Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_109941954.1 DLD82_RS15135 acetate--CoA ligase
Query= BRENDA::Q2XNL6 (634 letters) >NCBI__GCF_003173335.1:WP_109941954.1 Length = 629 Score = 684 bits (1765), Expect = 0.0 Identities = 328/635 (51%), Positives = 455/635 (71%), Gaps = 7/635 (1%) Query: 1 MSKDTSVLLEEKRVFKPHYTVVEEAHIKNWEAELEKG-KDHENYWAEKAERLEWFRKWDR 59 MS++ V ++ K + P E++ + +++A ++ +D + +W+ A+ +EW + W + Sbjct: 1 MSENFEVKVDSKS-YIPDPAYREQSFLGDYKAVYKEFIQDPDEFWSRMAKEIEWIKPWTK 59 Query: 60 VLDESNRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREV 119 VL E N P+ RWF G +N+T + +DR + +RN++A+++ E G+ER TY +L+R+V Sbjct: 60 VL-EWNHPYARWFTGGTLNITTSCLDRHVKEGRRNKLALIWRGEDGEERVYTYRQLHRDV 118 Query: 120 SRTANALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLND 179 R ANALK +G++KGD + Y+P+ PE ++++LACA+IGA+HS++Y+G AL R+ D Sbjct: 119 MRFANALKKIGVQKGDRICFYMPLVPEHIIALLACARIGAIHSIVYAGFGAEALHSRIRD 178 Query: 180 ARAKIIITADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLF 239 A AK++ITAD RRG VI L+ IVD+A+ P++E +V+ +E+ S E F Sbjct: 179 AEAKVVITADVGKRRGKVISLRSIVDDAVRNAPSVEKVIVLCREKCSVEL--YSEMEEDF 236 Query: 240 DKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHN 299 L+EG C EEMDAE+PLFILYTSG+TG PKG++H+ GGY GV T + FD+ Sbjct: 237 YSLLEGVSADCSPEEMDAEEPLFILYTSGTTGMPKGIVHSCGGYATGVHYTAKYLFDLKE 296 Query: 300 GDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTA 359 D+ WCTAD GWITGHSY+VYGPL +G T ++ E PD+PDPG+WWSI+E+ GVT FYTA Sbjct: 297 NDVIWCTADTGWITGHSYIVYGPLSVGATVVITETTPDWPDPGIWWSIIEELGVTLFYTA 356 Query: 360 PTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTE 419 PTAIR MR G++ P +YNL+SL+I+G+VGEP+NPEA+ WYYR IG+ +CPI+DTWWQTE Sbjct: 357 PTAIRMFMRVGEEWPNKYNLDSLRIIGSVGEPLNPEAFEWYYRVIGKMRCPILDTWWQTE 416 Query: 420 TGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLF 479 TGMH+I P+KPG P+PGI ADVVDE G+ +P G+GG LVI+KPWP+M RT++ Sbjct: 417 TGMHMITTPLGEPMKPGFAGVPIPGIIADVVDEEGNSLPPGQGGLLVIKKPWPSMMRTVY 476 Query: 480 NDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFV 539 +++RY YW QI Y AGD+A KDEDGYF I GR+DD++ +AGH +GTAEVES V Sbjct: 477 RNDERY-KKYWNQIK-DYYAAGDLAVKDEDGYFMILGRADDIIIVAGHNLGTAEVESALV 534 Query: 540 AHPAVAEAAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMV 599 H AVAEAAVIG D IKG+ +KAF+IL KG+ + L+ EL H+R +GP+A+ + Sbjct: 535 EHEAVAEAAVIGVPDEIKGQAVKAFVILVKGYTPSQKLVSELTYHVRMSIGPIAMPAAIE 594 Query: 600 QVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634 VD+LP+TRSGKIMRRIL+A+E DLGDTSTLEE Sbjct: 595 FVDTLPRTRSGKIMRRILKAKEMNMDLGDTSTLEE 629 Lambda K H 0.319 0.138 0.428 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: 1240 Number of extensions: 59 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: 634 Length of database: 629 Length adjustment: 38 Effective length of query: 596 Effective length of database: 591 Effective search space: 352236 Effective search space used: 352236 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate WP_109941954.1 DLD82_RS15135 (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.2601236.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-268 877.2 0.2 3.6e-268 876.9 0.2 1.0 1 NCBI__GCF_003173335.1:WP_109941954.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003173335.1:WP_109941954.