Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_089322819.1 CHB58_RS03975 acetate--CoA ligase
Query= BRENDA::Q2XNL6 (634 letters) >NCBI__GCF_900188395.1:WP_089322819.1 Length = 631 Score = 732 bits (1889), Expect = 0.0 Identities = 356/628 (56%), Positives = 467/628 (74%), Gaps = 6/628 (0%) Query: 8 LLEEKRVFKPHYTVVEEAHIKNWEAELEKGKDH-ENYWAEKAERLEWFRKWDRVLDESNR 66 LL + KP V A++KN+E E +K D+ E +WA+ A+ L W+ KWD+VL E N Sbjct: 9 LLHLGTIIKPPEEFVRNANVKNYEEEYKKFLDNPEEFWAKVADELFWYEKWDKVL-EWNL 67 Query: 67 PFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTANAL 126 P+ +WFVNGK N+T NA+DR + ++N+VA + +E G+E+ +TY LY V++ ANAL Sbjct: 68 PYAKWFVNGKTNITVNALDRHVKNGRKNKVAFFWEDEFGNEKVVTYGSLYTLVNKLANAL 127 Query: 127 KSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKIII 186 K+ GIKKGD V +Y+P+ E V +MLACA+IGAVHSV+Y+G SV AL R+ DA+AK++I Sbjct: 128 KNAGIKKGDRVVIYMPLVVEQVAAMLACARIGAVHSVVYAGFSVPALRHRIEDAQAKMVI 187 Query: 187 TADGTYRRGGVIKLKPIVDEAILQCPTIETTVVVKHTDIDIEMSDISGREMLFDKLIEGE 246 TAD T RRG I LK IVDEA+ +E VV++ +++ I +E+ F + I+ Sbjct: 188 TADMTIRRGRAIPLKQIVDEAVRGLDNVEKVVVLRRLKPKVDL--IGEKEIDFYEFIKDA 245 Query: 247 GDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLWWCT 306 C+ E MD+EDPLF+LYTSGSTGKPKGV+HTTGGYMVG +++ FD+ D++WCT Sbjct: 246 DTYCEPEVMDSEDPLFMLYTSGSTGKPKGVIHTTGGYMVGTYYSMKTVFDLKEDDIYWCT 305 Query: 307 ADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAIRHL 366 AD GWITGHSY+VYGPL+ G T +L EGAP+YPD G WWS++EKYGVT FYTAPTAIR Sbjct: 306 ADPGWITGHSYIVYGPLVAGATQVLAEGAPNYPDFGRWWSLIEKYGVTIFYTAPTAIRMF 365 Query: 367 MRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMHLIA 426 MR G+ P++Y+L SL++LG+VGEPINPEAWMWY+R IG+E+CPI+DTWWQTETG +I Sbjct: 366 MRAGEHWPEKYDLSSLRLLGSVGEPINPEAWMWYFRVIGKERCPIVDTWWQTETGAVMIT 425 Query: 427 PLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDEQRYI 486 + P+KPG KP+PG+ ADVVD+ G+PV KGGFLV+R PWP+M RT+ ++++Y Sbjct: 426 TIDGLPMKPGRAGKPVPGVVADVVDKEGNPVEPNKGGFLVVRNPWPSMMRTIHKNKEKY- 484 Query: 487 DVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPAVAE 546 + YW IP G Y AGD+A KDEDGY I GR+DDV+N++GHRIGT EVES V+HP+VAE Sbjct: 485 ESYWNTIP-GCYFAGDVATKDEDGYIMILGRADDVINVSGHRIGTMEVESALVSHPSVAE 543 Query: 547 AAVIGKADPIKGEVIKAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDSLPK 606 AAVIGK DP+KGE IKAF+ILK+G + L+ LK+H+R ELG +AV E+ VD LPK Sbjct: 544 AAVIGKPDPVKGERIKAFVILKEGESPSEELVNSLKKHVRTELGALAVPSEIEFVDKLPK 603 Query: 607 TRSGKIMRRILRAREEGEDLGDTSTLEE 634 TRSGKIMRR+L+A+E G D GD STLE+ Sbjct: 604 TRSGKIMRRVLKAKELGMDPGDLSTLED 631 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: 1241 Number of extensions: 59 Number of successful extensions: 6 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: 631 Length adjustment: 38 Effective length of query: 596 Effective length of database: 593 Effective search space: 353428 Effective search space used: 353428 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_089322819.1 CHB58_RS03975 (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.3808178.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-279 914.4 0.3 1.8e-279 914.2 0.3 1.0 1 NCBI__GCF_900188395.1:WP_089322819.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900188395.1:WP_089322819.