Query T0542 NH3-DEPENDENT NAD+ SYNTHETASE, STREPTOMYCES AVERMITILIS, 590 residues
Match_columns 590
No_of_seqs 250 out of 3532
Neff 7.5
Searched_HMMs 11830
Date Fri May 21 18:09:36 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0542.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0542.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02540 NAD_synthase: NAD syn 100.0 0 0 481.5 19.9 237 309-557 1-241 (242)
2 PF00795 CN_hydrolase: Carbon- 100.0 1.1E-29 9.4E-34 210.9 14.4 167 6-189 1-184 (184)
3 PF03054 tRNA_Me_trans: tRNA m 99.4 1.4E-12 1.1E-16 98.3 9.1 144 327-475 1-186 (356)
4 PF01171 ATP_bind_3: PP-loop f 98.6 3E-07 2.5E-11 63.1 11.5 137 328-473 1-160 (182)
5 PF06508 ExsB: ExsB; InterPro 98.3 4.2E-07 3.5E-11 62.1 5.9 63 328-392 1-63 (137)
6 PF00733 Asn_synthase: Asparag 98.3 1.9E-06 1.6E-10 57.8 8.9 134 309-445 2-139 (269)
7 PF02568 ThiI: Thiamine biosyn 98.2 1.9E-05 1.6E-09 51.1 12.1 144 327-475 4-162 (197)
8 PF01507 PAPS_reduct: Phosphoa 98.0 5.5E-05 4.7E-09 48.2 11.0 144 328-473 1-152 (174)
9 PF00764 Arginosuc_synth: Argi 96.7 0.0078 6.6E-07 34.0 9.3 140 330-474 1-156 (389)
10 PF01902 ATP_bind_4: ATP-bindi 95.6 0.011 9.4E-07 32.9 5.9 61 328-391 2-68 (218)
11 PF04273 DUF442: Putative phos 74.6 1.7 0.00015 18.5 4.8 93 331-425 9-108 (110)
12 PF05201 GlutR_N: Glutamyl-tRN 47.7 0.7 5.9E-05 21.1 -1.8 20 422-441 33-52 (152)
13 PF10042 DUF2278: Uncharacteri 40.5 6.7 0.00057 14.6 3.6 21 230-250 175-195 (206)
14 PF01488 Shikimate_DH: Shikima 38.3 7.3 0.00061 14.4 5.4 59 324-393 11-70 (135)
15 PF10871 DUF2748: Protein of u 35.1 7.2 0.00061 14.4 1.8 53 417-470 307-361 (447)
16 PF01156 IU_nuc_hydro: Inosine 31.9 9.2 0.00077 13.7 6.4 15 373-388 177-191 (312)
17 PF01121 CoaE: Dephospho-CoA k 30.8 9.5 0.00081 13.6 2.4 102 329-439 1-117 (180)
18 PF10649 DUF2478: Protein of u 27.7 11 0.00091 13.3 4.0 40 174-218 87-129 (159)
19 PF01553 Acyltransferase: Acyl 24.6 12 0.001 12.9 2.7 14 35-48 91-104 (135)
20 PF01888 CbiD: CbiD; InterPro 23.6 13 0.0011 12.8 2.8 31 413-443 185-216 (261)
21 PF06711 DUF1198: Protein of u 21.9 14 0.0012 12.6 4.8 31 368-400 23-53 (148)
22 PF09086 DUF1924: Domain of un 20.4 15 0.0012 12.4 1.9 23 537-559 66-88 (98)
No 1
>PF02540 NAD_synthase: NAD synthase; InterPro: IPR003694 NAD+ synthase (6.3.5.1 from EC) catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide and is induced by stress factors such as heat shock and glucose limitation. The three-dimensional structure of NH3-dependent NAD+ synthetase from Bacillus subtilis, in its free form and in complex with ATP shows that the enzyme consists of a tight homodimer with alpha/beta subunit topology .; GO: 0003952 NAD+ synthase (glutamine-hydrolyzing) activity, 0005524 ATP binding, 0009435 NAD biosynthetic process; PDB: 1xng_B 1xnh_A 2dpl_B 2z0c_B 2vxo_A 1gpm_C 2e18_A 3hmq_A 1wxe_A 1wxi_A ....
Probab=100.00 E-value=0 Score=481.54 Aligned_cols=237 Identities=48% Similarity=0.743 Sum_probs=230.0
Q ss_pred HHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEC
Q ss_conf 88999999999998415683489705883689999999851695517988778889828779999999997198479834
Q T0542 309 VYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVS 388 (590)
Q Consensus 309 ~~~a~~~~l~d~~~~~g~~~~viglSGGiDS~~~~~la~~a~g~~~v~~~~mp~~~~s~~~~~~a~~la~~lg~~~~~i~ 388 (590)
+|++++.+|+||++++|++++|||||||+||||+|+||++|+|++||+|++||+.++++.+.++|+.+|+.||+++.+++
T Consensus 1 ~i~~l~~~L~~~v~~~g~~~vvlglSGGvDSav~A~La~~AlG~~~v~~v~~p~~~~~~~~~~~a~~la~~lgi~~~~i~ 80 (242)
T PF02540_consen 1 IIEALVEFLRDYVKKSGAKGVVLGLSGGVDSAVVAALAVKALGPDNVLAVFMPSGFSSKEDIEDAKELAKKLGINHIVID 80 (242)
T ss_dssp -HHHHHHHHHHHHHHTTT-EEEEEE----HHHHHHHHHHHHHTCGEEEEEEEESSSTTHHHHHHHHHHHHHHTSEEEEEE
T ss_pred CHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHHCCEEEEEE
T ss_conf 98999999999999819980999757987899999999997631341476248888987899999999998299189997
Q ss_pred HHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHHHHHHHHHCCEEEECCCHHHHHHHHHHHCCCCCCCHHHCCCCCHHHHH
Q ss_conf 59999999986183--5740665556578999999997619789874866777552033306771112230688788999
Q T0542 389 IEPMFDAYMASLGL--TGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIF 466 (590)
Q Consensus 389 i~~~~~~~~~~~~~--~~~~~~N~qaR~R~~~l~~~a~~~~~lvl~t~n~sE~~lG~~t~~Gd~~~~~~p~~~l~Kt~v~ 466 (590)
|+++++++.+.+.. .+++.+|+|||+||.+||++||..|++|+||||+||.++||+|+|||+++|++||++|||++|+
T Consensus 81 i~~~~~~~~~~~~~~~~~~~~~Ni~aR~R~~~ly~~A~~~~~lVlgT~n~sE~~~Gy~Tk~GD~~~di~Pi~~L~K~eV~ 160 (242)
T PF02540_consen 81 ISEIFDAFLKGLEPAEKDIARGNIQARIRMTILYALANKLGYLVLGTGNKSELLLGYFTKYGDGAGDIAPIADLYKTEVR 160 (242)
T ss_dssp SHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHT-EB----CHHHHH----S-------SBETTTTS-HHHHH
T ss_pred CHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCHHHHHHCCCCCCCCCCCCEEEECCCCHHHHH
T ss_conf 90899853566530000355543568999999999988549769878738677608765457677550135896989999
Q ss_pred HHHHHHHHCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCC-CHHHHHHHHHHHHHCCCCHHHHHH-CCCCHHHHHHH
Q ss_conf 9999861002111332135377725888866678888600257-866899999999856898799986-17899899999
Q T0542 467 RLAEWRNRAAAERGQTPPIPEASITKPPSAELRPGQVDTDSLP-DYPVLDAILELYVDRDTGADAIVA-AGYDRELVVKT 544 (590)
Q Consensus 467 ~la~~~~~~~~~~~~~~~~p~~i~~~~psaeL~~~q~de~~lg-~y~~lD~~l~~~~~~~~~~~~i~~-~~~~~~~v~~~ 544 (590)
+||+|++ +|++|++|+||||||++|+||++|| ||+++|.||+ +++++.++++|.. .+++++.++++
T Consensus 161 ~La~~l~-----------ip~~ii~k~Psa~L~~~q~DE~elg~~Y~~lD~~l~-~~~~~~~~~~i~~~~~~~~~~~~~i 228 (242)
