sum_probs=54.0
Q ss_pred HHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhhhcc---CCchHHHHhccC
Q 024072 68 AEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRFAVT---DHLPHGLLDSLL 144 (273)
Q Consensus 68 i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~~~v---~~~~~~ll~~~~ 144 (273)
..+.+.+|.-++.|.+|...- +|.-.+--..+.|+++|++-.+-...-.+.+-.+++.++.+ |..+.+.+.+..
T Consensus 79 MaEtAkIL~p~k~VllP~~~A---gC~mAd~~~~~~i~~lk~~~p~a~vVaYvNssaeVKA~aD~~cTSSnAl~iv~~~~ 155 (319)
T PRK09375 79 MAETAKILSPEKTVLLPDLEA---GCSLADMCPAEEFRAFKEAHPDATVVTYVNTSAAVKARADIVCTSSNAVKIVEALP 155 (319)
T ss_pred hhhhHHhcCCCCeEECCCCCC---CCcccccCCHHHHHHHHHHCCCCEEEEEeCCCHHHHHhCCeEEeCHHHHHHHhccC
Confidence 457889999999999998833 45444444456666666654344455556677777877764 545666777664
Q ss_pred CCCeEEEEcc
Q 024072 145 PGPVTVVLSR 154 (273)
Q Consensus 145 PgpiTvIl~~ 154 (273)
++-.++.+|-
T Consensus 156 ~~~~IlF~PD 165 (319)
T PRK09375 156 QGKKILFLPD 165 (319)
T ss_pred CCCeEEEeCc
Confidence 5665555553
No 23
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=28.13 E-value=21 Score=27.17 Aligned_cols=16 Identities=19% Similarity=0.111 Sum_probs=12.8
Q ss_pred CcCCC-CCCCCCCCCce
Q 024072 35 NRRFP-KKMAFSLENGQ 50 (273)
Q Consensus 35 ~RRfh-~~~ac~~cgp~ 50 (273)
.+-|| |...|..||=.
T Consensus 24 ~~syH~QKstC~~CGYp 40 (92)
T KOG3475|consen 24 RRSYHIQKSTCSSCGYP 40 (92)
T ss_pred chhhhhhcccccccCCc
Confidence 45699 99999999843
No 24
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=27.97 E-value=86 Score=22.95 Aligned_cols=34 Identities=18% Similarity=0.144 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHHhcCceEEE-ec-CceEEEEeecCC
Q 024072 64 TEAHAEEAIQALKTGKVIAV-PT-DTLYGFACDACS 97 (273)
Q Consensus 64 ~~~~i~~a~~~L~~G~Ivai-pt-dtgYgL~cda~n 97 (273)
+...+.++.+.|++.|+|-- +| .|||.|+.+|.+
T Consensus 38 ~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~~ 73 (83)
T PF02082_consen 38 SPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPEE 73 (83)
T ss_dssp -HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CCG
T ss_pred CHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHHH
Confidence 35678899999988777654 55 499999998744
No 25
>PF00926 DHBP_synthase: 3,4-dihydroxy-2-butanone 4-phosphate synthase; InterPro: IPR000422 3,4-dihydroxy-2-butanone 4-phosphate synthase (4.1.99.12 from EC) (DHBP synthase) (RibB) catalyses the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate, the latter serving as the biosynthetic precursor for the xylene ring of riboflavin []. In Photobacterium leiognathi, the riboflavin synthesis genes ribB (DHBP synthase), ribE (riboflavin synthase), ribH (lumazone synthase) and ribA (GTP cyclohydrolase II) all reside in the lux operon []. RibB is sometimes found as a bifunctional enzyme with GTP cyclohydrolase II that catalyses the first committed step in the biosynthesis of riboflavin (IPR000926 from INTERPRO). No sequences with significant homology to DHBP synthase are found in the metazoa.; GO: 0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity, 0009231 riboflavin biosynthetic process; PDB: 1K4O_A 1K4L_A 1K4P_A 1K49_A 1K4I_A 1TKU_A 1TKS_B 2RIS_A 2RIU_A 3MIO_A ....
