Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Echvi_1268 Echvi_1268 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__Cola:Echvi_1268 Length = 632 Score = 721 bits (1861), Expect = 0.0 Identities = 356/618 (57%), Positives = 441/618 (71%), Gaps = 6/618 (0%) Query: 28 YQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVDIKWFADGTLNVSYNCLDRHLA 87 YQ+SV P+ FW A W K + V + F+ D+KWF +G +N++ N L+RHL Sbjct: 15 YQKSVTEPEQFWARIADSFHWKKRWDKVLEWDFEGP--DVKWFVNGKVNITENILERHLF 72 Query: 88 ERGDQIAIIWEGDDPSES-RNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIPEAV 146 GD+ AIIWE +DP+E R +TYR+L+ EVCKF+NAL+ + + +GD V IYMPM+PEA Sbjct: 73 IMGDRPAIIWEPNDPNEEGRTLTYRQLYHEVCKFSNALKAKGIGKGDKVIIYMPMVPEAA 132 Query: 147 VAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANVDDAL 206 +AMLAC RIGA+HSVVF GFS ALA RI DC++K V+T+D R KKI +K VD+AL Sbjct: 133 IAMLACARIGAVHSVVFAGFSSSALADRINDCEAKAVLTSDGNFRGTKKIAVKDLVDEAL 192 Query: 207 TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAGTVCAPKEMGAEEALFILYTSG 266 +T +I+ VIV +RT +K + RDIW+ D + + M +E+ LFILYTSG Sbjct: 193 E--KTKTIETVIVYQRTKQEVKMVEGRDIWWHDAIDGQPDTNEAEVMDSEDMLFILYTSG 250 Query: 267 STGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTADVGWVTGHSYIVYGPLANGAT 326 STGKPKGV HTT GY++Y+ T E VF Y PG+VYWCTAD+GW+TGHSYIVYGPL GAT Sbjct: 251 STGKPKGVVHTTGGYMVYSKYTFENVFQYSPGDVYWCTADIGWITGHSYIVYGPLLAGAT 310 Query: 327 TLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSV 386 +++FEGVP YPD R ++DK++V+ YTAPTAIRA+ A GT +E SL++LGSV Sbjct: 311 SIMFEGVPTYPDAGRFWAIVDKYQVNQFYTAPTAIRALEAHGTKPIEPYKLDSLKVLGSV 370 Query: 387 GEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISPLPGATALKPGSATRPFFGVVP 446 GEPIN EAW WY+ +VGK RCPIVDTWWQTETGG+++SP+ G T KP AT P GV Sbjct: 371 GEPINEEAWHWYHTHVGKNRCPIVDTWWQTETGGIMVSPIAGITPNKPAYATMPLPGVQL 430 Query: 447 ALVDNLGNLIEG-AAEGNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDGARRD 505 A+VD G ++G A EGNL I WPG RT YGDHDR TYF + GMYFTGDG +RD Sbjct: 431 AIVDPEGKELKGKAVEGNLCIKFPWPGMLRTTYGDHDRCKQTYFSAYPGMYFTGDGVKRD 490 Query: 506 EDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTL 565 DGYY I GRVDDV+NVSGHRMGTAEIE+A+ HPKV E+AVVG PH++KGQGIY YV Sbjct: 491 HDGYYRILGRVDDVINVSGHRMGTAEIENAINEHPKVIESAVVGYPHEVKGQGIYAYVIC 550 Query: 566 NAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEYDG 625 + T E L E+K+ + K IGPIA PD IQ PGLPKTRSGKIMRRILRK+A +D Sbjct: 551 DLKNRTEENLIGEIKDTITKSIGPIAKPDKIQIVPGLPKTRSGKIMRRILRKVAEGSFDN 610 Query: 626 LGDISTLADPGVVAHLIE 643 +GD STL DP VV +IE Sbjct: 611 MGDTSTLLDPAVVEEIIE 628 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: 1327 Number of extensions: 59 Number of successful extensions: 5 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: 632 Length adjustment: 38 Effective length of query: 613 Effective length of database: 594 Effective search space: 364122 Effective search space used: 364122 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 Echvi_1268 Echvi_1268 (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.29463.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-294 961.3 1.0 1.1e-293 961.1 1.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_1268 Echvi_1268 acetate--CoA ligase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_1268 Echvi_1268 acetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 961.1 1.0 1.1e-293 1.1e-293 4 628 .. 