Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PP_4487 PP_4487 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__Putida:PP_4487 Length = 696 Score = 1243 bits (3216), Expect = 0.0 Identities = 597/651 (91%), Positives = 623/651 (95%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MSAA LYPVRPEVAA+TLTDEATYKAMYQQSV+NPDGFWREQA+R+DWIKPFT VKQTSF Sbjct: 44 MSAAPLYPVRPEVAATTLTDEATYKAMYQQSVINPDGFWREQAQRIDWIKPFTKVKQTSF 103 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 DDHHVDIKWFADGTLNVS NCLDRHL ERGDQ+AIIWEGDDPSE RNITYRELHE+VCKF Sbjct: 104 DDHHVDIKWFADGTLNVSSNCLDRHLEERGDQLAIIWEGDDPSEHRNITYRELHEQVCKF 163 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLAC RIGAIHSVVFGGFSPEALAGRIIDCKS Sbjct: 164 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKS 223 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 KVVITADEGVR G++ PLKANVD ALTNPETSS+QK+IVCKRT G+I W+QHRDIWYEDL Sbjct: 224 KVVITADEGVRGGRRTPLKANVDLALTNPETSSVQKIIVCKRTGGDIAWHQHRDIWYEDL 283 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 MKVA + CAPKEMGAEEALFILYTSGSTGKPKGV HTT GYL+YAALTHERVFDY+PGEV Sbjct: 284 MKVASSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEV 343 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRV+K++DKHKV+ILYTAPTA Sbjct: 344 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTA 403 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IRAMMA G AAVEGADGSSLRLLGSVGEPINPEAW+WYYK VGKERCPIVDTWWQTETGG Sbjct: 404 IRAMMAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIVDTWWQTETGG 463 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LISPLPGAT LKPGSATRPFFGVVPALVDNLGNLI+GAAEGNLVILDSWPGQ+R+LYGD Sbjct: 464 ILISPLPGATGLKPGSATRPFFGVVPALVDNLGNLIDGAAEGNLVILDSWPGQSRSLYGD 523 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 HDRFVDTYFKTF GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH Sbjct: 524 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHS 583 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 KVAEAAVVGVPHDIKGQGIYVYVTLNAG E SE LRLELKNWVRKEIGPIASPDVIQWAP Sbjct: 584 KVAEAAVVGVPHDIKGQGIYVYVTLNAGIEASEQLRLELKNWVRKEIGPIASPDVIQWAP 643 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651 GLPKTRSGKIMRRILRKIAT EYD LGDISTLADPGVV HLI+THK MN+A Sbjct: 644 GLPKTRSGKIMRRILRKIATGEYDALGDISTLADPGVVQHLIDTHKAMNLA 694 Lambda K H 0.318 0.135 0.418 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: 1751 Number of extensions: 57 Number of successful extensions: 1 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: 651 Length of database: 696 Length adjustment: 39 Effective length of query: 612 Effective length of database: 657 Effective search space: 402084 Effective search space used: 402084 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 PP_4487 PP_4487 (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.4035251.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1018.9 0.1 0 1018.6 0.1 1.0 1 FitnessBrowser__Putida:PP_4487 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Putida:PP_4487 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1018.6 0.1 0 0 3 628 .. 63 686 .. 61 687 .. 0.98 Alignments for each domain: == domain 1 score: 1018.6 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaiiw 78 + +yk++y++++ +p+ fw+++a+ +++w+kpf+kv+++s+++ ++kWf+dg+lnvs nc+drh+e+r d++aiiw FitnessBrowser__Putida:PP_4487 63 DEATYKAMYQQSVINPDGFWREQAQ-RIDWIKPFTKVKQTSFDDhhvDIKWFADGTLNVSSNCLDRHLEERGDQLAIIW 140 5679*********************.5*************99887789******************************* PP TIGR02188 79 egdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRi 157 egd+++e +r++tY+el+++vc++an+l+ + v++gd v+iY+pmipeav+amlacaRiGa+hsvvf+Gfs+eala Ri FitnessBrowser__Putida:PP_4487 141 EGDDPSE-HRNITYRELHEQVCKFANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRI 218 *****96.*********************************************************************** PP TIGR02188 158 vdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepek 235 +d+++k+vitadeg+Rgg++++lk++vd al++ e+ sv+k++v+krtg ++a w++ rD+w+e+l++ as++c+p++ FitnessBrowser__Putida:PP_4487 219 IDCKSKVVITADEGVRGGRRTPLKANVDLALTNPETsSVQKIIVCKRTGGDIA-WHQHRDIWYEDLMKV-ASSHCAPKE 295 *********************************9998**************77.**************5.********* PP TIGR02188 236 ldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfe 314 +++e+ lfiLYtsGstGkPkGvlhttgGyl++aalt++ vfd+++++++wCtaDvGWvtGhsYivygPLanGattllfe FitnessBrowser__Putida:PP_4487 296 MGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEVYWCTADVGWVTGHSYIVYGPLANGATTLLFE 374 ******************************************************************************* PP TIGR02188 315 gvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpiv 393 gvp+ypd r+ ++++k+kv+i+YtaPtaiRa+m++g+++v+ d sslr+lgsvGepinpeaw+Wyy++vGke+cpiv FitnessBrowser__Putida:PP_4487 375 GVPNYPDITRVSKIVDKHKVNILYTAPTAIRAMMAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIV 453 ******************************************************************************* PP TIGR02188 394 dtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvet 472 dtwWqtetGgili+plpg at lkpgsat+P+fG+ +++vd+ g+ ++ +e g Lvi ++wP++ r++ygd++rfv+t FitnessBrowser__Putida:PP_4487 454 DTWWQTETGGILISPLPG-ATGLKPGSATRPFFGVVPALVDNLGNLIDGAAE-GNLVILDSWPGQSRSLYGDHDRFVDT 530 ******************.6****************************8777.79************************ PP TIGR02188 473 YfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551 Yfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGhr+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l+ FitnessBrowser__Putida:PP_4487 531 YFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHSKVAEAAVVGVPHDIKGQGIYVYVTLN 609 ******************************************************************************* PP TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +g+e++e +l+ elk++vrkeigpia+pd i++++ lPktRsGkimRR+lrkia+ge ++lgd+stl+dp vv++l++ FitnessBrowser__Putida:PP_4487 610 AGIEASE-QLRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIATGEyDALGDISTLADPGVVQHLID 686 ****999.6*****************************************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (696 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 18.94 // [ok]
This GapMind analysis is from Apr 09 2024. 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