Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 8501039 DvMF_1775 acetate/CoA ligase (RefSeq)
Query= SwissProt::Q8ZKF6 (652 letters) >FitnessBrowser__Miya:8501039 Length = 667 Score = 748 bits (1932), Expect = 0.0 Identities = 370/627 (59%), Positives = 468/627 (74%), Gaps = 10/627 (1%) Query: 22 EQYETKYKQSINDPDTFWGEQGK-ILDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAAN 80 ++Y +++ DP+ FWG++ + +LDW TP+ KV + I+W++ TLN+A N Sbjct: 38 DEYLAHRERADKDPEGFWGDRARQLLDWFTPWDKVMDADM--NEPRIEWFKGATLNVAYN 95 Query: 81 CLDRHLQENGDRT--AIIWEGDDTSQSKHISYRELHRDVCRFANTLLDLGIKKGDVVAIY 138 CLDRHL NG R AIIW+G+ + ++Y+ L+ +VCRFA+ L LG++KGD VA+Y Sbjct: 96 CLDRHLV-NGRRNKAAIIWQGEPEDDVRVLTYQMLYDEVCRFASVLQGLGVQKGDRVALY 154 Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPL 198 MPM+PE AVAMLACARIGAVHS++F GFS ++ RI D +++V+TAD +RAGRSIPL Sbjct: 155 MPMIPELAVAMLACARIGAVHSIVFAGFSAVSLQNRIQDCEAKVVVTADAVLRAGRSIPL 214 Query: 199 KKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRD-LIEKASPEHQPEA-MNAE 256 K NVD+ALK+ SVE V+V+ R S+ +EGRD+WW + + ++ P A M++E Sbjct: 215 KVNVDEALKD--CPSVERVVVVDRAHSNCAMREGRDMWWHEAMADRTLDTSCPCAKMDSE 272 Query: 257 DPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYL 316 D LFILYTSGSTGKPKGV+HTTGGYL YAA T ++VFD H D+YWCTAD+GW+TGHSY+ Sbjct: 273 DMLFILYTSGSTGKPKGVVHTTGGYLAYAAHTTQWVFDLHDDDVYWCTADIGWITGHSYI 332 Query: 317 LYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTD 376 +YGPLA G TTLMFEGVP+WP P R +V+K +VNI YTAPT IRALM EG + D Sbjct: 333 VYGPLALGGTTLMFEGVPSWPGPDRFWHIVEKFRVNIFYTAPTVIRALMREGAHWTQKHD 392 Query: 377 RSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGS 436 SSLR+LGSVGEPINPEAW WY + IG + P+VDTWWQTETGG MI+ LP A LK GS Sbjct: 393 LSSLRVLGSVGEPINPEAWMWYHEHIGHSRLPIVDTWWQTETGGIMISALPYATTLKPGS 452 Query: 437 ATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMY 496 AT P G+ A+V +G P G+LV+ WPG R +FG ER++ TYF F MY Sbjct: 453 ATMPLPGIDAAVVKADGTPCGPNEGGHLVVRKPWPGMLRGVFGSPERYKSTYFERFPGMY 512 Query: 497 FSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKG 556 SGDGAR DEDGY W+ GR+DDV+NVSGHR+GTAE+ESALV+HP +AEAAVVG+PHAIKG Sbjct: 513 ESGDGARTDEDGYTWVMGRLDDVINVSGHRMGTAEVESALVSHPAVAEAAVVGMPHAIKG 572 Query: 557 QAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616 +AIYAYVTL+ G E + EL A +R WVRKEIGP+ATP+V+ + + LPKTRSGKIMRRILR Sbjct: 573 EAIYAYVTLSAGTEETEELRAALRTWVRKEIGPIATPEVIQFAEGLPKTRSGKIMRRILR 632 Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLE 643 KIA+G S+ GDTSTLADPGVV+ L+E Sbjct: 633 KIASGAGSDFGDTSTLADPGVVQDLIE 659 Lambda K H 0.317 0.135 0.423 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: 1442 Number of extensions: 62 Number of successful extensions: 6 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: 652 Length of database: 667 Length adjustment: 38 Effective length of query: 614 Effective length of database: 629 Effective search space: 386206 Effective search space used: 386206 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate 8501039 DvMF_1775 (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.1333.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-304 996.4 0.0 2.7e-304 996.2 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501039 DvMF_1775 acetate/CoA ligase (Re Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501039 DvMF_1775 acetate/CoA ligase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 996.2 0.0 2.7e-304 2.7e-304 3 628 .. 