Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_009764094.1 MICLODRAFT_RS22300 acetate--CoA ligase
Query= SwissProt::Q8ZKF6 (652 letters) >NCBI__GCF_000262405.1:WP_009764094.1 Length = 651 Score = 822 bits (2122), Expect = 0.0 Identities = 381/642 (59%), Positives = 495/642 (77%), Gaps = 2/642 (0%) Query: 5 HKHAIPANIADRCLINPEQYETKYKQSINDPDTFWGEQGKILDWITPYQKVKNTSFAPGN 64 H +P+ +A ++ + Y+ Y++SI+DP+ FW EQ +ILDW+ P+ +VKNT ++P + Sbjct: 4 HVFPVPSALASTAHVDRQAYQDLYQRSIDDPEAFWREQARILDWVKPFTRVKNTRYSPED 63 Query: 65 VSIKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDTSQSKHISYRELHRDVCRFANTL 124 V+I+W+ DGTLN + NCLDRH ++ GD AI+WEGD +++ +++ +L R V R AN L Sbjct: 64 VTIEWFADGTLNASFNCLDRHARDRGDEAAILWEGDTPGETRKVTWTDLQRQVSRLANAL 123 Query: 125 LDLGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVI 184 LG+KKGD V++Y+P+VPEA AMLACARIGAVHSV+F GFS EA+AGRI D SR++I Sbjct: 124 ARLGVKKGDFVSVYLPVVPEAIAAMLACARIGAVHSVVFSGFSAEALAGRIEDCRSRVLI 183 Query: 185 TADEGVRAGRSIPLKKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRDLIEKA 244 TADEG+RAG+ +PLKKN D AL+N + VEHV+V++RTG D+ GRD W+ + + + Sbjct: 184 TADEGLRAGKHVPLKKNADAALQN--LPFVEHVLVVRRTGRDVPMVAGRDRWYDEALAEV 241 Query: 245 SPEHQPEAMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCT 304 E P A+ AEDPLF+LYTSGSTGKPKG+LHTTGGYLV+AAT+F+ +FDYHPGDI++CT Sbjct: 242 PEECAPVAVGAEDPLFVLYTSGSTGKPKGMLHTTGGYLVHAATSFRAMFDYHPGDIHFCT 301 Query: 305 ADVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRAL 364 ADVGWVT H+YL+YGPLA GAT ++FEGVP WP +R Q+V+ ++VNI YTAPTAIR+L Sbjct: 302 ADVGWVTAHTYLIYGPLANGATIVLFEGVPTWPDSSRWWQIVETYKVNIFYTAPTAIRSL 361 Query: 365 MAEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMIT 424 M +G+ + D SSLR+LGSVGEPINPEAW WY + +G +CP+VDT+WQTETG ++ Sbjct: 362 MRDGEGPVRRHDLSSLRVLGSVGEPINPEAWLWYHEVVGGGRCPIVDTYWQTETGAALLC 421 Query: 425 PLPGAIELKAGSATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERF 484 PLPGA++LK GSAT+PFFGV+PAL+ ++ EG GNL DSWPGQART+ GD ERF Sbjct: 422 PLPGAMDLKPGSATKPFFGVRPALLGSDATVVEGEGAGNLCFADSWPGQARTILGDRERF 481 Query: 485 EQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAE 544 +TYFSTF YF+GDGARRD DGYYWITGR+DDV+NVSGHRLGT E+ESAL +HP +AE Sbjct: 482 LKTYFSTFPGYYFTGDGARRDADGYYWITGRLDDVINVSGHRLGTVEVESALASHPSVAE 541 Query: 545 AAVVGIPHAIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPK 604 AAVVG+PH IKGQ I+A+VTL G + +L ++ VR IGP+ATPD + W LPK Sbjct: 542 AAVVGMPHEIKGQGIFAFVTLKEGIAENDDLRRDLIQVVRTRIGPIATPDRIEWASQLPK 601 Query: 605 TRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646 RSGKI+RRIL +IAAGD N GDTST+ADP VV +++ Q Sbjct: 602 NRSGKILRRILARIAAGDYENHGDTSTVADPTVVAEIVRRVQ 643 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: 1409 Number of extensions: 49 Number of successful extensions: 2 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: 651 Length adjustment: 38 Effective length of query: 614 Effective length of database: 613 Effective search space: 376382 Effective search space used: 376382 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_009764094.1 MICLODRAFT_RS22300 (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.961863.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-291 954.5 0.0 1.4e-291 954.2 0.0 1.0 1 NCBI__GCF_000262405.1:WP_009764094.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000262405.1:WP_009764094.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 954.2 0.0 1.4e-291 1.4e-291 4 627 .. 20 639 .. 17 641 .. 0.98 Alignments for each domain: == domain 1 score: 954.2 bits; conditional E-value: 1.4e-291 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 ++y++ly+++i+dpe+fw+++a+ l+w+kpf++v+++ +p +++Wf+dg+ln+s+nc+drh+++r d+ NCBI__GCF_000262405.1:WP_009764094.1 20 RQAYQDLYQRSIDDPEAFWREQAR-ILDWVKPFTRVKNTRYSPedvTIEWFADGTLNASFNCLDRHARDRGDE 91 689*********************.6************9988877899************************* PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 +ai wegd +ge +rk+t+++l+r+v+rlan+l +lGvkkgd v++Ylp++pea++amlacaRiGavhsvvf+ NCBI__GCF_000262405.1:WP_009764094.1 92 AAILWEGDTPGE-TRKVTWTDLQRQVSRLANALARLGVKKGDFVSVYLPVVPEAIAAMLACARIGAVHSVVFS 163 **********96.************************************************************ PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219 Gfsaeala Ri+d++++++itadeglR gk+++lkk++d+al++ + ve+vlvv+rtg++v ++ grD w+ NCBI__GCF_000262405.1:WP_009764094.1 164 GFSAEALAGRIEDCRSRVLITADEGLRAGKHVPLKKNADAALQNLP-FVEHVLVVRRTGRDVP-MVAGRDRWY 234 *********************************************9.7*************66.********* PP TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292 +e++++ +++ec+p ++++edplf+LYtsGstGkPkG+lhttgGyl++aa++++ +fd++++di++CtaDvGW NCBI__GCF_000262405.1:WP_009764094.1 235 DEALAE-VPEECAPVAVGAEDPLFVLYTSGSTGKPKGMLHTTGGYLVHAATSFRAMFDYHPGDIHFCTADVGW 306 *****6.****************************************************************** PP TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365 vt h+Y++ygPLanGat +lfegvpt+pd+sr+w+++e ykv+ifYtaPtaiR+lm+ ge v++hdlsslrv NCBI__GCF_000262405.1:WP_009764094.1 307 VTAHTYLIYGPLANGATIVLFEGVPTWPDSSRWWQIVETYKVNIFYTAPTAIRSLMRDGEGPVRRHDLSSLRV 379 ************************************************************************* PP TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438 lgsvGepinpeaw Wy+evvG ++cpivdt+WqtetG++l+ plpg a++lkpgsat+P+fG++++++ ++++ NCBI__GCF_000262405.1:WP_009764094.1 380 LGSVGEPINPEAWLWYHEVVGGGRCPIVDTYWQTETGAALLCPLPG-AMDLKPGSATKPFFGVRPALLGSDAT 451 **********************************************.6************************9 PP TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511 ve e g L++ ++wP+++rti gd erf +tYf++++g+yftGDgarrd+dGy+wi+GR+DdvinvsGhr NCBI__GCF_000262405.1:WP_009764094.1 452 VVEGEGA-GNLCFADSWPGQARTILGDRERFLKTYFSTFPGYYFTGDGARRDADGYYWITGRLDDVINVSGHR 523 9996655.79*************************************************************** PP TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilv 584 lgt+e+esal sh++vaeaavvg+p+eikg+ i+afv+lkeg++e+++ l+++l+++vr++igpia+pd+i++ NCBI__GCF_000262405.1:WP_009764094.1 524 LGTVEVESALASHPSVAEAAVVGMPHEIKGQGIFAFVTLKEGIAENDD-LRRDLIQVVRTRIGPIATPDRIEW 595 ********************************************9995.************************ PP TIGR02188 585 veelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627 +++lPk RsGki+RR+l +ia+g+ e+ gd+st++dp+vv+e+ NCBI__GCF_000262405.1:WP_009764094.1 596 ASQLPKNRSGKILRRILARIAAGDyENHGDTSTVADPTVVAEIV 639 ****************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (651 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: 25.45 // [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