T PF02540_consen 161 ELARYLG-----------IPESIIDKPPSAELWPGQTDEDELGFSYEELDAILY-LIEEGLSPEEIAEELGIDKEIVERI 228 (242)
T ss_dssp HHHHHTT-------------HHHHHS--BHHCSTT-BHHHH----HHHHHHHHH-HCTSS---HHHHHC----HHHHHHH
T ss_pred HHHHHHC-----------CHHHHHCCCCCCCCCCCCCCHHHHCCCHHHHHHHHH-HHHCCCCHHHHHHHCCCCHHHHHHH
T ss_conf 9999978-----------669995699998889999789883979999999999-9874999999987529999999999
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 9999851566863
Q T0542 545 LRMVDTAEYKRRQ 557 (590)
Q Consensus 545 ~~~~~~~~~KR~~ 557 (590)
.+++.+|+|||++
T Consensus 229 ~~~~~~~~hKr~~ 241 (242)
T PF02540_consen 229 LRLVKRSEHKRRQ 241 (242)
T ss_dssp HHHHHHTGGGGSS
T ss_pred HHHHHHHHHCCCC
T ss_conf 9999951242279
No 2
>PF00795 CN_hydrolase: Carbon-nitrogen hydrolase The Prosite family is specific to nitrilases The Prosite family is specific to UPF0012; InterPro: IPR003010 This family contains nitrilases that break carbon-nitrogen bonds and appear to be involved in the reduction of organic nitrogen compounds and ammonia production . They all have distinct substrate specificity and include cyanide hydratases, aliphatic amidases, beta-alanine synthase, and a few other proteins with unknown molecular function. Sequence conservation over the entire length, as well as the similarity in the reactions catalyzed by the known enzymes in this family, points to a common catalytic mechanism. They have an invariant cysteine that is part of the catalytic site in nitrilases. Another highly conserved motif includes an invariant glutamic acid that might also be involved in catalysis .; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0006807 nitrogen compound metabolic process; PDB: 1ems_B 2e11_D 2e2k_E 2dyu_A 2e2l_E 2dyv_B 2plq_A 2uxy_A 2vhh_D 2vhi_C ....
Probab=99.96 E-value=1.1e-29 Score=210.95 Aligned_cols=167 Identities=35% Similarity=0.547 Sum_probs=133.5
Q ss_pred EEEEEECCC--CCCCHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCH--HHHHHHHH-H----HHHHHHHHHHHHHH
Q ss_conf 899996067--416889999999999999996799699826400378881--23331068-8----99999999999998
Q T0542 6 RLALNQIDS--TVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPV--EDLALRSS-F----VEASRTALRELAAR 76 (590)
Q Consensus 6 kIAlaQ~~~--~~gD~~~N~~ki~~~i~~A~~~gadLVVfPEl~ltGY~~--~Dl~~~~~-~----~~~~~~~l~~la~~ 76 (590)
|||++|+++ ..+|.++|++++.+++++|+++|++||||||++++||+. .+...... . .......+.++++
T Consensus 1 ~vA~~Q~~~~~~~~~~~~n~~~~~~~~~~a~~~~~~liv~PE~~l~g~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~a~- 79 (184)
T PF00795_consen 1 KVALVQLNPDQSWGDIEENLERILRLIEEAARAGADLIVFPELALPGYPFWCWDDAADADEFAESLDGPELARLRELAR- 79 (184)
T ss_dssp EEEEEEB---SSCCHHHHHHHHHHHHHHHHHHHTESEEEB-TTTTS-SGGSCCSSHHHHHCHCBSSCCHHHHHHHHHHH-
T ss_pred CEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEECCHHHHHCCCHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_conf 9999989856776899999999999999999879979992704430030100100677888777630279999999999-
Q ss_pred HHHHCCCCEEEEEEEEECCCCCCCCCCCCCCCEEEEEEEEEC-CEEEEEECCEECCCCCCCC-CHHHCCCC-CCCCEEEE
Q ss_conf 652010881899832110355433444578823889999818-8179987327707987643-01220169-96106886
Q T0542 77 LAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHR-GRVALTFAKHHLPNYGVFD-EFRYFVPG-DTMPIVRL 153 (590)
Q Consensus 77 ~~~~~~~~i~ivvG~~~~~~~~~~~~~~~~g~lyNsa~vi~~-G~ii~~y~K~~Lp~~~~~~-E~r~f~~G-~~~~v~~~ 153 (590)
..++.+++|.+++. ++++||+++++++ |++++.|+|+||++++++. |++||.+| ...++|++
T Consensus 80 -----~~~~~i~~G~~~~~----------~~~~~N~~~~~~~~g~~~~~y~K~~lvpf~~~~Pe~~~~~~~~~~~~~~~~ 144 (184)
T PF00795_consen 80 -----KYGIYIVFGAPERD----------DGRLYNSAVVIDPDGEIIGRYRKRHLVPFGEYIPERRYFSPGGQELPVFDT 144 (184)
T ss_dssp -----HHTSEEEEEEEEEC----------TCEEEEEEEEE-----EEEEEE-SS-ESECTTTTHHHHSB----EE-EEEE
T ss_pred -----HCCCCCCCCCCEEE----------CCCEEEEEEEEECCCCCCCEECCCCCCCCCCEEEEEEEECCCCCCCEEEEC
T ss_conf -----65980005852132----------485224799997998621164144413211200000264133552126740
Q ss_pred -----CCEEEEEEEEHHHHCCHHHHHHHHHCCCCEEEEECC
Q ss_conf -----785788562023414418999999637978998327
Q T0542 154 -----HGVDIALAICEDLWQDGGRVPAARSAGAGLLLSVNA 189 (590)
Q Consensus 154 -----~g~riGi~IC~D~w~~~~~~~~la~~Gadlii~psa 189 (590)
+++|+|++||||.|| ++..+.++.+|+|++++|||
T Consensus 145 ~~~~~~g~~ig~~ICyd~~f-p~~~~~~~~~ga~il~~psa 184 (184)
T PF00795_consen 145 PVFDIGGGRIGILICYDIRF-PELARILAAKGADILLNPSA 184 (184)
T ss_dssp TETC---EEEEEEEGGGGGS-HHHHHHHHH----EEEEEE-
T ss_pred CCEEECCCEEEEEEECCCCC-HHHHHHHHHCCCCEEEECCC
T ss_conf 52430241799999521172-29999999879989997689
No 3
>PF03054 tRNA_Me_trans: tRNA methyl transferase; InterPro: IPR004506 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (2.1.1.61 from EC) catalyses the addition of 5-methylaminomethyl-2-thiouridylate to tRNAs using S-adenosyl-L-methionine as a substrate and releasing S-adenosyl-L-homocysteine. The enzyme is cytoplasmic and is involved in tRNA processing.; GO: 0004808 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 2der_A 2deu_A 2det_A 2hma_A.
Probab=99.36 E-value=1.4e-12 Score=98.31 Aligned_cols=144 Identities=20% Similarity=0.270 Sum_probs=99.1
Q ss_pred CCEEEECCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCC---------CHHHHHHHHHHHHHCCCCEEEECHHHHHHH--
Q ss_conf 834897058836899999998516955179887788898---------287799999999971984798345999999--
Q T0542 327 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYS---------SDHSKGDAAELARRTGLNFRTVSIEPMFDA-- 395 (590)
Q Consensus 327 ~~~viglSGGiDS~~~~~la~~a~g~~~v~~~~mp~~~~---------s~~~~~~a~~la~~lg~~~~~i~i~~~~~~-- 395 (590)
++|++++|||+|||++|+|..++ | -+|+|++|-.-.. ++.+..+|+.+|+.|||++.++|++..+..