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 914.2 0.3 1.8e-279 1.8e-279 3 619 .. 27 631 .] 25 631 .] 0.98 Alignments for each domain: == domain 1 score: 914.2 bits; conditional E-value: 1.8e-279 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.rkdkv 74 ++++y+e y++ ++pe+fwak a el w ++++kvl+++ p +kWf++g++n+++n++drhv++ rk+kv NCBI__GCF_900188395.1:WP_089322819.1 27 NVKNYEEEYKKFLDNPEEFWAKVAD-ELFWYEKWDKVLEWN-LPYAKWFVNGKTNITVNALDRHVKNgRKNKV 97 7899********************9.5*************9.569**************************** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 a we + g+ ++ +tY l++ v++lan+lk++G+kkgdrv+iY+p+++e v+amlacaRiGavhsvv+aG NCBI__GCF_900188395.1:WP_089322819.1 98 AFFWEDE-FGN-EKVVTYGSLYTLVNKLANALKNAGIKKGDRVVIYMPLVVEQVAAMLACARIGAVHSVVYAG 168 *****98.554.7************************************************************ PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220 fs al++Ri+da+ak+vitad ++R+g++i+lk+ivdea++ + +vekv+v++r + +v + ++++ + NCBI__GCF_900188395.1:WP_089322819.1 169 FSVPALRHRIEDAQAKMVITADMTIRRGRAIPLKQIVDEAVRGLD-NVEKVVVLRRLKPKVD-LIGEKEIDFY 239 *******************************************98.7*************76.9999****** PP TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293 e +++ a+++cepe +dsedplf+LYtsGstGkPkGv+httgGy++ +++++k+vfd+k++di+wCtaD GW+ NCBI__GCF_900188395.1:WP_089322819.1 240 EFIKD-ADTYCEPEVMDSEDPLFMLYTSGSTGKPKGVIHTTGGYMVGTYYSMKTVFDLKEDDIYWCTADPGWI 311 ****7.******************************************************************* PP TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366 tGhsYivygPL++Gat++l eg+p+ypd +r+w++ieky+vtifYtaPtaiR++m++ge++++k+dlsslr+l NCBI__GCF_900188395.1:WP_089322819.1 312 TGHSYIVYGPLVAGATQVLAEGAPNYPDFGRWWSLIEKYGVTIFYTAPTAIRMFMRAGEHWPEKYDLSSLRLL 384 ************************************************************************* PP TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439 gsvGepinpeaw+Wy++v+Gke+cpivdtwWqtetG+++it++ g +++kpg a +P++G+ a+vvd+eg++ NCBI__GCF_900188395.1:WP_089322819.1 385 GSVGEPINPEAWMWYFRVIGKERCPIVDTWWQTETGAVMITTIDG--LPMKPGRAGKPVPGVVADVVDKEGNP 455 *********************************************..5************************* PP TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512 ve++++ g+Lv+++pwPsm+rti++++e++ e+Y+++++g+yf+GD a++d+dGyi+ilGR+DdvinvsGhr+ NCBI__GCF_900188395.1:WP_089322819.1 456 VEPNKG-GFLVVRNPWPSMMRTIHKNKEKY-ESYWNTIPGCYFAGDVATKDEDGYIMILGRADDVINVSGHRI 526 ***999.8********************98.68**************************************** PP TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585 gt+e+esalvsh++vaeaav+g+pd +kge i afv+lkeg++++ee l ++lkk+vr+e+g++a p++i++v NCBI__GCF_900188395.1:WP_089322819.1 527 GTMEVESALVSHPSVAEAAVIGKPDPVKGERIKAFVILKEGESPSEE-LVNSLKKHVRTELGALAVPSEIEFV 598 *********************************************95.************************* PP TIGR02188 586 eelPktRsGkimRRllrkiaegeellgdvstled 619 ++lPktRsGkimRR+l++ g gd+stled NCBI__GCF_900188395.1:WP_089322819.1 599 DKLPKTRSGKIMRRVLKAKELG-MDPGDLSTLED 631 ****************986655.5567*****98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (631 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: 00:00:00.01 # Mc/sec: 25.40 // [ok]
This GapMind analysis is from Apr 09 2024. 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