Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF4676 PS417_23925 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__WCS417:GFF4676 Length = 645 Score = 816 bits (2107), Expect = 0.0 Identities = 398/640 (62%), Positives = 476/640 (74%), Gaps = 5/640 (0%) Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63 S +P V + + YK +Y+QS+ PD FW EQAK LDWI P+ TV+++ + Sbjct: 5 STFPTADAVRRAAQLSQEDYKRLYRQSIEQPDTFWAEQAKGFLDWITPWHTVQRSDINTG 64 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123 WFA G LNVSYNC+DRHLA+R +Q A IWEGDDP++S ITYR+LH+ V + AN Sbjct: 65 AAH--WFAGGQLNVSYNCIDRHLAQRAEQPAFIWEGDDPAKSCKITYRQLHQNVSRLANV 122 Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183 L+ + V +GD V IYMPMIPEA AMLACTRIGA+HSVVFGGFSP+AL RI D + V Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDALRDRIQDADCRTV 182 Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243 ITADEGVR GK + LK NVD AL + ++ V+V +RT + W++ RD+ Y+ + Sbjct: 183 ITADEGVRGGKPVALKQNVDKALAS--CPNVSTVLVVERTGATVNWSEGRDLKYQQALDA 240 Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303 A C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ GEV+WC Sbjct: 241 ASDNCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWC 300 Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363 TADVGWVTGHSYIVYGPLANGAT+L+FEGVP+YPD +R +VIDKHKV+I YTAPTA+RA Sbjct: 301 TADVGWVTGHSYIVYGPLANGATSLMFEGVPSYPDSSRFWQVIDKHKVNIFYTAPTALRA 360 Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423 +M G A +E +SLRLLGSVGEPINPEAWDWY+ VG++RCPIVDTWWQTETGG+++ Sbjct: 361 LMREGHAPLESTSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIML 420 Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483 SPL A +KPG AT+P FGV P L+D G GA G L I SWPGQ R++YGD R Sbjct: 421 SPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEFSGAGSGVLAIKASWPGQIRSVYGDPQR 480 Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543 +DTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H VA Sbjct: 481 MIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDLVA 540 Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603 EAAVVG PHD+KGQGIY +VT G E +AL+ L V KEIG A P++IQWAP LP Sbjct: 541 EAAVVGYPHDVKGQGIYAFVTPMNGVEPDDALKRHLLELVSKEIGSFAKPELIQWAPALP 600 Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 KTRSGKIMRRILRKIA E D LGD STLADP VV LI+ Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVEGLID 640 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: 1340 Number of extensions: 63 Number of successful extensions: 3 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: 645 Length adjustment: 38 Effective length of query: 613 Effective length of database: 607 Effective search space: 372091 Effective search space used: 372091 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 GFF4676 PS417_23925 (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.26810.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 1017.0 0.0 0 1016.7 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF4676 PS417_23925 acetyl-CoA synthetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4676 PS417_23925 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1016.7 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.99 Alignments for each domain: == domain 1 score: 1016.7 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvai 76 ++e+yk+ly+++ie+p++fwa++ak l+w++p+++v++++ ++ ++Wf++g+lnvsync+drh+++r+++ a lcl|FitnessBrowser__WCS417:GFF4676 20 SQEDYKRLYRQSIEQPDTFWAEQAKGFLDWITPWHTVQRSDINTgAAHWFAGGQLNVSYNCIDRHLAQRAEQPAF 94 5789*************************************99999***************************** PP TIGR02188 77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151 iwegd++ + s k+tY++l+++v+rlanvlk+ Gvkkgdrv+iY+pmipea++amlac+RiGavhsvvf+Gfs++ lcl|FitnessBrowser__WCS417:GFF4676 95 IWEGDDPAK-SCKITYRQLHQNVSRLANVLKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPD 168 *******96.9**************************************************************** PP TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelveke 226 al++Ri+da++++vitadeg+Rggk ++lk++vd+al++++ +v++vlvv+rtg+ v+ w+egrD++++++++ lcl|FitnessBrowser__WCS417:GFF4676 169 ALRDRIQDADCRTVITADEGVRGGKPVALKQNVDKALASCP-NVSTVLVVERTGATVN-WSEGRDLKYQQALDA- 240 ****************************************9.6*************66.**************5. PP TIGR02188 227 asaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivy 301 as++c+pe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyv d++d+++fwCtaDvGWvtGhsYivy lcl|FitnessBrowser__WCS417:GFF4676 241 ASDNCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWCTADVGWVTGHSYIVY 315 *************************************************************************** PP TIGR02188 302 gPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpe 376 gPLanGat+l+fegvp+ypd+srfw+vi+k+kv+ifYtaPta+Ralm++g++ ++++++ slr+lgsvGepinpe lcl|FitnessBrowser__WCS417:GFF4676 316 GPLANGATSLMFEGVPSYPDSSRFWQVIDKHKVNIFYTAPTALRALMREGHAPLESTSRASLRLLGSVGEPINPE 390 *************************************************************************** PP TIGR02188 377 aweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvi 451 aw+Wy++ vG+++cpivdtwWqtetGgi+++pl + a +kpg+at+P+fG++++++de+gke++ + gvL+i lcl|FitnessBrowser__WCS417:GFF4676 391 AWDWYFNAVGEQRCPIVDTWWQTETGGIMLSPLVS-AQRIKPGCATQPMFGVQPVLLDEQGKEFSGAGS-GVLAI 463 ***********************************.6***************************98777.8**** PP TIGR02188 452 kkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvshea 526 k +wP+++r++ygd++r+++tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esalv h+ lcl|FitnessBrowser__WCS417:GFF4676 464 KASWPGQIRSVYGDPQRMIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDL 538 *************************************************************************** PP TIGR02188 527 vaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRll 601 vaeaavvg+p+++kg+ i+afv+ ++gve+d+ +l+++l +lv+keig++akp+ i+++++lPktRsGkimRR+l lcl|FitnessBrowser__WCS417:GFF4676 539 VAEAAVVGYPHDVKGQGIYAFVTPMNGVEPDD-ALKRHLLELVSKEIGSFAKPELIQWAPALPKTRSGKIMRRIL 612 ********************************.5***************************************** PP TIGR02188 602 rkiaege.ellgdvstledpsvveelke 628 rkia +e ++lgd+stl+dpsvve l++ lcl|FitnessBrowser__WCS417:GFF4676 613 RKIACNElDSLGDTSTLADPSVVEGLID 640 ************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (645 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: 00:00:00.03 # 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