Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF2607 Psest_2657 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__psRCH2:GFF2607 Length = 651 Score = 1132 bits (2927), Expect = 0.0 Identities = 534/648 (82%), Positives = 588/648 (90%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 M AAS+YPV PE A +LTDEA Y+AMYQQSV+NP+GFWREQA RL+WI+PFT VK+TSF Sbjct: 1 MCAASVYPVSPEAAKHSLTDEAAYRAMYQQSVINPEGFWREQAARLNWIRPFTEVKRTSF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 DDHHVDIKWFADGTLNVS NCLDRHLAERGDQ+AIIWEGD+PSE R ITYREL++EVCKF Sbjct: 61 DDHHVDIKWFADGTLNVSANCLDRHLAERGDQVAIIWEGDEPSEHREITYRELYQEVCKF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANALRGQDVHRGDVVTIYMPMIPEA VAMLAC RIGAIHSVVFGGFSPEALAGRIID +S Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSPEALAGRIIDGQS 180 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 KVVITADEG+R GK IPLK NVD+ALT+P+T +QK+IV +RT +I+W+ HRD+ Y+DL Sbjct: 181 KVVITADEGIRGGKPIPLKENVDEALTHPQTRCVQKIIVVRRTGADIRWHPHRDVCYDDL 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 M+VAG VCAPKEMGAEE LFILYTSGSTGKPKGV HT GYLLYAALTHERVFDY+PG+V Sbjct: 241 MRVAGEVCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDV 300 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTAD+GW+TGHSY++YGPLANGATTL++EGVPNYPD+TR+A++IDKH+V+ILYTAPTA Sbjct: 301 YWCTADIGWITGHSYLIYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTA 360 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IRAMMA G AA+EGADGSSLRLLG+VGEPINPEAW WYY+ VG+ RCPIVDTWWQTETGG Sbjct: 361 IRAMMAEGAAAMEGADGSSLRLLGTVGEPINPEAWHWYYETVGRSRCPIVDTWWQTETGG 420 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LISPLPGATALKPGSATRP FGVVP LVDNLGNL+EG AEGNLVILDSWPGQ RT+Y D Sbjct: 421 ILISPLPGATALKPGSATRPLFGVVPGLVDNLGNLLEGPAEGNLVILDSWPGQMRTIYRD 480 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 HDRFVDTYFKTF GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHA 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 KVAEAA VGVPH +KGQ IYVYVTL AG E S+ LR EL+ WVR EIGPIA PD IQWAP Sbjct: 541 KVAEAAAVGVPHALKGQAIYVYVTLVAGVEPSDTLRQELQQWVRHEIGPIAVPDTIQWAP 600 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTM 648 GLPKTRSGKIMRR+LRKIAT +YD LGD STLADPGVV LIE H+ + Sbjct: 601 GLPKTRSGKIMRRLLRKIATDDYDALGDTSTLADPGVVDQLIEAHEAV 648 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: 1625 Number of extensions: 60 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: 651 Length adjustment: 38 Effective length of query: 613 Effective length of database: 613 Effective search space: 375769 Effective search space used: 375769 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 GFF2607 Psest_2657 (acetate--CoA ligase)
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.11765.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-307 1005.5 0.0 4.8e-307 1005.3 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF2607 Psest_2657 acetate--CoA ligase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF2607 Psest_2657 acetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1005.3 0.0 4.8e-307 4.8e-307 4 628 .. 21 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1005.3 bits; conditional E-value: 4.8e-307 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 +y+++y++++ +pe fw+++a +l+w++pf++v+++s+++ ++kWf+dg+lnvs+nc+drh+++r d+va lcl|FitnessBrowser__psRCH2:GFF2607 21 EAAYRAMYQQSVINPEGFWREQAA-RLNWIRPFTEVKRTSFDDhhvDIKWFADGTLNVSANCLDRHLAERGDQVA 94 678*********************.5*************99887789**************************** PP TIGR02188 76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150 iiwegde++e +r++tY+el++evc++an+l+ + v++gd v+iY+pmipea++amlacaRiGa+hsvvf+Gfs+ lcl|FitnessBrowser__psRCH2:GFF2607 95 IIWEGDEPSE-HREITYRELYQEVCKFANALRGQDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSP 168 ********96.**************************************************************** PP TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelve 224 eala Ri+d ++k+vitadeg+Rggk i+lk++vdeal++ ++ v+k++vv+rtg+++ w+ rDv +++l++ lcl|FitnessBrowser__psRCH2:GFF2607 169 EALAGRIIDGQSKVVITADEGIRGGKPIPLKENVDEALTHPQTrCVQKIIVVRRTGADIR-WHPHRDVCYDDLMR 242 ****************************************99889*************76.************** PP TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYi 299 a + c+p+++++e+plfiLYtsGstGkPkGvlht gGyll+aalt++ vfd++++d++wCtaD+GW+tGhsY+ lcl|FitnessBrowser__psRCH2:GFF2607 243 V-AGEVCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDVYWCTADIGWITGHSYL 316 5.************************************************************************* PP TIGR02188 300 vygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepin 374 +ygPLanGattl++egvp+ypd r++++i+k++v+i+YtaPtaiRa+m++g ++++ d sslr+lg+vGepin lcl|FitnessBrowser__psRCH2:GFF2607 317 IYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTAIRAMMAEGAAAMEGADGSSLRLLGTVGEPIN 391 *************************************************************************** PP TIGR02188 375 peaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvL 449 peaw+Wyye+vG+++cpivdtwWqtetGgili+plpg at+lkpgsat+PlfG+ + +vd+ g+ +e +e g L lcl|FitnessBrowser__psRCH2:GFF2607 392 PEAWHWYYETVGRSRCPIVDTWWQTETGGILISPLPG-ATALKPGSATRPLFGVVPGLVDNLGNLLEGPAE-GNL 464 *************************************.6****************************7666.68* PP TIGR02188 450 vikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsh 524 vi ++wP+++rtiy+d++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGhr+gtaeiesa+v+h lcl|FitnessBrowser__psRCH2:GFF2607 465 VILDSWPGQMRTIYRDHDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 539 *************************************************************************** PP TIGR02188 525 eavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRR 599 +vaeaa+vgvp+ +kg+ai+++v+l +gve++++ l++el+++vr+eigpia pd+i++++ lPktRsGkimRR lcl|FitnessBrowser__psRCH2:GFF2607 540 AKVAEAAAVGVPHALKGQAIYVYVTLVAGVEPSDT-LRQELQQWVRHEIGPIAVPDTIQWAPGLPKTRSGKIMRR 613 **********************************5.*************************************** PP TIGR02188 600 llrkiaege.ellgdvstledpsvveelke 628 llrkia+++ ++lgd+stl+dp vv++l+e lcl|FitnessBrowser__psRCH2:GFF2607 614 LLRKIATDDyDALGDTSTLADPGVVDQLIE 643 *********9*****************987 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 8.27 // [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