Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 7025363 Shewana3_2523 acetyl-CoA synthetase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__ANA3:7025363 Length = 650 Score = 993 bits (2567), Expect = 0.0 Identities = 460/649 (70%), Positives = 541/649 (83%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MS+ SLY V +AA+ L + YK MYQ+S+VNP+GFWRE KR+DWIKP+T +K+T+F Sbjct: 1 MSSQSLYKVSGNIAANALVNNDQYKKMYQESIVNPEGFWREHGKRIDWIKPYTKIKKTTF 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 DDH++ I WF DGTLN S NCLDRHLAE D++AIIWEGD+ SE R ITY ELH +VCKF Sbjct: 61 DDHNLSINWFYDGTLNASANCLDRHLAEHSDRVAIIWEGDNASEQRQITYGELHTQVCKF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANALR Q V RGD+VTIYMPM+PEA VAMLAC RIGA+HSVVFGGFSP+++A R+ID KS Sbjct: 121 ANALRSQGVRRGDIVTIYMPMVPEAAVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 KVVITADEG+R G+ IPLK N+DDAL +P+ +S++KVIV KRT G + W + RD+W+ L Sbjct: 181 KVVITADEGMRGGRAIPLKRNIDDALKHPDVTSVEKVIVLKRTGGKVDWVEGRDVWWHSL 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 ++ A CA +EMGAE+ LF+LYTSGSTG PKGV HTT GY++YA++THE VFDYKPGE+ Sbjct: 241 VETASEHCAIEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYASMTHEYVFDYKPGEI 300 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTADVGW+TGHSY+VYGPLANGAT L+ EG+PNYP R+ ++ID+HKV+ILYTAPT Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATVLIHEGIPNYPSPARLGEMIDRHKVNILYTAPTL 360 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IRA+MA G + DGSSLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG Sbjct: 361 IRALMAEGKQHFDKYDGSSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LI+PLPGAT KPGSATRPFFGV PALVDN+GN++EGA EGNLV+LDSWPGQ RT+YGD Sbjct: 421 ILITPLPGATDTKPGSATRPFFGVQPALVDNMGNILEGATEGNLVLLDSWPGQMRTVYGD 480 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 H+RFV TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+H Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVSHE 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 VAEAAVVG PHDIKGQGIY YVTL G E SE LR EL+ WVRKEIG +A+PD+IQWA Sbjct: 541 LVAEAAVVGYPHDIKGQGIYAYVTLTRGTEESEELRQELRQWVRKEIGALATPDLIQWAT 600 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMN 649 GLPKTRSGKIMRR LRKIA E LGD STLADP V+ LIET N Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIETLIETRLNRN 649 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: 1448 Number of extensions: 53 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: 650 Length adjustment: 38 Effective length of query: 613 Effective length of database: 612 Effective search space: 375156 Effective search space used: 375156 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 7025363 Shewana3_2523 (acetyl-CoA synthetase (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.18915.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 1039.5 0.3 0 1039.3 0.3 1.0 1 lcl|FitnessBrowser__ANA3:7025363 Shewana3_2523 acetyl-CoA synthet Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7025363 Shewana3_2523 acetyl-CoA synthetase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1039.3 0.3 0 0 3 628 .. 20 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1039.3 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvai 76 ++++yk++y+e+i +pe fw++++k +++w+kp++k++++++++ +++Wf dg+ln+s+nc+drh+++++d+vai lcl|FitnessBrowser__ANA3:7025363 20 NNDQYKKMYQESIVNPEGFWREHGK-RIDWIKPYTKIKKTTFDDhnlSINWFYDGTLNASANCLDRHLAEHSDRVAI 95 789**********************.5************998876789***************************** PP TIGR02188 77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaeal 153 iwegd+++e +r++tY el+++vc++an+l+++Gv++gd v+iY+pm+pea++amlacaRiGavhsvvf+Gfs++++ lcl|FitnessBrowser__ANA3:7025363 96 IWEGDNASE-QRQITYGELHTQVCKFANALRSQGVRRGDIVTIYMPMVPEAAVAMLACARIGAVHSVVFGGFSPDSI 171 *****9885.******************************************************************* PP TIGR02188 154 aeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasa 229 a+R++d ++k+vitadeg+Rgg++i+lk+++d+al++ + svekv+v+krtg +v w+egrDvww++lve+ as+ lcl|FitnessBrowser__ANA3:7025363 172 ASRVIDGKSKVVITADEGMRGGRAIPLKRNIDDALKHPDVtSVEKVIVLKRTGGKVD-WVEGRDVWWHSLVET-ASE 246 *************************************9999**************66.**************6.*** PP TIGR02188 230 ecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLan 306 +c+ e++++edplf+LYtsGstG+PkGvlhttgGy+++a++t++yvfd+k+++i+wCtaDvGW+tGhsY+vygPLan lcl|FitnessBrowser__ANA3:7025363 247 HCAIEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYASMTHEYVFDYKPGEIYWCTADVGWITGHSYMVYGPLAN 323 ***************************************************************************** PP TIGR02188 307 GattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyye 383 Gat l++eg+p+yp+++r+ e+i+++kv+i+YtaPt+iRalm++g+++++k+d sslr++gsvGepinpeaw+Wy+e lcl|FitnessBrowser__ANA3:7025363 324 GATVLIHEGIPNYPSPARLGEMIDRHKVNILYTAPTLIRALMAEGKQHFDKYDGSSLRIMGSVGEPINPEAWRWYHE 400 ***************************************************************************** PP TIGR02188 384 vvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlr 460 v+G+e+cpivdtwWqtetGgilitplpg at++kpgsat+P+fG+++++vd+ g+ +e +e g Lv+ ++wP+++r lcl|FitnessBrowser__ANA3:7025363 401 VIGHEHCPIVDTWWQTETGGILITPLPG-ATDTKPGSATRPFFGVQPALVDNMGNILEGATE-GNLVLLDSWPGQMR 475 ****************************.6****************************8777.79************ PP TIGR02188 461 tiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpd 537 t+ygd+erfv tYfk+++g+yftGDgarrd+dGy+wi+GRvDdvinvsGhrlgtae+esalvshe vaeaavvg+p+ lcl|FitnessBrowser__ANA3:7025363 476 TVYGDHERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVSHELVAEAAVVGYPH 552 ***************************************************************************** PP TIGR02188 538 eikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgd 613 +ikg+ i+a+v+l++g+ee+e el++el+++vrkeig++a+pd i++++ lPktRsGkimRR+lrkia++e ++lgd lcl|FitnessBrowser__ANA3:7025363 553 DIKGQGIYAYVTLTRGTEESE-ELRQELRQWVRKEIGALATPDLIQWATGLPKTRSGKIMRRFLRKIAANEvTNLGD 628 ******************999.5****************************************************** PP TIGR02188 614 vstledpsvveelke 628 stl+dp+v+e+l+e lcl|FitnessBrowser__ANA3:7025363 629 ASTLADPAVIETLIE 643 ***********9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (650 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: 11.92 // [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