T Consensus 1 ~rV~vamSGGVDSsvaa~LL~e~-G-~~V~gv~m~~~~~~~~~~~~C~~~~d~~da~~va~~LgIp~~v~d~~~~f~~~V 78 (356)
T PF03054_consen 1 KRVAVAMSGGVDSSVAAALLKEQ-G-YDVIGVTMRNWDDEDEPGGSCCSEEDIEDARKVAEQLGIPHYVVDLREEFWEEV 78 (356)
T ss_dssp -EEE-------HHHHHHHHHHH-----EEE--EEE-SS-----H-HHHHHHHHHHHHHHHHH------EEETHHHHHHHT
T ss_pred CEEEEECCCCHHHHHHHHHHHHH-C-CCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHH
T ss_conf 94999836778999999999972-8-774069999961677666678746679999999998699889988799998999
Q ss_pred ---HHHHC----CC-CCCHHHHHHHHHHHHHHHHHHHH-HCCEEEECCCHHHHHHHH-----H-----HHCCCCCC----
Q ss_conf ---99861----83-57406655565789999999976-197898748667775520-----3-----33067711----
Q T0542 396 ---YMASL----GL-TGLAEENLQSRLRGTTLMAISNQ-EGHIVLAPGNKSELAVGY-----S-----TLYGDSVG---- 452 (590)
Q Consensus 396 ---~~~~~----~~-~~~~~~N~qaR~R~~~l~~~a~~-~~~lvl~t~n~sE~~lG~-----~-----t~~Gd~~~---- 452 (590)
|.+.. .+ .++ .=| .++.--.|+..|.. .|.=-+.||+..-..-+- . -..=|++-
T Consensus 79 i~~f~~~Y~~G~TPNPcv-~CN--~~IKFg~l~~~a~~~~g~d~iATGHYAr~~~~~~~~~~~L~r~~D~~KDQSYFL~~ 155 (356)
T PF03054_consen 79 IDPFVDEYKKGRTPNPCV-LCN--RHIKFGALLERADEGLGADYIATGHYARIVEDEEDGRYRLLRGKDPNKDQSYFLSR 155 (356)
T ss_dssp HHHHHHHHH------HHH-HHH--HHTTTTHHHHHHHTT----EEE-----EEEE------EEEE----TTC--GGGGTT
T ss_pred HHHHHHHHHCCCCCCCHH-HHC--CHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCEEEEECCCCCCCCEEEEEC
T ss_conf 999999986899999313-547--32039999999997659996466637996405779957993558998886558963
Q ss_pred --------CHHHCCCCCHHHHHHHHHHHHHC
Q ss_conf --------12230688788999999986100
Q T0542 453 --------AYGPIKDVYKTSIFRLAEWRNRA 475 (590)
Q Consensus 453 --------~~~p~~~l~Kt~v~~la~~~~~~ 475 (590)
-+=|||+++|.+|+++|+-++-.
T Consensus 156 l~q~~L~~~iFPLG~~~K~eVR~~A~~~gl~ 186 (356)
T PF03054_consen 156 LPQEQLSRLIFPLGELTKEEVREIAREAGLP 186 (356)
T ss_dssp --HHHHCCEE-------HHHHHHHHHH---T
T ss_pred CCHHHHHHHHCCCCCCCHHHHHHHHHHCCCC
T ss_conf 8999984352567668789999999986998
No 4
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This group of proteins belongs to the PP-loop superfamily . ; PDB: 2e89_B 2e21_C 1wy5_A 1ni5_A.
Probab=98.62 E-value=3e-07 Score=63.12 Aligned_cols=137 Identities=21% Similarity=0.212 Sum_probs=93.7
Q ss_pred CEEEECCCCHHHHHHHHHHHHCCCC--CCEEEEECC--CCCCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHHHHCCCC
Q ss_conf 3489705883689999999851695--517988778--889828779999999997198479834599999999861835
Q T0542 328 SVLIGLSGGIDSALVAAIACDALGA--QNVYGVSMP--SKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLT 403 (590)
Q Consensus 328 ~~viglSGGiDS~~~~~la~~a~g~--~~v~~~~mp--~~~~s~~~~~~a~~la~~lg~~~~~i~i~~~~~~~~~~~~~~ 403 (590)
+++||+|||.||.+.+.++.+-... -++.+++.- -...|....+..+.+++.+|+++.+..++. . ...
T Consensus 1 kilvavSGGkDS~~Ll~ll~~~~~~~~~~~~~~~vdh~~~~~s~~~~~~v~~~~~~~gi~~~~~~~~~------~--~~~ 72 (182)
T PF01171_consen 1 KILVAVSGGKDSMALLHLLKDLNRRLGIKLIVVHVDHGIRSESDEEAEFVEEYCEKLGIPLIIKRLDE------S--KQK 72 (182)
T ss_dssp EEEEE-----HHHHHHHHHHHHCTTTT-EEEEEEE--SSSTCHHHHHHHHHHHHHHTT-EEEEE---H------H--HHT
T ss_pred CEEEEECCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEE------H--HCC
T ss_conf 99999767799999999999999867997899998478886444899999999998199769999876------1--025
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHCCEEEECCC----HHHHHHHHHHHCCCC---------------CCCHHHCCCCCHHH
Q ss_conf 74066555657899999999761978987486----677755203330677---------------11122306887889
Q T0542 404 GLAEENLQSRLRGTTLMAISNQEGHIVLAPGN----KSELAVGYSTLYGDS---------------VGAYGPIKDVYKTS 464 (590)
Q Consensus 404 ~~~~~N~qaR~R~~~l~~~a~~~~~lvl~t~n----~sE~~lG~~t~~Gd~---------------~~~~~p~~~l~Kt~ 464 (590)
....++..-+.|-..+..+|.+.|+-+|-||+ ..|..+.-... |.+ .--+=|+-.++|.+
T Consensus 73 ~~~~e~~aR~~R~~~l~~~a~~~~~~~l~~gHh~dD~~Et~l~~l~~-g~~~~~l~~~~~~~~~~~~~iiRPLl~~~~~e 151 (182)
T PF01171_consen 73 GSNFEACARKLRYQFLNEIARENGADKLATGHHLDDQAETFLMNLLR-GGGLRGLSGMPPVSEREGIRIIRPLLYVSKKE 151 (182)
T ss_dssp T--TTTHHHHHHHHHHHHCHHH----EEE---BHHHHHHHHHHHHC-------------SEEE---TCEE-CCCT--HHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHH-HHCCCCCCCCCCCCCCCCCEEECCCHHCCHHH
T ss_conf 78989999999999999876540000132236751689999999998-70545567686101356744860540085999
Q ss_pred HHHHHHHHH
Q ss_conf 999999861
Q T0542 465 IFRLAEWRN 473 (590)
Q Consensus 465 v~~la~~~~ 473 (590)
+.++++..+
T Consensus 152 i~~~~~~~~ 160 (182)
T PF01171_consen 152 IEAYARENG 160 (182)
T ss_dssp HHHHHHHTT
T ss_pred HHHHHHHCC
T ss_conf 999999879
No 5
>PF06508 ExsB: ExsB; InterPro: IPR004479 This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Sinorhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA , . In Arthrobacter viscosus, the homologous gene is designated alu1 and is associated with an aluminum tolerance phenotype. When expressed in Escherichia coli, it conferred aliminium tolerance . The entry also contains the gene queC, which is responsible for the conversion of GTP to 7-cyano-7-deazaguanine (preQ0). The biosynthesis of hypermodified tRNA nucleoside queuosine only occurs in eubacteria. It occupies the wobble position for all known tRNAs that are specific for Asp, Asn, His or Tyr .; PDB: 3bl5_E 2pg3_A.
