Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_106712619.1 CU102_RS18670 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_003010955.1:WP_106712619.1 Length = 650 Score = 897 bits (2319), Expect = 0.0 Identities = 430/639 (67%), Positives = 506/639 (79%), Gaps = 3/639 (0%) Query: 6 LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65 +YPV L D TY Y+QS+ +P+ FW + KR+DW KP+T VK TSF+ V Sbjct: 5 VYPVLASAKKDALIDNETYLNWYKQSIKDPEKFWAKHGKRIDWFKPYTKVKNTSFEGK-V 63 Query: 66 DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125 IKWF DG NVSYNC+DRHL +RGDQ+AIIWEGD+P + ITY EL+E+VC+ AN L+ Sbjct: 64 AIKWFEDGVTNVSYNCIDRHLKKRGDQVAIIWEGDNPYLDKKITYNELYEQVCRLANVLK 123 Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185 V +GD VTIYMPMIPEA AMLACTRIGAIHSVVFGGFSP+ALAGRI+DC+S VIT Sbjct: 124 KHGVKKGDRVTIYMPMIPEASYAMLACTRIGAIHSVVFGGFSPDALAGRIVDCESTFVIT 183 Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSI--QKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243 +DEG+R GK IPLK N D A+ + + V+V +RT G W RD+WY + + Sbjct: 184 SDEGMRGGKPIPLKDNTDKAIDIAARHHVMVKNVLVVRRTGGKTGWAPGRDLWYHEEIAS 243 Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303 C P++M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY G++YWC Sbjct: 244 VKPECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGDIYWC 303 Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363 TADVGWVTGHSYIVYGPLANGATTL+FEGVPNYP ++R VIDKHKV+I YTAPTAIRA Sbjct: 304 TADVGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWDVIDKHKVNIFYTAPTAIRA 363 Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423 +M++G V+ SLR+LGSVGEPINPEAW+WYY+ VG +R PIVDTWWQTETGG+LI Sbjct: 364 LMSAGDEPVKKTSRKSLRILGSVGEPINPEAWEWYYQVVGDKRSPIVDTWWQTETGGILI 423 Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483 +PLPGATALKPGSATRPFFGV P LVDN G+++EGAA+GNL I+DSWPGQ RT+YGDH R Sbjct: 424 TPLPGATALKPGSATRPFFGVQPQLVDNEGDVLEGAADGNLCIIDSWPGQMRTVYGDHKR 483 Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543 F++TYF T+ G YFTGDG RRD+DGYYWITGRVDDVLNVSGHRMGTAE+ESA+V+H V+ Sbjct: 484 FIETYFSTYKGKYFTGDGCRRDKDGYYWITGRVDDVLNVSGHRMGTAEVESALVSHDTVS 543 Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603 EAAVVG PHD+KGQGIY YVTL AG + ++ LR EL VRKEIGPIASPD IQ+AP LP Sbjct: 544 EAAVVGYPHDLKGQGIYCYVTLMAGLDGTDELRKELVTHVRKEIGPIASPDKIQFAPSLP 603 Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642 KTRSGKIMRRILRKIA ++ LGD STLADP VV LI Sbjct: 604 KTRSGKIMRRILRKIAEDDFGALGDTSTLADPAVVDDLI 642 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: 1473 Number of extensions: 71 Number of successful extensions: 3 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: 650 Length adjustment: 38 Effective length of query: 613 Effective length of database: 612 Effective search space: 375156 Effective search space used: 375156 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_106712619.1 CU102_RS18670 (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.2263171.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1050.3 0.1 0 1050.1 0.1 1.0 1 NCBI__GCF_003010955.1:WP_106712619.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106712619.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1050.1 0.1 0 0 3 628 .. 19 643 .. 17 644 .. 0.98 Alignments for each domain: == domain 1 score: 1050.1 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 ++e+y ++y+++i+dpekfwak++k +++w+kp++kv+++s+e +kWfedg +nvsync+drh++kr d+ NCBI__GCF_003010955.1:WP_106712619.1 19 DNETYLNWYKQSIKDPEKFWAKHGK-RIDWFKPYTKVKNTSFEGkvAIKWFEDGVTNVSYNCIDRHLKKRGDQ 90 6789*********************.5**************9987789************************* PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 vaiiwegd++ +k+tY+el+++vcrlanvlk++Gvkkgdrv+iY+pmipea +amlac+RiGa+hsvvf+ NCBI__GCF_003010955.1:WP_106712619.1 91 VAIIWEGDNPYL-DKKITYNELYEQVCRLANVLKKHGVKKGDRVTIYMPMIPEASYAMLACTRIGAIHSVVFG 162 ********9996.9*********************************************************** PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrD 216 Gfs++ala Rivd+e+ +vit+deg+Rggk i+lk+++d+a++ a + +v++vlvv+rtg + + w grD NCBI__GCF_003010955.1:WP_106712619.1 163 GFSPDALAGRIVDCESTFVITSDEGMRGGKPIPLKDNTDKAIDIAARhhvMVKNVLVVRRTGGK-TGWAPGRD 234 *****************************************9877655579*************.56****** PP TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289 +w++e++++ ++ ec+pek+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++d+di+wCtaD NCBI__GCF_003010955.1:WP_106712619.1 235 LWYHEEIAS-VKPECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGDIYWCTAD 306 ********6.*************************************************************** PP TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362 vGWvtGhsYivygPLanGattl+fegvp+yp+ srfw+vi+k+kv+ifYtaPtaiRalm +g+e vkk++++s NCBI__GCF_003010955.1:WP_106712619.1 307 VGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWDVIDKHKVNIFYTAPTAIRALMSAGDEPVKKTSRKS 379 ************************************************************************* PP TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435 lr+lgsvGepinpeaweWyy+vvG++++pivdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd+ NCBI__GCF_003010955.1:WP_106712619.1 380 LRILGSVGEPINPEAWEWYYQVVGDKRSPIVDTWWQTETGGILITPLPG-ATALKPGSATRPFFGVQPQLVDN 451 *************************************************.6********************** PP TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508 eg+ +e ++ g L+i ++wP+++rt+ygd++rf+etYf+++kg yftGDg+rrdkdGy+wi+GRvDdv+nvs NCBI__GCF_003010955.1:WP_106712619.1 452 EGDVLEGAAD-GNLCIIDSWPGQMRTVYGDHKRFIETYFSTYKGKYFTGDGCRRDKDGYYWITGRVDDVLNVS 523 *****98777.79************************************************************ PP TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581 Ghr+gtae+esalvsh++v+eaavvg+p+++kg+ i+++v+l++g + ++ el+kel ++vrkeigpia+pdk NCBI__GCF_003010955.1:WP_106712619.1 524 GHRMGTAEVESALVSHDTVSEAAVVGYPHDLKGQGIYCYVTLMAGLDGTD-ELRKELVTHVRKEIGPIASPDK 595 ***********************************************999.5********************* PP TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 i+++++lPktRsGkimRR+lrkiae++ +lgd+stl+dp+vv++l++ NCBI__GCF_003010955.1:WP_106712619.1 596 IQFAPSLPKTRSGKIMRRILRKIAEDDfGALGDTSTLADPAVVDDLIA 643 ********************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (650 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: 00:00:00.02 # Mc/sec: 19.38 // [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