8 628 .. 5 629 .. 0.98 Alignments for each domain: == domain 1 score: 961.1 bits; conditional E-value: 1.1e-293 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvai 76 l+ y + y++++++pe+fwa+ a +++w+k ++kvl++++e +vkWf++g++n++ n ++rh+ d+ ai lcl|FitnessBrowser__Cola:Echvi_1268 8 LSGYFHEYQKSVTEPEQFWARIAD-SFHWKKRWDKVLEWDFEGpDVKWFVNGKVNITENILERHLFIMGDRPAI 80 6678899****************9.6***************988****************************** PP TIGR02188 77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150 iwe ++++e+ r+ltY++l++evc+++n+lk+ G+ kgd+v+iY+pm+pea+iamlacaRiGavhsvvfaGfs+ lcl|FitnessBrowser__Cola:Echvi_1268 81 IWEPNDPNEEGRTLTYRQLYHEVCKFSNALKAKGIGKGDKVIIYMPMVPEAAIAMLACARIGAVHSVVFAGFSS 154 ************************************************************************** PP TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelve 224 +ala+Ri+d+eak v+t+d+++Rg k+i++k+ vdealek++ ++e+v+v++rt++ev+ ++egrD+ww+++++ lcl|FitnessBrowser__Cola:Echvi_1268 155 SALADRINDCEAKAVLTSDGNFRGTKKIAVKDLVDEALEKTK-TIETVIVYQRTKQEVK-MVEGRDIWWHDAID 226 ****************************************98.7*************76.************** PP TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298 +++++ e+e +dsed+lfiLYtsGstGkPkGv+httgGy+++ ++t++ vf++ ++d++wCtaD+GW+tGhsY lcl|FitnessBrowser__Cola:Echvi_1268 227 -GQPDTNEAEVMDSEDMLFILYTSGSTGKPKGVVHTTGGYMVYSKYTFENVFQYSPGDVYWCTADIGWITGHSY 299 .6************************************************************************ PP TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGep 372 ivygPL++Gat+++fegvptypda+rfw++++ky+v++fYtaPtaiRal + g++ ++ ++l+sl+vlgsvGep lcl|FitnessBrowser__Cola:Echvi_1268 300 IVYGPLLAGATSIMFEGVPTYPDAGRFWAIVDKYQVNQFYTAPTAIRALEAHGTKPIEPYKLDSLKVLGSVGEP 373 ************************************************************************** PP TIGR02188 373 inpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeg 446 in eaw+Wy+++vGk++cpivdtwWqtetGgi+++p++g +t+ kp+ at+Pl+G++ ++vd egke++ ++ + lcl|FitnessBrowser__Cola:Echvi_1268 374 INEEAWHWYHTHVGKNRCPIVDTWWQTETGGIMVSPIAG-ITPNKPAYATMPLPGVQLAIVDPEGKELKGKAVE 446 ***************************************.5****************************77777 PP TIGR02188 447 gvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesa 520 g L+ik pwP+mlrt ygd++r +tYf++++g+yftGDg++rd+dGy+ ilGRvDdvinvsGhr+gtaeie+a lcl|FitnessBrowser__Cola:Echvi_1268 447 GNLCIKFPWPGMLRTTYGDHDRCKQTYFSAYPGMYFTGDGVKRDHDGYYRILGRVDDVINVSGHRMGTAEIENA 520 9************************************************************************* PP TIGR02188 521 lvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsG 594 + +h++v e+avvg+p+e+kg+ i+a+v+ +++++e +l e+k++++k+igpiakpdki++v+ lPktRsG lcl|FitnessBrowser__Cola:Echvi_1268 521 INEHPKVIESAVVGYPHEVKGQGIYAYVICDLKNRTEE-NLIGEIKDTITKSIGPIAKPDKIQIVPGLPKTRSG 593 ******************************99999888.5********************************** PP TIGR02188 595 kimRRllrkiaege.ellgdvstledpsvveelke 628 kimRR+lrk+aeg+ +++gd+stl dp+vvee++e lcl|FitnessBrowser__Cola:Echvi_1268 594 KIMRRILRKVAEGSfDNMGDTSTLLDPAVVEEIIE 628 ********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (632 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: 11.05 // [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