Probab=27.15 E-value=1.4e+02 Score=26.07 Aligned_cols=57 Identities=33% Similarity=0.344 Sum_probs=32.9
Q ss_pred HHHHHHHHhcCceEEEecCc------eEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhh
Q 024072 68 AEEAIQALKTGKVIAVPTDT------LYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRF 129 (273)
Q Consensus 68 i~~a~~~L~~G~Ivaiptdt------gYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~ 129 (273)
|++|++.|++|+.|++=.+. -+-+.+..-+.+.|.-+.+- .+-+.-+.-+.+.+.++
T Consensus 1 ie~ai~al~~G~~Viv~D~~~rE~egdlv~aAe~~t~e~v~fm~~~-----~~Glicva~~~~~~~~L 63 (194)
T PF00926_consen 1 IEEAIEALKAGKPVIVVDDEDRENEGDLVFAAEFVTPEKVNFMIRH-----ASGLICVAMPEERADRL 63 (194)
T ss_dssp HHHHHHHHHTTS-EEEECSSTTT-EEEEEEEGGG--HHHHHHHHHH-----BCSEEEEEEEHHHHHHT
T ss_pred CHHHHHHHHCCCeEEEEeCCCCCcceeEEeEHHhCCHHHHHHHHHh-----cCCCeEecCCHHHHhHC
Confidence 57899999999999998754 45555555666666655442 23333333344555544
No 26
>TIGR00506 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase. Several members of the family are bifunctional, involving both ribA and ribB function. In these cases, ribA tends to be on the C-terminal end of the protein and ribB tends to be on the N-terminal.
Probab=26.50 E-value=1.4e+02 Score=26.22 Aligned_cols=58 Identities=21% Similarity=0.220 Sum_probs=39.6
Q ss_pred HHHHHHHHHhcCceEEEecCce------EEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhh
Q 024072 67 HAEEAIQALKTGKVIAVPTDTL------YGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRF 129 (273)
Q Consensus 67 ~i~~a~~~L~~G~Ivaiptdtg------YgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~ 129 (273)
.+++|++.|++|+.|++=.+-. +-+.+...+++.|..+.+- .+-++-+.-+.+.++++
T Consensus 4 ~ie~ai~al~~G~~Viv~Dd~~REnEgdlv~aAe~~T~e~v~fm~~~-----~~GliC~~~~~~~a~~L 67 (199)
T TIGR00506 4 RVEEALEALKKGEIVLVYDDEDRENEGDLIVAAEFITPEQIAFMRRH-----AGGLICVAITPDIADKL 67 (199)
T ss_pred hHHHHHHHHHCCCeEEEEeCCCCCccEeEEEEhhhCCHHHHHHHHHh-----CCCCEEEECCHHHHhhC
Confidence 4889999999999999976533 4566666777777766542 24455555556666554
No 27
>PF00639 Rotamase: PPIC-type PPIASE domain; InterPro: IPR000297 Peptidylprolyl isomerase (5.2.1.8 from EC) is an enzyme that accelerates protein folding by catalyzing the cis-trans isomerization of proline imidic peptide bonds in oligopeptides []. It has been reported in bacteria and eukayotes. Synonyms for proteins with this domain are: Peptidylprolyl isomerase, Peptidyl-prolyl cis-trans isomerase, PPIase, rotamase, cyclophilin, FKBP65.; GO: 0016853 isomerase activity; PDB: 2JZV_A 2PV3_B 1M5Y_A 2PV2_B 2PV1_A 1JNS_A 1JNT_A 3KAB_A 2ZR6_A 2XPB_A ....