36 659 .. 34 660 .. 0.98 Alignments for each domain: == domain 1 score: 996.2 bits; conditional E-value: 2.7e-304 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvek.rkdkvaii 77 ++ey + e+a +dpe fw++ a++ l+w++p++kv+d+++++ +++Wf++++lnv+ync+drh+ + r++k+aii lcl|FitnessBrowser__Miya:8501039 36 GMDEYLAHRERADKDPEGFWGDRARQLLDWFTPWDKVMDADMNEpRIEWFKGATLNVAYNCLDRHLVNgRRNKAAII 112 6899***********************************998877*********************999******** PP TIGR02188 78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaeala 154 w g+ +++d+r ltY+ l++evcr+a vl+ lGv+kgdrva+Y+pmipe+++amlacaRiGavhs+vfaGfsa +l+ lcl|FitnessBrowser__Miya:8501039 113 WQGE-PEDDVRVLTYQMLYDEVCRFASVLQGLGVQKGDRVALYMPMIPELAVAMLACARIGAVHSIVFAGFSAVSLQ 188 ****.5568******************************************************************** PP TIGR02188 155 eRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvek.easae 230 +Ri+d+eak+v+tad lR g++i+lk +vdeal++++ sve+v+vv r+ ++ a ++egrD+ww+e++++ + +++ lcl|FitnessBrowser__Miya:8501039 189 NRIQDCEAKVVVTADAVLRAGRSIPLKVNVDEALKDCP-SVERVVVVDRAHSNCA-MREGRDMWWHEAMADrTLDTS 263 *************************************9.7*************55.**************977899* PP TIGR02188 231 cepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanG 307 c+++k+dsed+lfiLYtsGstGkPkGv+httgGyl +aa t+++vfd++d+d++wCtaD+GW+tGhsYivygPLa G lcl|FitnessBrowser__Miya:8501039 264 CPCAKMDSEDMLFILYTSGSTGKPKGVVHTTGGYLAYAAHTTQWVFDLHDDDVYWCTADIGWITGHSYIVYGPLALG 340 ***************************************************************************** PP TIGR02188 308 attllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyev 384 ttl+fegvp++p ++rfw+++ek++v+ifYtaPt+iRalm++g ++++khdlsslrvlgsvGepinpeaw+Wy+e+ lcl|FitnessBrowser__Miya:8501039 341 GTTLMFEGVPSWPGPDRFWHIVEKFRVNIFYTAPTVIRALMREGAHWTQKHDLSSLRVLGSVGEPINPEAWMWYHEH 417 ***************************************************************************** PP TIGR02188 385 vGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrt 461 +G+++ pivdtwWqtetGgi+i++lp at lkpgsat+Pl+Gi+a+vv+ +g+++ ++e+ g Lv++kpwP+mlr+ lcl|FitnessBrowser__Miya:8501039 418 IGHSRLPIVDTWWQTETGGIMISALPY-ATTLKPGSATMPLPGIDAAVVKADGTPCGPNEG-GHLVVRKPWPGMLRG 492 ***************************.6*****************************999.8************** PP TIGR02188 462 iygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpde 538 ++g +er+ +tYf++++g+y +GDgar+d+dGy w++GR+DdvinvsGhr+gtae+esalvsh+avaeaavvg+p+ lcl|FitnessBrowser__Miya:8501039 493 VFGSPERYKSTYFERFPGMYESGDGARTDEDGYTWVMGRLDDVINVSGHRMGTAEVESALVSHPAVAEAAVVGMPHA 569 ***************************************************************************** PP TIGR02188 539 ikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdv 614 ikgeai+a+v+l++g+ee+e el++ l+++vrkeigpia+p+ i+++e lPktRsGkimRR+lrkia+g+ + gd+ lcl|FitnessBrowser__Miya:8501039 570 IKGEAIYAYVTLSAGTEETE-ELRAALRTWVRKEIGPIATPEVIQFAEGLPKTRSGKIMRRILRKIASGAgSDFGDT 645 *****************999.5************************************************99***** PP TIGR02188 615 stledpsvveelke 628 stl+dp vv++l+e lcl|FitnessBrowser__Miya:8501039 646 STLADPGVVQDLIE 659 **********9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (667 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: 8.48 // [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