Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 6937938 Sama_2079 acetyl-CoA synthetase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__SB2B:6937938 Length = 650 Score = 973 bits (2516), Expect = 0.0 Identities = 453/644 (70%), Positives = 533/644 (82%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 MS SLY V ++AA+ L + Y+ MYQ+SV NP+GFW E AKR+DWIKPFT VK TS+ Sbjct: 1 MSTQSLYSVPADIAANALVNNEQYQKMYQESVANPEGFWGEHAKRIDWIKPFTQVKDTSY 60 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 DD ++ IKWF DGTLN S NCLDRHLA +GD +AIIWEGDD SE R +TYRELH EVC+F Sbjct: 61 DDQNLYIKWFHDGTLNASANCLDRHLASKGDDVAIIWEGDDASEQRKVTYRELHAEVCQF 120 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 ANAL+ + V RGDVVTIYMPM+ EA VAMLAC RIGA+HSVVFGGFSP+++A R+ID KS Sbjct: 121 ANALKAEGVKRGDVVTIYMPMVVEATVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 K++ITADEGVR G+KIPLK N+D+AL P+ ++++ VIV KRT G + W + RD W+ + Sbjct: 181 KLLITADEGVRGGRKIPLKGNIDEALNRPDVTTVETVIVLKRTGGAVNWVEGRDKWWHQV 240 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 A T CA +EMGAE+ LF+LYTSGSTG PKGV HTT GYL+YA++THE VFDYKPGEV Sbjct: 241 TDGAATECAVEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKPGEV 300 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 YWCTADVGW+TGHSY+VYGPLANGAT L+ EG+PN+P R+ +++D+H+V+ILYTAPT Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATILIHEGIPNFPSPARLGEIVDRHQVNILYTAPTL 360 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 IRA+MA G + DG SLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG Sbjct: 361 IRALMAEGKQHFDNFDGKSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LI+PLPGAT KPGSATRPFFGV PALVDN GN++EGA EGNLV+LDSWPGQ RT+YGD Sbjct: 421 ILITPLPGATDTKPGSATRPFFGVQPALVDNEGNILEGATEGNLVLLDSWPGQMRTVYGD 480 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 H+RFV TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAH Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHD 540 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 VAEAAVVG PHDIKGQGIY YVTL G E +E LR EL+ WVRKEIG +A+PD+IQWA Sbjct: 541 LVAEAAVVGYPHDIKGQGIYAYVTLTKGTEATEELRQELRQWVRKEIGALATPDLIQWAS 600 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIET 644 GLPKTRSGKIMRR LRKIA E LGD STLADP V+ LIE+ Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEITNLGDASTLADPSVIDTLIES 644 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: 1440 Number of extensions: 48 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 6937938 Sama_2079 (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.1020949.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 1025.3 0.2 0 1025.1 0.2 1.0 1 FitnessBrowser__SB2B:6937938 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6937938 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1025.1 0.2 0 0 3 628 .. 20 643 .. 18 644 .. 0.98 Alignments for each domain: == domain 1 score: 1025.1 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaiiweg 80 ++e+y+++y+e++++pe fw+++ak+ ++w+kpf++v+d+s ++ +kWf+dg+ln+s+nc+drh++++ d vaiiweg FitnessBrowser__SB2B:6937938 20 NNEQYQKMYQESVANPEGFWGEHAKR-IDWIKPFTQVKDTSYDDqnlYIKWFHDGTLNASANCLDRHLASKGDDVAIIWEG 99 789**********************5.************9987666789******************************** PP TIGR02188 81 deegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivdae 161 d+++e +rk+tY+el++evc++an+lk+ Gvk+gd v+iY+pm++ea++amlacaRiGavhsvvf+Gfs++++a+R++d + FitnessBrowser__SB2B:6937938 100 DDASE-QRKVTYRELHAEVCQFANALKAEGVKRGDVVTIYMPMVVEATVAMLACARIGAVHSVVFGGFSPDSIASRVIDGK 179 *9985.*************************************************************************** PP TIGR02188 162 aklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedp 241 +kl+itadeg+Rgg++i+lk ++deal++ + +ve+v+v+krtg v+ w+egrD+ww+++++ +a +ec++e++++edp FitnessBrowser__SB2B:6937938 180 SKLLITADEGVRGGRKIPLKGNIDEALNRPDVtTVETVIVLKRTGGAVN-WVEGRDKWWHQVTD-GAATECAVEEMGAEDP 258 *****************************9988**************66.*************9.6*************** PP TIGR02188 242 lfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypda 322 lf+LYtsGstG+PkGvlhttgGyl++a++t++yvfd+k+++++wCtaDvGW+tGhsY+vygPLanGat l++eg+p++p++ FitnessBrowser__SB2B:6937938 259 LFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKPGEVYWCTADVGWITGHSYMVYGPLANGATILIHEGIPNFPSP 339 ********************************************************************************* PP TIGR02188 323 srfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGg 403 +r+ e++++++v+i+YtaPt+iRalm++g++++++ d +slr++gsvGepinpeaw+Wy+ev+G+e+cpivdtwWqtetGg FitnessBrowser__SB2B:6937938 340 ARLGEIVDRHQVNILYTAPTLIRALMAEGKQHFDNFDGKSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420 ********************************************************************************* PP TIGR02188 404 ilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftG 484 ilitplpg at++kpgsat+P+fG+++++vd+eg+ +e +e g Lv+ ++wP+++rt+ygd+erfv tYfk+++g+yftG FitnessBrowser__SB2B:6937938 421 ILITPLPG-ATDTKPGSATRPFFGVQPALVDNEGNILEGATE-GNLVLLDSWPGQMRTVYGDHERFVLTYFKTFRGMYFTG 499 ********.6****************************8777.79************************************ PP TIGR02188 485 DgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekel 565 Dgarrd+dGy+wi+GRvDdvinvsGhrlgtae+esalv+h+ vaeaavvg+p++ikg+ i+a+v+l++g+e++e el++el FitnessBrowser__SB2B:6937938 500 DGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHDLVAEAAVVGYPHDIKGQGIYAYVTLTKGTEATE-ELRQEL 579 ***********************************************************************999.5***** PP TIGR02188 566 kklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +++vrkeig++a+pd i++++ lPktRsGkimRR+lrkia++e ++lgd stl+dpsv+++l+e FitnessBrowser__SB2B:6937938 580 RQWVRKEIGALATPDLIQWASGLPKTRSGKIMRRFLRKIAANEiTNLGDASTLADPSVIDTLIE 643 ************************************************************9986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 37.59 // [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