Probab=98.31 E-value=4.2e-07 Score=62.14 Aligned_cols=63 Identities=19% Similarity=0.360 Sum_probs=55.0
Q ss_pred CEEEECCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEECHHHH
Q ss_conf 34897058836899999998516955179887788898287799999999971984798345999
Q T0542 328 SVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPM 392 (590)
Q Consensus 328 ~~viglSGGiDS~~~~~la~~a~g~~~v~~~~mp~~~~s~~~~~~a~~la~~lg~~~~~i~i~~~ 392 (590)
++|+-+|||+||+++++++.+. | .+|++++.-.........+.|+.+|+.||+++.+++++.+
T Consensus 1 Kavvl~SGG~DSt~~l~~a~~~-~-~~v~altfdYGqr~~~El~~a~~ia~~lgv~h~vidl~~l 63 (137)
T PF06508_consen 1 KAVVLFSGGLDSTTLLYLAKKE-G-YEVYALTFDYGQRHRKELEAAKKIAEKLGVEHEVIDLSFL 63 (137)
T ss_dssp EEEEE-----HHHHHHHHHHHH---SEEEEEEEESS-TTCHHHHHHHHHHHH----EEEEE-GGC
T ss_pred CEEEEECCCHHHHHHHHHHHHC-C-CEEEEEEEECCCCCHHHHHHHHHHHHHCCCCEEEECHHHH
T ss_conf 9899917858999999999985-9-9699999988999799999999999982998799551788
No 6
>PF00733 Asn_synthase: Asparagine synthase; InterPro: IPR001962 This domain is always found associated with (IPR000583 from INTERPRO). Family members that contain this domain catalyse the conversion of aspartate to asparagine. Asparagine synthetase B (6.3.5.4 from EC) catalyzes the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine. The three-dimensional architecture of the N-terminal domain of asparagine synthetase B is similar to that observed for glutamine phosphoribosylpyrophosphate amidotransferase while the molecular motif of the C-domain is reminiscent to that observed for GMP synthetase .; GO: 0004066 asparagine synthase (glutamine-hydrolyzing) activity, 0006529 asparagine biosynthetic process; PDB: 1mbz_B 1mc1_B 1jgt_A 1mb9_B 1m1z_B 1q15_B 1q19_B 1ct9_A.
Probab=98.29 E-value=1.9e-06 Score=57.78 Aligned_cols=134 Identities=23% Similarity=0.228 Sum_probs=79.1
Q ss_pred HHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEC
Q ss_conf 88999999999998415683489705883689999999851695517988778889828779999999997198479834
Q T0542 309 VYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVS 388 (590)
Q Consensus 309 ~~~a~~~~l~d~~~~~g~~~~viglSGGiDS~~~~~la~~a~g~~~v~~~~mp~~~~s~~~~~~a~~la~~lg~~~~~i~ 388 (590)
+-+++-.+++.+++ .-..+.+-||||+||+.+++++... ...++.+++.-..........-|+.+|+.+|+++.+++
T Consensus 2 ~r~~l~~av~~rl~--~~~~v~~~LSGGlDSs~ia~~~~~~-~~~~~~~~t~~~~~~~~~E~~~a~~va~~~g~~~~~v~ 78 (269)
T PF00733_consen 2 LRELLDEAVRRRLR--SDKPVGVLLSGGLDSSAIAALAARQ-SGPPIKTFTIGFEGAEYDEREYARKVAEHLGLEHHEVE 78 (269)
T ss_dssp HHHHHHHHHHHHCG--GSSEEEEE-----HHHHHHHHHHH--CSSEEEEEE---TSSH--HHHHHHHHHHHHT-EEEE--
T ss_pred HHHHHHHHHHHHHH--CCCCEEEECCCHHHHHHHHHHHHHH-HCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEC
T ss_conf 79999999999985--6997899899809999999999985-39997279987699861389999999873386575414
Q ss_pred HHHHH--HHHHHHCCCCCCHHHH-HHHHHHHHHHHHHHHHHCCEEEECCC-HHHHHHHHHH
Q ss_conf 59999--9999861835740665-55657899999999761978987486-6777552033
Q T0542 389 IEPMF--DAYMASLGLTGLAEEN-LQSRLRGTTLMAISNQEGHIVLAPGN-KSELAVGYST 445 (590)
Q Consensus 389 i~~~~--~~~~~~~~~~~~~~~N-~qaR~R~~~l~~~a~~~~~lvl~t~n-~sE~~lG~~t 445 (590)
+++.- +.....+...+-...+ ...-.=...++..|...|.-|+=||. -+|+.-||..
T Consensus 79 ~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~a~~~g~~v~lsG~GgDelf~Gy~~ 139 (269)
T PF00733_consen 79 LSPDDFLDDLEEALRHLDEPFPTADSSSFPLYLLARAARESGVRVLLSGEGGDELFGGYSR 139 (269)
T ss_dssp --HHHHHTTHHHHHHHHT---HHHHHHHHHHHHHHHHHHH---SEEE-----TTT------
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCHHCCCCHH
T ss_conf 5899999999999999648633542048999999998746598399963671120146136
No 7
>PF02568 ThiI: Thiamine biosynthesis protein (ThiI); InterPro: IPR003720 Thiamine pyrophosphate (TPP) is synthesized de novo in many bacteria and is a required cofactor for many enzymes in the cell. ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway . Almost all the proteins in this group have an N-terminal THUMP domain (see IPR004114 from INTERPRO).; GO: 0009228 thiamin biosynthetic process; PDB: 2c5s_A 1vbk_B.
Probab=98.18 E-value=1.9e-05 Score=51.13 Aligned_cols=144 Identities=19% Similarity=0.245 Sum_probs=93.9
Q ss_pred CCEEEECCCCHHHHHHHHHHHHCCCCCCEEEEECC-CCCCCHHHHHHHHHHHHHC-------CCCEEEECHHHHHHHHHH
Q ss_conf 83489705883689999999851695517988778-8898287799999999971-------984798345999999998
Q T0542 327 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP-SKYSSDHSKGDAAELARRT-------GLNFRTVSIEPMFDAYMA 398 (590)
Q Consensus 327 ~~~viglSGGiDS~~~~~la~~a~g~~~v~~~~mp-~~~~s~~~~~~a~~la~~l-------g~~~~~i~i~~~~~~~~~ 398 (590)
.+++.=+||||||.|++.+..+. |- .|++|+.- .+++++.+.+.++.+++.| .+++.++++.+.......
T Consensus 4 gk~l~LlSGGiDSpVAa~lmmkr-G~-~V~~v~f~s~~~~~~~~~~k~~~l~~~l~~~~~~~~~~l~~v~~~~~~~~i~~ 81 (197)
T PF02568_consen 4 GKALALLSGGIDSPVAAWLMMKR-GV-EVIAVHFDSPPFTSEKAREKVEDLARLLSEYGGGHKIRLYVVDFTEVQKEIIR 81 (197)
T ss_dssp --EEEE-SSHHHHHHHHHHHHC------EEEEEEE-TTTS-CCCHHHHHHHHHHHHCCSS---EEEEEECHHHHHHHHHH
T ss_pred CEEEEEECCCCCHHHHHHHHHHC-CC-EEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECHHHHHHHHHH
T ss_conf 63999856862099999999988-99-79999997999998899999999999999956755651798351898899985
Q ss_pred HCCCCCCHHHHHHHHHH-HHHHHHHHHHHCCEEEECCCH-----HHHHHHHHHHC-CCCCCCHHHCCCCCHHHHHHHHHH
Q ss_conf 61835740665556578-999999997619789874866-----77755203330-677111223068878899999998
Q T0542 399 SLGLTGLAEENLQSRLR-GTTLMAISNQEGHIVLAPGNK-----SELAVGYSTLY-GDSVGAYGPIKDVYKTSIFRLAEW 471 (590)
Q Consensus 399 ~~~~~~~~~~N~qaR~R-~~~l~~~a~~~~~lvl~t~n~-----sE~~lG~~t~~-Gd~~~~~~p~~~l~Kt~v~~la~~ 471 (590)
..... +..+--|.- +-+...+|...|+..+-||.- |...-.-.+.. +-..--+-|+.++.|.++.++||-
T Consensus 82 ~~~~~---~~ci~crr~M~r~A~~ia~~~ga~~ivTGEsLGQvaSQTl~nL~~i~~~~~~pIlRPLi~~DK~EIi~~Ar~ 158 (197)
T PF02568_consen 82 NVKEK---YPCIDCRRFMYRIAEEIAEEEGADAIVTGESLGQVASQTLENLNVIERASDLPILRPLIGMDKEEIIEIARE 158 (197)
T ss_dssp HS-GG---GHHHHHHHHHHHHHHHHHHHTT--EEE-------TTS--HHHHHHHGGG--S-EE-TTTT--HHHHHHHHHH
T ss_pred CCCCC---CCCHHHHHHHHHHHHHHHHHCCCCEEEECCCHHHHHCCCHHHHHHHHHHCCCCEECCCCCCCHHHHHHHHHH
T ss_conf 17754---621999999999999999985992999785968865063889999887549844505667999999999998
Q ss_pred HHHC
Q ss_conf 6100
Q T0542 472 RNRA 475 (590)
Q Consensus 472 ~~~~ 475 (590)
++..
T Consensus 159 IGTy 162 (197)
T PF02568_consen 159 IGTY 162 (197)
T ss_dssp ---H
T ss_pred HCHH
T ss_conf 6938
No 8
>PF01507 PAPS_reduct: Phosphoadenosine phosphosulfate reductase family; InterPro: IPR002500 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases . The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) , . It is also found in NodP nodulation protein P from Rhizobium meliloti which has ATP sulphurylase activity (sulphate adenylate transferase) .; GO: 0016740 transferase activity, 0008152 metabolic process; PDB: 2o8v_A 1sur_A 2goy_H 2oq2_A 3g5a_E 3g6k_C 3fwk_A 3g59_A 1zun_A.
Probab=97.97 E-value=5.5e-05 Score=48.16 Aligned_cols=144 Identities=19% Similarity=0.215 Sum_probs=87.8
Q ss_pred CEEEECCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEECHHHHHHHHHHHCCCCCCHH
Q ss_conf 34897058836899999998516955179887788898287799999999971984798345999999998618357406
Q T0542 328 SVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAE 407 (590)
Q Consensus 328 ~~viglSGGiDS~~~~~la~~a~g~~~v~~~~mp~~~~s~~~~~~a~~la~~lg~~~~~i~i~~~~~~~~~~~~~~~~~~ 407 (590)
.++++.|||-||++++.|+.++..+ +..+++-+...-+++.+-.+.+++.+|++...+.............+...-..
T Consensus 1 ~ivvs~SGGKDS~v~l~l~~~~~~~--~~v~~~dTg~e~pet~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 78 (174)
T PF01507_consen 1 NIVVSFSGGKDSTVLLHLAREAGRP--IPVVFVDTGWEFPETYEFVDELAERYGIEIHVYRPPPTFERQIIPYGIPSRLW 78 (174)
T ss_dssp SEEEE-----HHHHHHHHHHHHHTT--CEEEEEE-STS-HHHHHHHHHHHHHTTCEEEEEETTSHHHHHHHHHH---GHH
T ss_pred CEEEEECCCHHHHHHHHHHHHHCCC--CCEEEEECCCCCHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHCCCCCCCCHH
T ss_conf 9599956878999999999996799--84799837977888999999999743985389637623566522335873110
Q ss_pred HH-HHHHHHHHHHHHHHHHHCCEEEECCC-HHHHHHHH--HHHCCCCC----CCHHHCCCCCHHHHHHHHHHHH
Q ss_conf 65-55657899999999761978987486-67775520--33306771----1122306887889999999861
Q T0542 408 EN-LQSRLRGTTLMAISNQEGHIVLAPGN-KSELAVGY--STLYGDSV----GAYGPIKDVYKTSIFRLAEWRN 473 (590)
Q Consensus 408 ~N-~qaR~R~~~l~~~a~~~~~lvl~t~n-~sE~~lG~--~t~~Gd~~----~~~~p~~~l~Kt~v~~la~~~~ 473 (590)
++ --......-+....+..+..++=+|- ++|..-.. .....+.. --++||.+....+|++..+..+
T Consensus 79 ~~~c~~~~K~~p~~~~~~~~~~~~~~~G~R~~Es~~R~~~~~~~~~~~~~~~~~~~PI~~Wt~~dVw~yi~~~~ 152 (174)
T PF01507_consen 79 RNWCCSILKVKPMRRALREYGEVVVITGVRADESAARAKLPRFEIDRENPKRLRVYPIIDWTEEDVWAYIRKHG 152 (174)
T ss_dssp HHHHHHHHTHHHHHHHHHHTT-SEEE----TTSSGGGGGSSSEEEETTT-SEEEE-TTTT--HHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHEECCCCCCCCEEEEECHHHCCHHHHHHHHHHCC
T ss_conf 38899999899999886436723347869877887775403011124668879995038599999999999778
No 9
>PF00764 Arginosuc_synth: Arginosuccinate synthase; InterPro: IPR001518 Argininosuccinate synthase (6.3.4.5 from EC) (AS) is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate , . In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterised by severe vomiting spells and mental retardation. AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.; GO: 0004055 argininosuccinate synthase activity, 0005524 ATP binding, 0006526 arginine biosynthetic process; PDB: 1j21_B 1kh1_A 1j1z_C 1kor_A 1j20_B 1kh2_C 1kh3_C 2nz2_A 1vl2_C 1k97_A ....
Probab=96.66 E-value=0.0078 Score=33.97 Aligned_cols=140 Identities=17% Similarity=0.280 Sum_probs=87.0
Q ss_pred EEECCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCC-CEEEECHHHHHH-HHH-HHCCCCCCH
Q ss_conf 89705883689999999851695517988778889828779999999997198-479834599999-999-861835740
Q T0542 330 LIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFD-AYM-ASLGLTGLA 406 (590)
Q Consensus 330 viglSGGiDS~~~~~la~~a~g~~~v~~~~mp~~~~s~~~~~~a~~la~~lg~-~~~~i~i~~~~~-~~~-~~~~~~~~~ 406 (590)
||.-|||+|+|+++....+..| ..|++++.-- ++.....+.+++-|..+|. ++.++|...-+- .+. ..+. .+..
T Consensus 1 VLAySGGLDTSv~l~wL~e~~~-~eVia~~aDv-Gq~~ed~~~i~~kA~~~GA~~~~v~D~r~ef~~~~i~~aI~-ana~ 77 (389)
T PF00764_consen 1 VLAYSGGLDTSVILKWLKEEYG-YEVIAVTADV-GQGEEDLEAIEEKALKLGASKHYVIDLRDEFVEDYIFPAIK-ANAL 77 (389)
T ss_dssp EEE-----HHHHHHHHHHHHHT--EEEEEEEE----T-S-HHHHHHHHHH----EEEEEE-HHHHHHHTHHHHHH-TT--
T ss_pred CEEECCCCHHHHHHHHHHHHCC-CEEEEEEEEC-CCCHHHHHHHHHHHHHCCCCEEEEEHHHHHHHHHHHHHHHH-HHHH
T ss_conf 9505777079999999997559-6499999989-99746654778999966994588724599999999999997-2122
Q ss_pred HHH----HH--HHHH-HHHHHHHHHHHCCEEEEC-----CCHHH-HHHHHHHHCCCCCCCHHHCCCCCHHHHHHHHHHHH
Q ss_conf 665----55--6578-999999997619789874-----86677-75520333067711122306887889999999861
Q T0542 407 EEN----LQ--SRLR-GTTLMAISNQEGHIVLAP-----GNKSE-LAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRN 473 (590)
Q Consensus 407 ~~N----~q--aR~R-~~~l~~~a~~~~~lvl~t-----~n~sE-~~lG~~t~~Gd~~~~~~p~~~l~Kt~v~~la~~~~ 473 (590)
+|| .- ||-- .-.+..+|.+.|.-.+.- ||.-- .-+.+.++ +-...-++|.-+.--+ -.+...|+.
