Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate 408300 DVU0748 acetyl-CoA synthetase
Query= BRENDA::Q2XNL6 (634 letters) >MicrobesOnline__882:408300 Length = 648 Score = 700 bits (1806), Expect = 0.0 Identities = 334/638 (52%), Positives = 454/638 (71%), Gaps = 14/638 (2%) Query: 8 LLEEKRVFKPHYTVVEEAHIKNWE---AELEKGKDHENYWAEKAERLEWFRKWDRVLDES 64 LL E+RVF+P VV +A + + A + G +W E AE LEWFR+WD VLD+S Sbjct: 11 LLREERVFRPLPRVVADAVVNPQDVARAREQAGTAPLAFWEEAAEELEWFRRWDGVLDDS 70 Query: 65 NRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTAN 124 N PF RWF N+ +NA+DR ++T R+++A+++ E GD R+ TY++LYREV+R AN Sbjct: 71 NAPFMRWFPGALCNIVHNALDRHIETSNRHRLALIWEGEPGDSRRFTYFDLYREVNRLAN 130 Query: 125 ALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKI 184 A++SLG+ KGD V +Y+P PE V +MLACAKIGAVHS ++ G S +L +R+ DAR + Sbjct: 131 AMRSLGVTKGDRVVIYMPPLPETVFAMLACAKIGAVHSTVFGGFSARSLCDRVEDARPTL 190 Query: 185 IITADGTYRRGGVIKLKPIVDEAILQCPT-----IETTVVVKHTDIDIEMSDISGREMLF 239 ++T DG YR G V+ LKP+ D+A+ + VVV ++ M D GR++ + Sbjct: 191 LLTVDGFYRNGRVVPLKPVADDAVDALSPEARAGLHHVVVVHRAHLETPMRD--GRDIWY 248 Query: 240 DKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHN 299 L+ G+ E + A DPLF+LYTSG+TGKPKG++H+ GGYMVGV T+ FD+ Sbjct: 249 HDLVRGQSTEALTEVLSANDPLFVLYTSGTTGKPKGLVHSHGGYMVGVHRTMRWVFDVRP 308 Query: 300 GDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTA 359 D++WCTA+ GWITGHSY VYGPL+ GTTT+LYEG P YP+ G WS+VE++GVT YT Sbjct: 309 TDIFWCTAEPGWITGHSYGVYGPLMAGTTTVLYEGHPLYPEAGRLWSMVERWGVTILYTV 368 Query: 360 PTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTE 419 PT IR LMRFG +P R+++ +L++L TVGEPI+PE W+W+YR IGR +CP++DTWWQTE Sbjct: 369 PTVIRMLMRFGPLYPARHDITTLRLLATVGEPISPETWVWFYRTIGRGRCPVLDTWWQTE 428 Query: 420 TGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLF 479 TGM +++PLPV+ LKPGSV +PLPG++ D+VD G PVP G+GG LV++ PWPAM +F Sbjct: 429 TGMIMVSPLPVSALKPGSVARPLPGVDVDIVDGEGAPVPPGRGGLLVVKNPWPAMACGVF 488 Query: 480 NDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFV 539 D++ + +YW++ PG Y GD+AR+D+DGY WIQGR+DDV+ IAGHRIGTAE+E+ Sbjct: 489 GDDEAFRRLYWERFPGW-YCTGDVARRDDDGYIWIQGRADDVILIAGHRIGTAEMEAALA 547 Query: 540 AHPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNA---ALIEELKRHLRHELGPVAVVG 596 +HPAVAE AVIG D +KGEV KAF++L+ + A AL L H+R ELGPVAV+ Sbjct: 548 SHPAVAECAVIGVPDRLKGEVGKAFVVLRDTEEAAAEEQALATSLVGHVRRELGPVAVIR 607 Query: 597 EMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634 ++V + LP+ RSGKIMRRILR+ E G + GD STLE+ Sbjct: 608 DVVFREGLPRNRSGKIMRRILRSEEMGVETGDLSTLED 645 Lambda K H 0.319 0.138 0.428 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1335 Number of extensions: 63 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 634 Length of database: 648 Length adjustment: 38 Effective length of query: 596 Effective length of database: 610 Effective search space: 363560 Effective search space used: 363560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate 408300 DVU0748 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02188.hmm # target sequence database: /tmp/gapView.6036.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02188 [M=629] Accession: TIGR02188 Description: Ac_CoA_lig_AcsA: acetate--CoA ligase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-248 809.8 0.0 8.1e-248 809.6 0.0 1.0 1 lcl|MicrobesOnline__882:408300 DVU0748 acetyl-CoA synthetase Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:408300 DVU0748 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 809.6 0.0 8.1e-248 8.1e-248 5 620 .. 