Probab=26.05 E-value=1.4e+02 Score=22.20 Aligned_cols=29 Identities=34% Similarity=0.393 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHhcCce-EEEecCceEEEEe
Q 024072 65 EAHAEEAIQALKTGKV-IAVPTDTLYGFAC 93 (273)
Q Consensus 65 ~~~i~~a~~~L~~G~I-vaiptdtgYgL~c 93 (273)
...+.+++..|+.|.| -.+.|..|||+.-
T Consensus 63 ~~~~~~~~~~l~~Gevs~pi~t~~G~~Ii~ 92 (95)
T PF00639_consen 63 PPEFEKALFALKPGEVSKPIETDNGYHIIK 92 (95)
T ss_dssp BHHHHHHHHTSTTTSBEEEEEETTEEEEEE
T ss_pred cHHHHHHHHhCCCCCcCCCEEECCEEEEEE
Confidence 3568999999999999 4589999999863
No 28
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=25.12 E-value=62 Score=25.63 Aligned_cols=48 Identities=15% Similarity=0.148 Sum_probs=27.4
Q ss_pred CCCCCCceeEEEcCCCcccCCCHHHHHHHH--HHHhcC---ceEEEecCceEEE
Q 024072 43 AFSLENGQVSVENKAGLVRPATEAHAEEAI--QALKTG---KVIAVPTDTLYGF 91 (273)
Q Consensus 43 ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~--~~L~~G---~IvaiptdtgYgL 91 (273)
-|+.||...+++-+... .++-.++++.-+ +...+| .-|-+...|.|-|
T Consensus 22 GCp~CG~nkF~yv~~e~-rpa~~e~~d~~vrde~~a~ge~ietIrI~~pG~Yei 74 (112)
T COG3364 22 GCPKCGCNKFLYVPEEK-RPAVAEAADPEVRDEDGAQGEPIETIRILRPGVYEI 74 (112)
T ss_pred cCccccchheEeccccc-ccchhhhcCCcccchhhcccCcceEEEEecCceEEE
Confidence 59999999887644321 111111111111 244456 6777888888876
No 29
>KOG2949 consensus Ketopantoate hydroxymethyltransferase [Coenzyme transport and metabolism]
Probab=23.67 E-value=67 Score=29.25 Aligned_cols=40 Identities=20% Similarity=0.217 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHH
Q 024072 62 PATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYE 106 (273)
Q Consensus 62 ~~~~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~ 106 (273)
....++++.|++.++.||.=++|-++|= ..--+++++|-+
T Consensus 113 S~~sda~knAv~vmk~~g~~~vK~EgGs-----~~~~~~~~~l~e 152 (306)
T KOG2949|consen 113 SSWSDAVKNAVRVMKEGGMDAVKLEGGS-----NSRITAAKRLVE 152 (306)
T ss_pred ccHHHHHHHHHHHHHhcCCceEEEccCc-----HHHHHHHHHHHH
Confidence 4456899999999999999999999983 333455666654
No 30
>COG5441 Uncharacterized conserved protein [Function unknown]
Probab=22.23 E-value=1.2e+02 Score=28.77 Aligned_cols=89 Identities=19% Similarity=0.223 Sum_probs=51.2
Q ss_pred hhccCcccc--ccccCCCeEEEEeecccCcCCCCCCCCCCCCceeEEEcCCCcccCCCHHHHHHHH-HHHh--cCce-EE
Q 024072 9 EKLPLLSSR--VSLIGVPKLWFVSFLHLNRRFPKKMAFSLENGQVSVENKAGLVRPATEAHAEEAI-QALK--TGKV-IA 82 (273)
Q Consensus 9 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~RRfh~~~ac~~cgp~~~~~~~~~~~~~~~~~~i~~a~-~~L~--~G~I-va 82 (273)
..||.++|+ +|-+.|+-.--|+..-.||+||..| |++.+.... ++.-.++.+.+ +.|+ +|-+ ++
T Consensus 264 t~lPyvgs~GAlDMVnf~a~~tVPeqyr~R~~~~HN------~~vtlmrts----pee~~ai~rwig~kLn~c~gpvrFl 333 (401)
T COG5441 264 TGLPYVGSCGALDMVNFGAPETVPEQYRDRLFYAHN------PQVTLMRTS----PEECRAIGRWIGAKLNLCAGPVRFL 333 (401)
T ss_pred cCCCccccccceeeecCCCcccChHHhcCcchhhcC------CceeEEeCC----HHHHHHHHHHHHHHHhhccCceEEE
Confidence 468999987 7888888877888888899999644 334553222 11112232222 3333 4544 56
Q ss_pred EecCceEEEEeec---CCHHHHHHHHHH
Q 024072 83 VPTDTLYGFACDA---CSSEAVNRIYEI 107 (273)
Q Consensus 83 iptdtgYgL~cda---~n~~AV~rLr~~ 107 (273)
+|+-|+-.|=... ++++|..-+++-
T Consensus 334 iPe~GvsalD~~G~pf~dpeA~aa~~~a 361 (401)
T COG5441 334 IPEGGVSALDAPGQPFHDPEADAALFEA 361 (401)
T ss_pred ecCCCcccccCCCCcCCChHHHHHHHHH
Confidence 7877775553221 355555555443
No 31
>TIGR02925 cis_trans_EpsD peptidyl-prolyl cis-trans isomerase, EpsD family. Members of this family belong to the peptidyl-prolyl cis-trans isomerase family and are found in loci associated with exopolysaccharide biosynthesis. All members are encoded near a homolog of EpsH, as detected by TIGR02602.
Probab=21.72 E-value=1e+02 Score=26.86 Aligned_cols=28 Identities=18% Similarity=0.113 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhcCceEEEecCceEEEEe
Q 024072 66 AHAEEAIQALKTGKVIAVPTDTLYGFAC 93 (273)
Q Consensus 66 ~~i~~a~~~L~~G~IvaiptdtgYgL~c 93 (273)
..+..++..|+.|++..+.|..|||+.=
T Consensus 194 ~~~~~a~~~l~~G~is~v~s~~G~hiik 221 (232)
T TIGR02925 194 AEILAVLAKLKPGAPLVVQGPNNVLILV 221 (232)
T ss_pred HHHHHHHHhCCCCCeEEeecCCceEEEE
Confidence 4578899999999999999999999865
No 32
>PRK05773 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated
Probab=21.64 E-value=2e+02 Score=25.76 Aligned_cols=57 Identities=18% Similarity=0.111 Sum_probs=41.5
Q ss_pred HHHHHHHHhcCceEEEecC------ceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEECCHHHHhhh
Q 024072 68 AEEAIQALKTGKVIAVPTD------TLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINRF 129 (273)
Q Consensus 68 i~~a~~~L~~G~Ivaiptd------tgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~~dl~~l~~~ 129 (273)
+++|++.|++|+.|++=-+ |-+-+.+..-+++.+..+++- ..-++-+.-+.+.++++
T Consensus 3 ie~ai~al~~G~~Viv~Dde~REnEgDlv~aAe~vT~e~i~fm~~~-----a~GliCval~~~~a~~L 65 (219)
T PRK05773 3 FEEARKALESGIPVLIYDFDGREEEVDMVFYAGAVTWKSIYTLRKN-----AGGLICYATSNSEGKTL 65 (219)
T ss_pred HHHHHHHHHCCCeEEEEECCCCCccccEEEEhhhCCHHHHHHHHHH-----CCceEEEeCCHHHHhhC
Confidence 6889999999998888753 667778888888888877652 34555555566666664
No 33
>COG0288 CynT Carbonic anhydrase [Inorganic ion transport and metabolism]
Probab=21.47 E-value=1.6e+02 Score=25.91 Aligned_cols=74 Identities=15% Similarity=0.105 Sum_probs=52.9
Q ss_pred ccccCCCeEEEEeecccCcCCCCCCCCCCCCce-eEEEcCCCcccC----CCHHHHHHHHHHHhcCceEEEecCceEEEE
Q 024072 18 VSLIGVPKLWFVSFLHLNRRFPKKMAFSLENGQ-VSVENKAGLVRP----ATEAHAEEAIQALKTGKVIAVPTDTLYGFA 92 (273)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~RRfh~~~ac~~cgp~-~~~~~~~~~~~~----~~~~~i~~a~~~L~~G~IvaiptdtgYgL~ 92 (273)
+.+.--|+.+|++=. |.|.+.+ -+-.++|. ++....-|.+++ ..-..++-|++.|+-..||++-....=+..