T Consensus 78 Yeg~Y~L~tslaRplIa~~lv~vA~~~ga~avaHG~TGKGNDQvRFe~~~~al-~P~l~iiaP~Rd~~~~-R~~~i~Ya~ 155 (389)
T PF00764_consen 78 YEGRYPLGTSLARPLIAKKLVEVAREEGADAVAHGCTGKGNDQVRFELAFKAL-APDLKIIAPWRDWDLS-REEEIEYAK 155 (389)
T ss_dssp BTCCB--TTTTHHHHHHHHHHHHHHH----EEE--------HHHHHHHHHHHH-STTSEEE-GGGHHHHH--HHHHHHHH
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHH-CCCCEEEEECCCCCCC-HHHHHHHHH
T ss_conf 07875255534689999999999998099599836777786268899999975-9997799614156767-999999999
Q ss_pred H
Q ss_conf 0
Q T0542 474 R 474 (590)
Q Consensus 474 ~ 474 (590)
+
T Consensus 156 ~ 156 (389)
T PF00764_consen 156 K 156 (389)
T ss_dssp H
T ss_pred H
T ss_conf 8
No 10
>PF01902 ATP_bind_4: ATP-binding region; InterPro: IPR002761 This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N-terminal. The structure of Q8U2K6 from Pyrococcus furiosus has been resolved to 2.7A and is suggested to be a putative N-type pytophosphatase. In some members of the family e.g. Q12429 from SWISSPROT, this domain is associated with IPR006175 from INTERPRO, another domain of unknown function. Proteins with this uncharacterised domain include two apparent ortholog families in the archaea, one of which is universal among the first four completed archaeal genomes. The domain comprises the full length of the archaeal proteins and the first third of fungal proteins. ; PDB: 1ru8_A 3h7e_A 2d13_A.
Probab=95.65 E-value=0.011 Score=32.95 Aligned_cols=61 Identities=26% Similarity=0.223 Sum_probs=43.1
Q ss_pred CEEEECCCCHHHHHHHHHHHHCCCCCCEEEE-EC-CCCCCC--HHH--HHHHHHHHHHCCCCEEEECHHH
Q ss_conf 3489705883689999999851695517988-77-888982--877--9999999997198479834599
Q T0542 328 SVLIGLSGGIDSALVAAIACDALGAQNVYGV-SM-PSKYSS--DHS--KGDAAELARRTGLNFRTVSIEP 391 (590)
Q Consensus 328 ~~viglSGGiDS~~~~~la~~a~g~~~v~~~-~m-p~~~~s--~~~--~~~a~~la~~lg~~~~~i~i~~ 391 (590)
++++-.|||-||++++..|.+. -.|.++ +| |....| -++ .+..+..|+.||++...+.+..
T Consensus 2 K~v~l~SGGKDS~~Al~~a~~~---~~V~~L~t~~~~~~~s~~~H~~~~~l~~~qA~algiPl~~~~~~g 68 (218)
T PF01902_consen 2 KVVALWSGGKDSTLALYRALRQ---HEVVCLLTMVPENGDSYMFHGVNLELLELQAEALGIPLIEIEISG 68 (218)
T ss_dssp EEEEE-----HHHHHHHHHHHT----EEEEEE---BSSSSTTTS-STSSTCHHHHHHH----EEE--B--
T ss_pred CEEEEECCCHHHHHHHHHHHHC---CCCCEEEEEECCCCCEECCCCCCHHHHHHHHHHCCCCEEEEECCC
T ss_conf 6999966868999999999872---974599999659986131535588999999997699789998578
No 11
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 This is a family of largely hypothetical proteins of unknown function. ; PDB: 3gxh_A.
Probab=74.57 E-value=1.7 Score=18.53 Aligned_cols=93 Identities=19% Similarity=0.299 Sum_probs=53.6
Q ss_pred EECCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEECHHH------HHHHHHHHCCC-C
Q ss_conf 9705883689999999851695517988778889828779999999997198479834599------99999986183-5
Q T0542 331 IGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEP------MFDAYMASLGL-T 403 (590)
Q Consensus 331 iglSGGiDS~~~~~la~~a~g~~~v~~~~mp~~~~s~~~~~~a~~la~~lg~~~~~i~i~~------~~~~~~~~~~~-~ 403 (590)
+.+||=+...=...|+. .|=+.|+...........-+..+-+..|+.+|+.|..+|+.. .+++|.+.+.. .
T Consensus 9 ~~va~Q~~~~di~~la~--~GfktVIn~Rpd~E~~~qp~~~~~~~~a~~~GL~y~~iPv~~~~~~~~~v~~f~~~l~~~~ 86 (110)
T PF04273_consen 9 LSVAGQPSPEDIAQLAA--QGFKTVINNRPDGEDPGQPSSAEEREAAEAAGLEYVHIPVDSGQITPEDVEAFAAALEELP 86 (110)
T ss_dssp EEEE----HHHHHHHHH------EEEE-S-TTSTTS-T---T---HHHH---EEEE----TTS--HHHHHHHHHHHHHT-
T ss_pred EEECCCCCHHHHHHHHH--CCCCEEEECCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHCC
T ss_conf 78858989999999997--8973999899898888997419999999986992899513788899999999999998489
Q ss_pred CCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 7406655565789999999976
Q T0542 404 GLAEENLQSRLRGTTLMAISNQ 425 (590)
Q Consensus 404 ~~~~~N~qaR~R~~~l~~~a~~ 425 (590)
+=.+-.-++-.|...||.+++.
T Consensus 87 ~PVL~hCrsG~Rs~~l~~l~~a 108 (110)
T PF04273_consen 87 GPVLAHCRSGTRSSALWALAQA 108 (110)
T ss_dssp --EEEE-SSSHHHHHHHHH---
T ss_pred CCEEEECCCCHHHHHHHHHHCC
T ss_conf 9999989998029999988602
No 12
>PF05201 GlutR_N: Glutamyl-tRNAGlu reductase, N-terminal domain; InterPro: IPR015895 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway . The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin . The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) . This entry represents the N-terminal domain of glutamyl-tRNA reductase (1.2.1.70 from EC), which reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway , . The enzyme requires NADPH as a cofactor.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process; PDB: 1gpj_A.
