Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate 8502070 DvMF_2783 acetate/CoA ligase (RefSeq)
Query= BRENDA::Q2XNL6 (634 letters) >FitnessBrowser__Miya:8502070 Length = 651 Score = 713 bits (1840), Expect = 0.0 Identities = 347/641 (54%), Positives = 458/641 (71%), Gaps = 17/641 (2%) Query: 8 LLEEKRVFKPHYTVVEEAHIKNWE---AELEKGKDHENYWAEKAERLEWFRKWDRVLDES 64 LL E+RVF+P VV A + + A D + YW E AE LEWFR+WD V D S Sbjct: 11 LLREERVFRPLPQVVAGAVVNPQDVARARARAAADPDGYWEEAAEELEWFRRWDAVHDGS 70 Query: 65 NRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTAN 124 N PF+RWF + N+ +NA+DR ++T +N++A+++ E GD R TYY+LYREV+R AN Sbjct: 71 NAPFHRWFTGARCNIVHNALDRHIETGTKNRLALIWEGESGDTRSFTYYQLYREVNRLAN 130 Query: 125 ALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKI 184 AL+ LG+ KGD V +Y+P PE V +MLA AKIGAVHS ++ G S +L +R+ DAR + Sbjct: 131 ALRGLGVGKGDRVIIYMPPLPETVFAMLAAAKIGAVHSTVFGGFSARSLRDRMEDARPAV 190 Query: 185 IITADGTYRRGGVIKLKPIVDEAILQCPT-----IETTVVVKHTDIDIEMSDISGREMLF 239 I+T DG YR G VI LKPI DEA+ P + VVV ++ M++ GR++ + Sbjct: 191 IVTVDGFYRNGRVIPLKPIADEAVATLPPDLAAGVRHMVVVHRAHVETPMTE--GRDIWY 248 Query: 240 DKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHN 299 + G+ E MD+ DPLF+LYTSG+TGKPKG +H GGYMVGV T+ FD+ Sbjct: 249 HDAVRGQHHEALTEIMDSTDPLFLLYTSGTTGKPKGHVHAHGGYMVGVHRTMRWVFDVKP 308 Query: 300 GDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTA 359 D++WCTA+ GWITGHSYVVYGPL+ GTTT+LYEG P YP+PG WS+VE+ G+T YTA Sbjct: 309 TDIFWCTAEPGWITGHSYVVYGPLMAGTTTVLYEGHPLYPEPGRVWSMVERLGITILYTA 368 Query: 360 PTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTE 419 PT +R LMR G +H R++L +L++LGTVGEPI+PEAW+W++R++GR +CP++DTWWQTE Sbjct: 369 PTLVRMLMRHGAQHVARHDLTTLRLLGTVGEPISPEAWLWFHRHVGRGRCPVLDTWWQTE 428 Query: 420 TGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLF 479 TGM +++PLPV+ LKPGSVT+PLPGIEADVVDE+G PV G GG LV+++PWPAM ++ Sbjct: 429 TGMIMLSPLPVSLLKPGSVTRPLPGIEADVVDEHGKPVGPGHGGLLVLQRPWPAMSCGVY 488 Query: 480 NDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFV 539 ND++ Y +YW++ PG Y GD+AR+DEDGYFWIQGR+DDVL IAGHRIGTAE+E+ Sbjct: 489 NDDESYRRLYWERFPGW-YCTGDVARRDEDGYFWIQGRADDVLLIAGHRIGTAEMEAALA 547 Query: 540 AHPAVAEAAVIGKADPIKGEVIKAFLILKKGH-----KLNA-ALIEELKRHLRHELGPVA 593 +H +VAE AVIG D ++GEV KAF++L H +NA L EL H+R ELGPVA Sbjct: 548 SHRSVAECAVIGVPDALRGEVAKAFVVLVDDHPPLGTMVNADELAAELVEHVRRELGPVA 607 Query: 594 VVGEMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634 V+ E+ + LP+ RSGKIMRR+LR+ E G D GD STLE+ Sbjct: 608 VIREVSFREGLPRNRSGKIMRRVLRSEELGRDTGDLSTLED 648 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: 1378 Number of extensions: 68 Number of successful extensions: 4 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: 651 Length adjustment: 38 Effective length of query: 596 Effective length of database: 613 Effective search space: 365348 Effective search space used: 365348 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 8502070 DvMF_2783 (acetate/CoA ligase (RefSeq))