T Consensus 30 ~~~~Q~P~~lii~C~--DSRv~~e-~i~~~~pGdlfV~RNaGniV~~~~~~~l~sleyAv~~L~v~~IiV~GH~~CGav~ 106 (207)
T COG0288 30 ADKGQSPKALIITCS--DSRVPPE-LITGLGPGDLFVIRNAGNIVTHPDGSVLRSLEYAVYVLGVKEIIVCGHTDCGAVK 106 (207)
T ss_pred hccCCCCcEEEEEEc--cCCCCHH-HHhCCCCccEEEEeecccccCCCccchhHHHHHHHHHcCCCEEEEecCCCcHHHH
Confidence 345578999999988 9999932 35567776 555555666664 223578999999999999999876654444
Q ss_pred ee
Q 024072 93 CD 94 (273)
Q Consensus 93 cd 94 (273)
+.
T Consensus 107 aa 108 (207)
T COG0288 107 AA 108 (207)
T ss_pred hc
Confidence 43
No 34
>PRK01130 N-acetylmannosamine-6-phosphate 2-epimerase; Provisional
Probab=21.39 E-value=5.3e+02 Score=22.19 Aligned_cols=43 Identities=12% Similarity=0.152 Sum_probs=27.4
Q ss_pred CHHHHHHHHHHHhcCceEEEecCceEEEEeecCCHHHHHHHHHHhCCCCCCCcEEEE
Q 024072 64 TEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICV 120 (273)
Q Consensus 64 ~~~~i~~a~~~L~~G~IvaiptdtgYgL~cda~n~~AV~rLr~~K~R~~~KPfavm~ 120 (273)
..+.+.+.++...+||..++-.. +.+.++++++ .. ++||..|.
T Consensus 21 ~~~~~~~~a~a~~~~G~~~~~~~----------~~~~i~~i~~---~~-~~Pil~~~ 63 (221)
T PRK01130 21 SPEIMAAMALAAVQGGAVGIRAN----------GVEDIKAIRA---VV-DVPIIGII 63 (221)
T ss_pred CHHHHHHHHHHHHHCCCeEEEcC----------CHHHHHHHHH---hC-CCCEEEEE
Confidence 34556778888888887666643 2455555544 33 58887664
No 35
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=20.57 E-value=1.3e+02 Score=24.77 Aligned_cols=30 Identities=17% Similarity=0.129 Sum_probs=25.5
Q ss_pred HHHHHHHHHhcCceEEEecCceEEEEeecC
Q 024072 67 HAEEAIQALKTGKVIAVPTDTLYGFACDAC 96 (273)
Q Consensus 67 ~i~~a~~~L~~G~IvaiptdtgYgL~cda~ 96 (273)
.++.+.+.|.+|+.|-+++.|.|.+.-.+.
T Consensus 58 l~~~i~~~L~~G~~V~L~gfGtF~~~~~s~ 87 (145)
T TIGR01201 58 LAYVLRRELANGKTVRLGEIGTFRLSATAK 87 (145)
T ss_pred HHHHHHHHHhCCCeEEeCCCEEEEEEeccC
Confidence 356667889999999999999999988654
Done!