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 876.9 0.2 3.6e-268 3.6e-268 6 619 .. 28 629 .] 24 629 .] 0.97 Alignments for each domain: == domain 1 score: 876.9 bits; conditional E-value: 3.6e-268 TIGR02188 6 eykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkvaii 77 +yk++y+e i+dp++fw+++ake +ew+kp++kvl+++ +p ++Wf++g+ln+++ c+drhv++ r++k+a+i NCBI__GCF_003173335.1:WP_109941954.1 28 DYKAVYKEFIQDPDEFWSRMAKE-IEWIKPWTKVLEWN-HPYARWFTGGTLNITTSCLDRHVKEgRRNKLALI 98 89********************5.*************9.789******************************* PP TIGR02188 78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150 w g++ + +r +tY++l+r+v r+an+lk++Gv+kgdr+++Y+p++pe +ia+lacaRiGa+hs+v+aGf a NCBI__GCF_003173335.1:WP_109941954.1 99 WRGEDGE--ERVYTYRQLHRDVMRFANALKKIGVQKGDRICFYMPLVPEHIIALLACARIGAIHSIVYAGFGA 169 ****664..7*************************************************************** PP TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelv 223 eal++Ri daeak+vitad g R+gkvi+l++ivd+a+++a+ svekv+v+ r + +v+ + ++++ + +l+ NCBI__GCF_003173335.1:WP_109941954.1 170 EALHSRIRDAEAKVVITADVGKRRGKVISLRSIVDDAVRNAP-SVEKVIVLCREKCSVE-LYSEMEEDFYSLL 240 *****************************************9.7*************77.6667778888899 PP TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGh 296 e ++sa+c+pe++d+e+plfiLYtsG+tG+PkG++h+ gGy++ +++t ky+fd+k++d+ wCtaD GW+tGh NCBI__GCF_003173335.1:WP_109941954.1 241 E-GVSADCSPEEMDAEEPLFILYTSGTTGMPKGIVHSCGGYATGVHYTAKYLFDLKENDVIWCTADTGWITGH 312 9.59********************************************************************* PP TIGR02188 297 sYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsv 369 sYivygPL++Gat ++ e++p++pd++ +w++ie+ +vt fYtaPtaiR++m++gee+++k++l+slr++gsv NCBI__GCF_003173335.1:WP_109941954.1 313 SYIVYGPLSVGATVVITETTPDWPDPGIWWSIIEELGVTLFYTAPTAIRMFMRVGEEWPNKYNLDSLRIIGSV 385 ************************************************************************* PP TIGR02188 370 GepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkevee 442 Gep+npea+eWyy+v+Gk +cpi dtwWqtetG ++it+ g ++kpg a +P++Gi a+vvdeeg+++ + NCBI__GCF_003173335.1:WP_109941954.1 386 GEPLNPEAFEWYYRVIGKMRCPILDTWWQTETGMHMITTPLG--EPMKPGFAGVPIPGIIADVVDEEGNSLPP 456 *************************************99888..5**************************** PP TIGR02188 443 eeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgta 515 +++ g+LvikkpwPsm+rt+y+++er+ +Y++++k++y +GD a++d+dGy++ilGR+Dd+i v+Gh+lgta NCBI__GCF_003173335.1:WP_109941954.1 457 GQG-GLLVIKKPWPSMMRTVYRNDERYK-KYWNQIKDYYAAGDLAVKDEDGYFMILGRADDIIIVAGHNLGTA 527 999.8*********************96.6******************************************* PP TIGR02188 516 eiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveel 588 e+esalv+heavaeaav+gvpdeikg+a+ afv+l +g+++++ +l +el+ +vr +igpia p+ i++v++l NCBI__GCF_003173335.1:WP_109941954.1 528 EVESALVEHEAVAEAAVIGVPDEIKGQAVKAFVILVKGYTPSQ-KLVSELTYHVRMSIGPIAMPAAIEFVDTL 599 *******************************************.5**************************** PP TIGR02188 589 PktRsGkimRRllrkiaegeellgdvstled 619 P+tRsGkimRR+l++ + lgd+stle+ NCBI__GCF_003173335.1:WP_109941954.1 600 PRTRSGKIMRRILKAKEM-NMDLGDTSTLEE 629 *************97544.57788*****85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (629 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 30.22 // [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