Probab=47.72 E-value=0.7 Score=21.12 Aligned_cols=20 Identities=20% Similarity=0.283 Sum_probs=16.3
Q ss_pred HHHHHCCEEEECCCHHHHHH
Q ss_conf 99761978987486677755
Q T0542 422 ISNQEGHIVLAPGNKSELAV 441 (590)
Q Consensus 422 ~a~~~~~lvl~t~n~sE~~l 441 (590)
.....+.++|+|+|++|.++
T Consensus 33 ~~~i~e~vvLsTCNR~EiY~ 52 (152)
T PF05201_consen 33 SPGISEAVVLSTCNRVEIYL 52 (152)
T ss_dssp H------EEEEETTEEEEEE
T ss_pred CCCCCCEEEEECCCEEEEEE
T ss_conf 47998779972788079999
No 13
>PF10042 DUF2278: Uncharacterized conserved protein (DUF2278)
Probab=40.47 E-value=6.7 Score=14.62 Aligned_cols=21 Identities=33% Similarity=0.333 Sum_probs=8.8
Q ss_pred ECCCEEECCCCCEEECCCCCC
Q ss_conf 467278847883432178998
Q T0542 230 DGDSIVVDRDGEVVARAPQFS 250 (590)
Q Consensus 230 ~G~S~Iidp~G~ila~~~~f~ 250 (590)
||+-+|--++|++.+---.|+
T Consensus 175 DGall~~~~d~~w~a~FlaF~ 195 (206)
T PF10042_consen 175 DGALLVHFADGQWAAIFLAFQ 195 (206)
T ss_pred CCEEEEEECCCEEEEEEEHHH
T ss_conf 786999915993875220254
No 14
>PF01488 Shikimate_DH: Shikimate / quinate 5-dehydrogenase; InterPro: IPR006151 This entry contains shikimate and quinate dehydrogenases, as well as glutamyl-tRNA reductases. Shikimate 5-dehydrogenase (1.1.1.25 from EC) catalyses the conversion of shikimate to 5-dehydroshikimate , . This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids . Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites, 3-dehydroquinate and dehydroshikimate. Glutamyl-tRNA reductase (1.2.1.70 from EC) catalyzes the first step of tetrapyrrole biosynthesis in plants, archaea and most bacteria. The dimeric enzyme has an unusual V-shaped architecture where each monomer consists of three domains linked by a long 'spinal' alpha-helix. The central catalytic domain specifically recognises the glutamate moiety of the substrate . ; GO: 0004764 shikimate 5-dehydrogenase activity, 0005737 cytoplasm; PDB: 1gpj_A 2d5c_A 2ev9_B 1wxd_A 2cy0_B 1nyt_A 1p74_A 1p77_A 2hk8_G 2hk9_B ....
Probab=38.26 E-value=7.3 Score=14.40 Aligned_cols=59 Identities=32% Similarity=0.479 Sum_probs=38.4
Q ss_pred CCCCCEEEECCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHC-CCCEEEECHHHHH
Q ss_conf 156834897058836899999998516955179887788898287799999999971-9847983459999
Q T0542 324 NGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRT-GLNFRTVSIEPMF 393 (590)
Q Consensus 324 ~g~~~~viglSGGiDS~~~~~la~~a~g~~~v~~~~mp~~~~s~~~~~~a~~la~~l-g~~~~~i~i~~~~ 393 (590)
.|.+-++|| +||.-.+++.+|+.. |..++.-+. .|.+.|+.|++.+ +.....++++..-
T Consensus 11 ~~k~vlviG-aGg~a~~v~~~L~~~--g~~~i~I~n--------Rt~~ka~~la~~~~~~~~~~~~~~~~~ 70 (135)
T PF01488_consen 11 KGKRVLVIG-AGGAARAVAAALAAL--GAKRITIVN--------RTPEKAEELAEEFGGKKIEVIPLEDLE 70 (135)
T ss_dssp TTSEEEEE------HHHHHHHHHHT--TSCEEEEEE--------SSHHHHHHHHHHHTCCSEEEEEEGGHH
T ss_pred CCCEEEEEC-CCHHHHHHHHHHHHC--CCCEEEEEE--------CCHHHHHHHHHHCCCCCCCEEEHHHHH
T ss_conf 799899999-829999999999986--999899994--------999999999997354663133387877
No 15
>PF10871 DUF2748: Protein of unknown function (DUF2748)
Probab=35.08 E-value=7.2 Score=14.43 Aligned_cols=53 Identities=21% Similarity=0.294 Sum_probs=34.8
Q ss_pred HHHHHHHHHHCCEEEECCCHHHH--HHHHHHHCCCCCCCHHHCCCCCHHHHHHHHH
Q ss_conf 99999997619789874866777--5520333067711122306887889999999
Q T0542 417 TTLMAISNQEGHIVLAPGNKSEL--AVGYSTLYGDSVGAYGPIKDVYKTSIFRLAE 470 (590)
Q Consensus 417 ~~l~~~a~~~~~lvl~t~n~sE~--~lG~~t~~Gd~~~~~~p~~~l~Kt~v~~la~ 470 (590)
.-|+.++++++.+.+--= |+|- +|=--.+.-|+.+.++|.+++||..-.+.-+
T Consensus 307 ~kL~~~~~~~~~iFvr~f-K~~~Y~~LMl~AM~~DM~~NLsP~AeVYK~~nPe~EE 361 (447)
T PF10871_consen 307 FKLLNYSSKNNLIFVRKF-KTDKYMALMLDAMFKDMQANLSPKAEVYKNKNPEIEE 361 (447)
T ss_pred HHHHHHHCCCCEEEEEEE-CCHHHHHHHHHHHHHHHHHCCCCCHHHHCCCCCCHHH
T ss_conf 999976401675999961-4157999999999999884379424665168923889
No 16
>PF01156 IU_nuc_hydro: Inosine-uridine preferring nucleoside hydrolase; InterPro: IPR001910 Inosine-uridine preferring nucleoside hydrolase (3.2.2.1 from EC) (IU-nucleoside hydrolase or IUNH) is an enzyme first identified in protozoan that catalyzes the hydrolysis of all of the commonly occuring purine and pyrimidine nucleosides into ribose and the associated base, but has a preference for inosine and uridine as substrates. This enzyme is important for these parasitic organisms, which are deficient in de novo synthesis of purines, to salvage the host purine nucleosides. IUNH from Crithidia fasciculata has been sequenced and characterised, it is an homotetrameric enzyme of subunits of 34 Kd. An histidine has been shown to be important for the catalytic mechanism, it acts as a proton donor to activate the hypoxanthine leaving group. A highly conserved region located in the N-terminal extremity contains four conserved aspartates that have been shown to be located in the active site cavity. IUNH is evolutionary related to a number of uncharacterised proteins from various biological sources.; PDB: 3b9g_B 3epw_B 2ff1_A 3epx_B 2ff2_A 1r4f_A 1kie_B 1kic_B 1hoz_A 1hp0_A ....
Probab=31.88 E-value=9.2 Score=13.74 Aligned_cols=15 Identities=20% Similarity=0.246 Sum_probs=5.7
Q ss_pred HHHHHHHCCCCEEEEC
Q ss_conf 9999997198479834
Q T0542 373 AAELARRTGLNFRTVS 388 (590)
Q Consensus 373 a~~la~~lg~~~~~i~ 388 (590)
|+.+-+. +++...++
T Consensus 177 A~~V~~s-~~~i~~vp 191 (312)
T PF01156_consen 177 AQIVFES-GIPITLVP 191 (312)
T ss_dssp HHHHHTS-SS-EEE--
T ss_pred HHHHHHC-CCCEEEEE
T ss_conf 9999944-89879982
No 17
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The cyrstal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases . ; GO: 0005524 ATP binding; PDB: 2f6r_A 2if2_C 1jjv_A 1viy_A 1n3b_A 1vht_C 1vhl_C 1t3h_A 2grj_F 1uf9_B ....
Probab=30.80 E-value=9.5 Score=13.62 Aligned_cols=102 Identities=22% Similarity=0.248 Sum_probs=44.0
Q ss_pred EEEECCCCHHH--HHHHHHHHHCCCCCCEE------EEECCCCCCCHHHHHHHHHHHHHCCCCE----EEECHHHHHHHH
Q ss_conf 48970588368--99999998516955179------8877888982877999999999719847----983459999999
Q T0542 329 VLIGLSGGIDS--ALVAAIACDALGAQNVY------GVSMPSKYSSDHSKGDAAELARRTGLNF----RTVSIEPMFDAY 396 (590)
Q Consensus 329 ~viglSGGiDS--~~~~~la~~a~g~~~v~------~~~mp~~~~s~~~~~~a~~la~~lg~~~----~~i~i~~~~~~~ 396 (590)
++|||.|||-| |+++.+..+ +|..-+- -++.|. ...-+.+.+.+|-.. -.+|-..+-+..
