Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate SMc04093 SMc04093 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__Smeli:SMc04093 Length = 649 Score = 885 bits (2286), Expect = 0.0 Identities = 423/638 (66%), Positives = 500/638 (78%), Gaps = 3/638 (0%) Query: 7 YPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66 YPV TL D ATY Y++SV +P+ FW E KR++W +P+T VK TSF+ V Sbjct: 6 YPVLEAAKNRTLLDNATYLEWYRESVADPEKFWGEHGKRIEWFEPYTKVKNTSFEGD-VS 64 Query: 67 IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALRG 126 IKWF DG NVSYNC+DRHL G++ AIIWEGD+P + ITY EL+++VC+ AN L+ Sbjct: 65 IKWFEDGLTNVSYNCIDRHLKTHGEKTAIIWEGDNPYLDKKITYNELYDKVCRLANVLKE 124 Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186 Q V +GD VTIYMPMIPEA AMLAC RIGAIHSVVFGGFSPEALAGRI+DC+S VIT Sbjct: 125 QGVKKGDRVTIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPEALAGRIVDCESTFVITC 184 Query: 187 DEGVRAGKKIPLKANVDDAL--TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244 DEGVR GK + LK N D A+ + ++ KV+V +RT G + W RD+WY A Sbjct: 185 DEGVRGGKPVALKENTDTAIDIAARQHVTVSKVLVVRRTGGKVGWAPGRDLWYHQETAAA 244 Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304 C P++M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY+ G++YWCT Sbjct: 245 EPHCPPEKMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYQDGDIYWCT 304 Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364 ADVGWVTGHSYIVYGPLAN ATTL+FEGVPN+PD R +V+DKHKV+I YTAPTAIR++ Sbjct: 305 ADVGWVTGHSYIVYGPLANAATTLMFEGVPNFPDAGRFWEVVDKHKVNIFYTAPTAIRSL 364 Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424 M +G V+ + SSLRLLG+VGEPINPEAW+WYY VG ERCP+VDTWWQTETGG+LI+ Sbjct: 365 MGAGDDFVKRSSRSSLRLLGTVGEPINPEAWEWYYHVVGDERCPVVDTWWQTETGGILIT 424 Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484 PLPGAT LKPGSATRPFFGV P +VD+ G +++GAA+GNL I DSWPGQ RT+YGDH+RF Sbjct: 425 PLPGATDLKPGSATRPFFGVQPQIVDSDGKVVDGAADGNLCITDSWPGQMRTVYGDHERF 484 Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544 + TYF T+ G YFTGDG RRDEDGYYWITGRVDDVLNVSGHR+GTAE+ESA+V+H V+E Sbjct: 485 IQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVSE 544 Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604 AAVVG PH IKGQGIY YV+L AGE + LR L VR EIGPIA+PD IQ+APGLPK Sbjct: 545 AAVVGYPHPIKGQGIYCYVSLMAGEVGDDELRQALVKHVRSEIGPIATPDKIQFAPGLPK 604 Query: 605 TRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642 TRSGKIMRRILRKIA ++ LGD STLADPGVV LI Sbjct: 605 TRSGKIMRRILRKIAEDDFGSLGDTSTLADPGVVDDLI 642 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: 1468 Number of extensions: 72 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: 649 Length adjustment: 38 Effective length of query: 613 Effective length of database: 611 Effective search space: 374543 Effective search space used: 374543 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 SMc04093 SMc04093 (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.27095.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 1034.6 0.0 0 1034.4 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc04093 SMc04093 acetyl-CoA synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc04093 SMc04093 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1034.4 0.0 0 0 4 628 .. 20 643 .. 17 644 .. 0.98 Alignments for each domain: == domain 1 score: 1034.4 bits; conditional E-value: 0 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdkvai 76 + +y e+y+e+++dpekfw++++k ++ew++p++kv+++s+e ++kWfedg +nvsync+drh++++ +k+ai lcl|FitnessBrowser__Smeli:SMc04093 20 NATYLEWYRESVADPEKFWGEHGK-RIEWFEPYTKVKNTSFEGdvSIKWFEDGLTNVSYNCIDRHLKTHGEKTAI 93 57899*******************.5***************987899**************************** PP TIGR02188 77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151 iwegd++ +k+tY+el+++vcrlanvlke+Gvkkgdrv+iY+pmipea++amlacaRiGa+hsvvf+Gfs+e lcl|FitnessBrowser__Smeli:SMc04093 94 IWEGDNPYL-DKKITYNELYDKVCRLANVLKEQGVKKGDRVTIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPE 167 *****9996.9**************************************************************** PP TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrDvwweelv 223 ala Rivd+e+ +vit deg+Rggk ++lk+++d a++ a + +v+kvlvv+rtg +v w grD+w+++++ lcl|FitnessBrowser__Smeli:SMc04093 168 ALAGRIVDCESTFVITCDEGVRGGKPVALKENTDTAIDIAARqhvTVSKVLVVRRTGGKVG-WAPGRDLWYHQET 241 ************************************9876554579*************76.************* PP TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298 + a+ +c+pek+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++d+di+wCtaDvGWvtGhsY lcl|FitnessBrowser__Smeli:SMc04093 242 AA-AEPHCPPEKMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYQDGDIYWCTADVGWVTGHSY 315 *5.************************************************************************ PP TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepi 373 ivygPLan attl+fegvp++pda+rfwev++k+kv+ifYtaPtaiR+lm +g+++vk+ ++sslr+lg+vGepi lcl|FitnessBrowser__Smeli:SMc04093 316 IVYGPLANAATTLMFEGVPNFPDAGRFWEVVDKHKVNIFYTAPTAIRSLMGAGDDFVKRSSRSSLRLLGTVGEPI 390 *************************************************************************** PP TIGR02188 374 npeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448 npeaweWyy+vvG+e+cp+vdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd++gk v+ ++ g lcl|FitnessBrowser__Smeli:SMc04093 391 NPEAWEWYYHVVGDERCPVVDTWWQTETGGILITPLPG-ATDLKPGSATRPFFGVQPQIVDSDGKVVDGAAD-GN 463 **************************************.6***************************98777.79 PP TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvs 523 L+i+++wP+++rt+ygd+erf++tYf+++kg yftGDg+rrd+dGy+wi+GRvDdv+nvsGhrlgtae+esalvs lcl|FitnessBrowser__Smeli:SMc04093 464 LCITDSWPGQMRTVYGDHERFIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVS 538 *************************************************************************** PP TIGR02188 524 heavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimR 598 h+ v+eaavvg+p+ ikg+ i+++v l++g+ d+ el++ l k+vr+eigpia+pdki++++ lPktRsGkimR lcl|FitnessBrowser__Smeli:SMc04093 539 HNLVSEAAVVGYPHPIKGQGIYCYVSLMAGEVGDD-ELRQALVKHVRSEIGPIATPDKIQFAPGLPKTRSGKIMR 612 *****************************999999.5************************************** PP TIGR02188 599 Rllrkiaege.ellgdvstledpsvveelke 628 R+lrkiae++ +lgd+stl+dp vv++l++ lcl|FitnessBrowser__Smeli:SMc04093 613 RILRKIAEDDfGSLGDTSTLADPGVVDDLIA 643 ***************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (649 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: 11.51 // [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