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.14015.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-252 825.5 0.0 1.5e-252 825.3 0.0 1.0 1 lcl|FitnessBrowser__Miya:8502070 DvMF_2783 acetate/CoA ligase (Re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8502070 DvMF_2783 acetate/CoA ligase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 825.3 0.0 1.5e-252 1.5e-252 5 620 .. 33 649 .. 29 651 .] 0.96 Alignments for each domain: == domain 1 score: 825.3 bits; conditional E-value: 1.5e-252 TIGR02188 5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaiiweg 80 ++ ++ ++a++dp+ +w++ a+ elew++ ++ v d s++p+ +Wf++++ n+ n++drh+e+ +k+++a+iweg lcl|FitnessBrowser__Miya:8502070 33 QDVARARARAAADPDGYWEEAAE-ELEWFRRWDAVHDGSNAPFHRWFTGARCNIVHNALDRHIETgTKNRLALIWEG 108 56677788999********9998.6**************************************************** PP TIGR02188 81 deegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRi 157 + +g d+r++tY++l+rev+rlan+l+ lGv kgdrv+iY+p +pe+v+amla+a+iGavhs vf+Gfsa +l++R+ lcl|FitnessBrowser__Miya:8502070 109 E-SG-DTRSFTYYQLYREVNRLANALRGLGVGKGDRVIIYMPPLPETVFAMLAAAKIGAVHSTVFGGFSARSLRDRM 183 *.44.58********************************************************************** PP TIGR02188 158 vdaeaklvitadeglRggkvielkkivdealekaee....svekvlvvkrtgeevaewkegrDvwweelvekeasae 230 +da+ +++t d+ +R+g+vi+lk i+dea+++ + v++++vv+r+ e ++++egrD+w++++v+ ++++e lcl|FitnessBrowser__Miya:8502070 184 EDARPAVIVTVDGFYRNGRVIPLKPIADEAVATLPPdlaaGVRHMVVVHRAHVE-TPMTEGRDIWYHDAVR-GQHHE 258 ********************************987656668*************.66**************.699** PP TIGR02188 231 cepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanG 307 +e +ds dplf+LYtsG+tGkPkG +h+ gGy++ ++ t+++vfd+k++difwCta+ GW+tGhsY+vygPL++G lcl|FitnessBrowser__Miya:8502070 259 ALTEIMDSTDPLFLLYTSGTTGKPKGHVHAHGGYMVGVHRTMRWVFDVKPTDIFWCTAEPGWITGHSYVVYGPLMAG 335 ***************************************************************************** PP TIGR02188 308 attllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyev 384 tt+l+eg p yp+++r+w+++e+ ++ti+YtaPt++R+lm+ g ++v++hdl +lr+lg+vGepi peaw W++++ lcl|FitnessBrowser__Miya:8502070 336 TTTVLYEGHPLYPEPGRVWSMVERLGITILYTAPTLVRMLMRHGAQHVARHDLTTLRLLGTVGEPISPEAWLWFHRH 412 ***************************************************************************** PP TIGR02188 385 vGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrt 461 vG+++cp+ dtwWqtetG i+++plp lkpgs t+Pl+Giea+vvde+gk+v ++++ g+Lv+++pwP+m + lcl|FitnessBrowser__Miya:8502070 413 VGRGRCPVLDTWWQTETGMIMLSPLPV--SLLKPGSVTRPLPGIEADVVDEHGKPVGPGHG-GLLVLQRPWPAMSCG 486 **************************9..589**************************999.8************** PP TIGR02188 462 iygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpde 538 +y+d+e + + Y+++++g y tGD arrd+dGy+wi+GR+Ddv+ ++Ghr+gtae+e+al sh +vae+av+gvpd lcl|FitnessBrowser__Miya:8502070 487 VYNDDESYRRLYWERFPGWYCTGDVARRDEDGYFWIQGRADDVLLIAGHRIGTAEMEAALASHRSVAECAVIGVPDA 563 ***************************************************************************** PP TIGR02188 539 ikgeaivafvvlkegve.....edeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeel 610 ++ge+ afvvl + + +++el++el ++vr+e+gp+a +++ + e lP+ RsGkimRR+lr+ g++ lcl|FitnessBrowser__Miya:8502070 564 LRGEVAKAFVVLVDDHPplgtmVNADELAAELVEHVRRELGPVAVIREVSFREGLPRNRSGKIMRRVLRSEELGRD- 639 ************997762222245569******************************************9877765. PP TIGR02188 611 lgdvstledp 620 +gd+stled lcl|FitnessBrowser__Miya:8502070 640 TGDLSTLEDG 649 56******96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (651 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 8.99 // [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