Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_066607468.1 V473_RS15130 acetate--CoA ligase
Query= SwissProt::Q8ZKF6 (652 letters) >NCBI__GCF_001046645.1:WP_066607468.1 Length = 647 Score = 848 bits (2190), Expect = 0.0 Identities = 406/642 (63%), Positives = 492/642 (76%), Gaps = 5/642 (0%) Query: 9 IPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSFAPGNVSIK 68 +P + A L++ + Y +SI D D +W E+ + LDWIT K +SFA G+ +K Sbjct: 8 VPESWAKGALMDRAARDADYARSIEDSDAYWLERAQRLDWITVPTKCNESSFAEGDFGVK 67 Query: 69 WYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDT-SQSKHISYRELHRDVCRFANTLLDL 127 W+ DG LN++ANC+DRHL + D+TAI+WE D +Q + SY +LH +VCR AN L Sbjct: 68 WFADGVLNVSANCIDRHLAQRADQTAILWEPDSPDAQPRRYSYAQLHEEVCRLANVLKAA 127 Query: 128 GIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITAD 187 G KKGD + IYMPM+PEAA A+LACARIGAVHSV+FGGFSP+A+AGRI D S +VITAD Sbjct: 128 GAKKGDRITIYMPMIPEAAFALLACARIGAVHSVVFGGFSPDALAGRIQDCDSNIVITAD 187 Query: 188 EGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKASPE 247 EG R G+++PLK NVD AL + SV+ VIV+K TG + Q+GRDLW + K SP+ Sbjct: 188 EGRRGGKAVPLKVNVDAALVH--CPSVKKVIVVKATGGTVTMQDGRDLWLHEEAAKTSPD 245 Query: 248 HQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADV 307 PE MNAEDPLFILYTSGSTGKPKGVLHTTGGYL++AA T + FDY PGDIYWC AD+ Sbjct: 246 CPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLWAALTHELCFDYRPGDIYWCAADI 305 Query: 308 GWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAE 367 GWVTGHSY++YGPLA GATTLM+EGVPNWPTP+R+ +VVD+HQV ++TAPTA+RALM E Sbjct: 306 GWVTGHSYIVYGPLANGATTLMYEGVPNWPTPSRIWEVVDRHQVQTIFTAPTALRALMKE 365 Query: 368 GDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLP 427 GD + T R+SLR+LG+VGEPINPEAW WY + +G+ +CP++DTWWQTETGG MI P P Sbjct: 366 GDGFVHSTSRASLRLLGTVGEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGGAMIAPTP 425 Query: 428 GAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERFEQT 487 GA +LK GSAT P GV P +VD EGH +GA EGNLVI SWPGQ RT++GDH+RF QT Sbjct: 426 GATDLKPGSATFPMPGVAPQIVDAEGHVLDGAAEGNLVIAQSWPGQMRTVWGDHDRFFQT 485 Query: 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAV 547 YF+TF Y +GDGARRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALV H +AEAAV Sbjct: 486 YFTTFPGKYTTGDGARRDGDGYYWITGRVDDVINVSGHRMGTAEVESALVLHESVAEAAV 545 Query: 548 VGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRS 607 VG PH IKGQ IYAYVTLN GEE + +L + WVR EIGP+ATPD + + LPKTRS Sbjct: 546 VGFPHDIKGQGIYAYVTLNSGEEATDDLRKTLVKWVRTEIGPIATPDAIQFAPGLPKTRS 605 Query: 608 GKIMRRILRKIAAGDTS--NLGDTSTLADPGVVEKLLEEKQA 647 GKIMRRILRKIA GD S LGDTSTLADP VV+ L+ +Q+ Sbjct: 606 GKIMRRILRKIAEGDVSAQALGDTSTLADPSVVDNLIANRQS 647 Lambda K H 0.317 0.135 0.423 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: 63 Number of successful extensions: 4 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: 652 Length of database: 647 Length adjustment: 38 Effective length of query: 614 Effective length of database: 609 Effective search space: 373926 Effective search space used: 373926 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 WP_066607468.1 V473_RS15130 (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.2463448.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-300 982.3 0.0 5e-300 982.1 0.0 1.0 1 NCBI__GCF_001046645.1:WP_066607468.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046645.1:WP_066607468.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 982.1 0.0 5e-300 5e-300 8 628 .. 24 643 .. 17 644 .. 0.98 Alignments for each domain: == domain 1 score: 982.1 bits; conditional E-value: 5e-300 TIGR02188 8 kelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaii 77 + y+++ied +++w + a+ +l+w++ +k ++s+++ vkWf+dg lnvs+nc+drh+++r+d++ai NCBI__GCF_001046645.1:WP_066607468.1 24 DADYARSIEDSDAYWLERAQ-RLDWITVPTKCNESSFAEgdfGVKWFADGVLNVSANCIDRHLAQRADQTAIL 95 566899**************.5***************9988789***************************** PP TIGR02188 78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150 we d+++ + r+++Ya+l++evcrlanvlk++G kkgdr++iY+pmipea++a+lacaRiGavhsvvf+Gfs+ NCBI__GCF_001046645.1:WP_066607468.1 96 WEPDSPDAQPRRYSYAQLHEEVCRLANVLKAAGAKKGDRITIYMPMIPEAAFALLACARIGAVHSVVFGGFSP 168 ******999**************************************************************** PP TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelv 223 +ala Ri+d+++++vitadeg Rggk+++lk +vd+al +++ sv+kv+vvk tg v+ +++grD+w++e+ NCBI__GCF_001046645.1:WP_066607468.1 169 DALAGRIQDCDSNIVITADEGRRGGKAVPLKVNVDAALVHCP-SVKKVIVVKATGGTVT-MQDGRDLWLHEEA 239 *****************************************9.7*************76.************* PP TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGh 296 +k +s +c+pe++++edplfiLYtsGstGkPkGvlhttgGyll+aalt+++ fd++++di+wC+aD+GWvtGh NCBI__GCF_001046645.1:WP_066607468.1 240 AK-TSPDCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLWAALTHELCFDYRPGDIYWCAADIGWVTGH 311 *7.********************************************************************** PP TIGR02188 297 sYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsv 369 sYivygPLanGattl++egvp++p++sr+wev+++++v++ +taPta+Ralmk+g+ +v+++++ slr+lg+v NCBI__GCF_001046645.1:WP_066607468.1 312 SYIVYGPLANGATTLMYEGVPNWPTPSRIWEVVDRHQVQTIFTAPTALRALMKEGDGFVHSTSRASLRLLGTV 384 ************************************************************************* PP TIGR02188 370 GepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkevee 442 Gepinpeaw+Wy+evvG+++cpi+dtwWqtetGg++i+p pg at+lkpgsat P++G+ +++vd eg+ ++ NCBI__GCF_001046645.1:WP_066607468.1 385 GEPINPEAWRWYHEVVGEGRCPIIDTWWQTETGGAMIAPTPG-ATDLKPGSATFPMPGVAPQIVDAEGHVLDG 456 ******************************************.6****************************8 PP TIGR02188 443 eeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgta 515 +e g Lvi ++wP+++rt++gd++rf++tYf++++g y tGDgarrd dGy+wi+GRvDdvinvsGhr+gta NCBI__GCF_001046645.1:WP_066607468.1 457 AAE-GNLVIAQSWPGQMRTVWGDHDRFFQTYFTTFPGKYTTGDGARRDGDGYYWITGRVDDVINVSGHRMGTA 528 777.79******************************************************************* PP TIGR02188 516 eiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveel 588 e+esalv he+vaeaavvg+p++ikg+ i+a+v+l++g+e++++ l+k+l k+vr+eigpia+pd i++++ l NCBI__GCF_001046645.1:WP_066607468.1 529 EVESALVLHESVAEAAVVGFPHDIKGQGIYAYVTLNSGEEATDD-LRKTLVKWVRTEIGPIATPDAIQFAPGL 600 ****************************************9995.**************************** PP TIGR02188 589 PktRsGkimRRllrkiaege...ellgdvstledpsvveelke 628 PktRsGkimRR+lrkiaeg+ ++lgd+stl+dpsvv++l++ NCBI__GCF_001046645.1:WP_066607468.1 601 PKTRSGKIMRRILRKIAEGDvsaQALGDTSTLADPSVVDNLIA 643 ******************98766789*************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (647 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 0.01s 00:00:00.02 Elapsed: 00:00:00.03 # Mc/sec: 12.46 // [ok]
This GapMind analysis is from Sep 24 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