T Consensus 1 miIGlTGgIgsGKStv~~~l~~-~G~~vidaD~i~~~l~~~~-------~~~~~~i~~~FG~~il~~~g~idR~~L~~~v 72 (180)
T PF01121_consen 1 MIIGLTGGIGSGKSTVAKILKE-LGAPVIDADEIAHELYEPG-------SPVYKKIVERFGEDILDEDGEIDRKKLAEIV 72 (180)
T ss_dssp EEEEEB-------HHHHHHHHH----EEEEHHHHHHHTTHHT-------HHHHHHHHHH-GGTTBB----B-HHHHHHHH
T ss_pred CEEEEECCCCCCHHHHHHHHHH-CCCCEEEHHHHHHHHHCCC-------HHHHHHHHHHHCHHHCCCCCCCCHHHHHHHH
T ss_conf 9899978875789999999997-7996997778999984598-------2899999999486641889758499999998
Q ss_pred HHHCCCCCCHHHH-HHHHHHHHHHHHHHHHH--CCEEEECCCHHHH
Q ss_conf 9861835740665-55657899999999761--9789874866777
Q T0542 397 MASLGLTGLAEEN-LQSRLRGTTLMAISNQE--GHIVLAPGNKSEL 439 (590)
Q Consensus 397 ~~~~~~~~~~~~N-~qaR~R~~~l~~~a~~~--~~lvl~t~n~sE~ 439 (590)
+.+-..-. .+++ +.+.+|-.+...+.... ..+|+-.--.-|.
T Consensus 73 F~d~~~~~-~Le~i~HP~I~~~~~~~i~~~~~~~~vv~e~pLL~E~ 117 (180)
T PF01121_consen 73 FSDPEKRK-KLESILHPLIREEIEKQIKEARKEKYVVVEIPLLFES 117 (180)
T ss_dssp HTSHHHHH-HHHHHHHHHHHHHHHHHHHHCHSSSEEEEE-TTTTTT
T ss_pred HCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCHHHHH
T ss_conf 58999999-9999876999999999997610388899970045530
No 18
>PF10649 DUF2478: Protein of unknown function (DUF2478)
Probab=27.71 E-value=11 Score=13.28 Aligned_cols=40 Identities=28% Similarity=0.244 Sum_probs=23.3
Q ss_pred HHHHHCCCCEEEEECCCCCCCCCHHHH---HHHHHHHHHHCCHHHHHH
Q ss_conf 999963797899832787657838999---999999998607264456
Q T0542 174 PAARSAGAGLLLSVNASPYERDKDDTR---LELVRKRAQEAGCTTAYL 218 (590)
Q Consensus 174 ~~la~~Gadlii~psasp~~~~~~~~r---~~~~~~rA~e~~~~vv~a 218 (590)
+..-..++|+++.. .+||++.- ....-..|...+.||+.+
T Consensus 87 ~~al~~~~dLlIvN-----kFGk~Ea~G~Glr~~i~~Al~~giPvLt~ 129 (159)
T PF10649_consen 87 RAALAAGPDLLIVN-----KFGKQEAEGRGLRAEIAEALAAGIPVLTA 129 (159)
T ss_pred HHHHHCCCCEEEEC-----CCHHHHHCCCCHHHHHHHHHHCCCCEEEE
T ss_conf 99984499899984-----42375614987799999998769988998
No 19
>PF01553 Acyltransferase: Acyltransferase; InterPro: IPR002123 This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function . This family also includes tafazzin subfamily (Q16635 from SWISSPROT) .; GO: 0008415 acyltransferase activity, 0008152 metabolic process; PDB: 1k30_A 1iuq_A.
Probab=24.61 E-value=12 Score=12.92 Aligned_cols=14 Identities=43% Similarity=0.681 Sum_probs=6.0
Q ss_pred HCCCCEEEECCCCC
Q ss_conf 67996998264003
Q T0542 35 EQGAHLVAFPEMAL 48 (590)
Q Consensus 35 ~~gadLVVfPEl~l 48 (590)
++|--+++|||-..
T Consensus 91 ~~g~~l~iFPEGt~ 104 (135)
T PF01553_consen 91 KKGQSLVIFPEGTR 104 (135)
T ss_dssp ----EEEE------
T ss_pred CCCCEEEEECCCCC
T ss_conf 47977999834125
No 20
>PF01888 CbiD: CbiD; InterPro: IPR002748 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CbiD, an essential protein for cobalamin biosynthesis in both S. typhimurium and B. megaterium. A deletion mutant of CbiD suggests that this enzyme is involved in C-1 methylation and deacylation reactions required during the ring contraction process in the anaerobic pathway to cobalamin (similar role as CobF) . The CbiD protein has a putative S-AdoMet binding site . CbiD has no counterpart in the aerobic pathway.; GO: 0016740 transferase activity, 0009236 cobalamin biosynthetic process; PDB: 1sr8_A.
Probab=23.61 E-value=13 Score=12.79 Aligned_cols=31 Identities=35% Similarity=0.494 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHCCEEEECCCHHH-HHHHH
Q ss_conf 57899999999761978987486677-75520
Q T0542 413 RLRGTTLMAISNQEGHIVLAPGNKSE-LAVGY 443 (590)
Q Consensus 413 R~R~~~l~~~a~~~~~lvl~t~n~sE-~~lG~ 443 (590)
.+|-.+-...|+....+|+.|||.+| ++.-+
T Consensus 185 si~~~l~va~a~g~~~lVl~~G~~g~~~a~~~ 216 (261)
T PF01888_consen 185 SIRQELDVARANGCDHLVLVPGNRGERFARRL 216 (261)
T ss_dssp HHHH------GGG-SSEEEE---HHHHHHHHH
T ss_pred HHHHHHCCHHCCCCCEEEEECCCCHHHHHHHH
T ss_conf 99886201000588739995184178999987
No 21
>PF06711 DUF1198: Protein of unknown function (DUF1198); InterPro: IPR009587 This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=21.91 E-value=14 Score=12.57 Aligned_cols=31 Identities=23% Similarity=0.342 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHCCCCEEEECHHHHHHHHHHHC
Q ss_conf 779999999997198479834599999999861
Q T0542 368 HSKGDAAELARRTGLNFRTVSIEPMFDAYMASL 400 (590)
Q Consensus 368 ~~~~~a~~la~~lg~~~~~i~i~~~~~~~~~~~ 400 (590)
.|+..-..|++.||| ..++|+.+.+++-+.-
T Consensus 23 dtRrAi~rLs~rL~I--~pv~iESMi~qmGk~~ 53 (148)
T PF06711_consen 23 DTRRAIDRLSERLKI--KPVPIESMIDQMGKRQ 53 (148)
T ss_pred CHHHHHHHHHHHHCC--CEEEHHHHHHHHCCHH
T ss_conf 448999999986198--0255999999974040
No 22
>PF09086 DUF1924: Domain of unknown function (DUF1924); InterPro: IPR015170 This entry is found in a set of bacterial proteins, including Cytochrome c-type protein. It is functionally uncharacterised. ; PDB: 1e8e_A 1oae_B 1gu2_A 1dw3_B 1dw1_A 1dw0_C 1dw2_A.
Probab=20.38 E-value=15 Score=12.37 Aligned_cols=23 Identities=22% Similarity=0.019 Sum_probs=16.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99899999999985156686378
Q T0542 537 DRELVVKTLRMVDTAEYKRRQYP 559 (590)
Q Consensus 537 ~~~~v~~~~~~~~~~~~KR~~~p 559 (590)
|.+.|+||++|--..-+.|.|.|
T Consensus 66 D~akvEKWf~RNC~dV~gReCTa 88 (98)
T PF09086_consen 66 DAAKVEKWFRRNCNDVLGRECTA 88 (98)
T ss_dssp SHHHHHHHHHHHHHHH------H
T ss_pred CHHHHHHHHHCCCHHHHCCCCCH
T ss_conf 88999999970047666235677
Done!