33 646 .. 29 648 .] 0.96 Alignments for each domain: == domain 1 score: 809.6 bits; conditional E-value: 8.1e-248 TIGR02188 5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiwegde 82 ++ ++ e+a + p +fw++ a+ elew++ ++ vld+s++p+++Wf ++ n+ n++drh+e+ +++++a+iweg+ lcl|MicrobesOnline__882:408300 33 QDVARAREQAGTAPLAFWEEAAE-ELEWFRRWDGVLDDSNAPFMRWFPGALCNIVHNALDRHIETsNRHRLALIWEGE- 109 6667788999999******9998.6****************************************999**********. PP TIGR02188 83 egedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivdae 161 +g dsr++tY +l+rev+rlan++++lGv kgdrv+iY+p +pe+v+amlaca+iGavhs vf+Gfsa +l +R++da+ lcl|MicrobesOnline__882:408300 110 PG-DSRRFTYFDLYREVNRLANAMRSLGVTKGDRVVIYMPPLPETVFAMLACAKIGAVHSTVFGGFSARSLCDRVEDAR 187 77.59************************************************************************** PP TIGR02188 162 aklvitadeglRggkvielkkivdealekaee....svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekl 236 l++t d+ +R+g+v++lk ++d+a+++ + +++v+vv+r+ e +++++grD+w+++lv+ ++s+e +e l lcl|MicrobesOnline__882:408300 188 PTLLLTVDGFYRNGRVVPLKPVADDAVDALSPearaGLHHVVVVHRAHLE-TPMRDGRDIWYHDLVR-GQSTEALTEVL 264 *************************99876543445799***********.66**************.6********** PP TIGR02188 237 dsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfeg 315 +++dplf+LYtsG+tGkPkG++h+ gGy++ ++ t+++vfd++++difwCta+ GW+tGhsY vygPL++G tt+l+eg lcl|MicrobesOnline__882:408300 265 SANDPLFVLYTSGTTGKPKGLVHSHGGYMVGVHRTMRWVFDVRPTDIFWCTAEPGWITGHSYGVYGPLMAGTTTVLYEG 343 ******************************************************************************* PP TIGR02188 316 vptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivd 394 p yp+a+r+w+++e+++vti+Yt Pt+iR+lm+ g +++hd+ +lr+l +vGepi pe+w W+y+++G+++cp+ d lcl|MicrobesOnline__882:408300 344 HPLYPEAGRLWSMVERWGVTILYTVPTVIRMLMRFGPLYPARHDITTLRLLATVGEPISPETWVWFYRTIGRGRCPVLD 422 ******************************************************************************* PP TIGR02188 395 twWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetY 473 twWqtetG i+++plp +lkpgs ++Pl+G+++++vd eg +v ++++ g+Lv+k+pwP+m+ +++gd+e f + Y lcl|MicrobesOnline__882:408300 423 TWWQTETGMIMVSPLPV--SALKPGSVARPLPGVDVDIVDGEGAPVPPGRG-GLLVVKNPWPAMACGVFGDDEAFRRLY 498 ****************9..69***************************999.8************************** PP TIGR02188 474 fkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlke 552 +++++g y tGD arrd+dGyiwi+GR+Ddvi ++Ghr+gtae+e+al sh+avae+av+gvpd +kge+ afvvl++ lcl|MicrobesOnline__882:408300 499 WERFPGWYCTGDVARRDDDGYIWIQGRADDVILIAGHRIGTAEMEAALASHPAVAECAVIGVPDRLKGEVGKAFVVLRD 577 ******************************************************************************9 PP TIGR02188 553 gveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledp 620 ++e+ +e +l+++l +vr+e+gp+a +++ + e lP+ RsGkimRR+lr+ g e +gd+stled lcl|MicrobesOnline__882:408300 578 TEEAAAEeqALATSLVGHVRRELGPVAVIRDVVFREGLPRNRSGKIMRRILRSEEMGVE-TGDLSTLEDA 646 9886554448******************************************9777655.67******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (648 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 10.27 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory