Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_011427293.1 RHE_RS21025 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_000092045.1:WP_011427293.1 Length = 651 Score = 883 bits (2282), Expect = 0.0 Identities = 427/648 (65%), Positives = 497/648 (76%), Gaps = 3/648 (0%) Query: 6 LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65 ++PV +V A L D+ Y Y++SV NPD FW + KR+DW KP+T VK TSF V Sbjct: 5 IHPVPKQVKAQALIDKEKYLKWYEESVENPDKFWGKHGKRIDWFKPYTKVKNTSFTGK-V 63 Query: 66 DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125 IKWF DG NVSYNC+DRHL GDQ+AIIWEGD+P + ITY EL+E VC+ AN L+ Sbjct: 64 SIKWFEDGQTNVSYNCIDRHLKTNGDQVAIIWEGDNPYIDKKITYNELYEHVCRMANVLK 123 Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185 V +GD VTIYMPMIPEA AMLAC RIGA+HSVVFGGFSPEALAGRI+DC+S VIT Sbjct: 124 KHGVKKGDRVTIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPEALAGRIVDCESTFVIT 183 Query: 186 ADEGVRAGKKIPLKANVDDAL--TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243 DEGVR GK +PLK N D A+ + ++ KV+V +RT G W RD+WY + Sbjct: 184 CDEGVRGGKPVPLKDNTDTAIHIAARQHVNVSKVLVVRRTGGKTGWAPGRDLWYHQEVAT 243 Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303 C P +M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++THE VFDY G++YWC Sbjct: 244 VKAECPPVKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHEYVFDYHHGDIYWC 303 Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363 TADVGWVTGHSYIVYGPL+N ATTL+FEGVPN+PD R +VIDKHKV+I YTAPTAIR+ Sbjct: 304 TADVGWVTGHSYIVYGPLSNCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRS 363 Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423 +M +G V + SSLRLLG+VGEPINPEAW+WYY VG +RCP++DTWWQTETGG +I Sbjct: 364 LMGAGDDFVTRSSRSSLRLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMI 423 Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483 +PLPGA LKPGSAT PFFGV P LVDN G ++EGAA+GNL I DSWPGQ RT+YGDH+R Sbjct: 424 TPLPGAIDLKPGSATVPFFGVKPELVDNEGKVLEGAADGNLCIADSWPGQMRTVYGDHER 483 Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543 F+ TYF T+ G YFTGDG RRDEDGYYWITGRVDDVLNVSGHR+GTAE+ESA+V+H V+ Sbjct: 484 FIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVS 543 Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603 EAAVVG PH IKGQGIY YVTL AG E ++ LR EL VR EIGPIASPD IQ+APGLP Sbjct: 544 EAAVVGYPHAIKGQGIYCYVTLMAGHEGTDTLRQELVKHVRAEIGPIASPDKIQFAPGLP 603 Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651 KTRSGKIMRRILRKIA ++ LGD STLADP VV LI + A Sbjct: 604 KTRSGKIMRRILRKIAEDDFGALGDTSTLADPAVVDDLIANRQNKATA 651 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: 1448 Number of extensions: 67 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: 651 Length of database: 651 Length adjustment: 38 Effective length of query: 613 Effective length of database: 613 Effective search space: 375769 Effective search space used: 375769 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_011427293.1 RHE_RS21025 (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.1600521.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 1038.3 0.1 0 1038.1 0.1 1.0 1 NCBI__GCF_000092045.1:WP_011427293.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000092045.1:WP_011427293.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1038.1 0.1 0 0 3 628 .. 19 643 .. 17 644 .. 0.98 Alignments for each domain: == domain 1 score: 1038.1 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 + e+y ++yee++e+p+kfw+k++k +++w+kp++kv+++s++ ++kWfedg++nvsync+drh++++ d+ NCBI__GCF_000092045.1:WP_011427293.1 19 DKEKYLKWYEESVENPDKFWGKHGK-RIDWFKPYTKVKNTSFTGkvSIKWFEDGQTNVSYNCIDRHLKTNGDQ 90 6789*********************.5**************9887799************************* PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 vaiiwegd++ +k+tY+el+++vcr+anvlk++Gvkkgdrv+iY+pmipea++amlacaRiGavhsvvf+ NCBI__GCF_000092045.1:WP_011427293.1 91 VAIIWEGDNPYI-DKKITYNELYEHVCRMANVLKKHGVKKGDRVTIYMPMIPEAAYAMLACARIGAVHSVVFG 162 ********9996.9*********************************************************** PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrD 216 Gfs+eala Rivd+e+ +vit deg+Rggk ++lk+++d a++ a + +v+kvlvv+rtg + + w grD NCBI__GCF_000092045.1:WP_011427293.1 163 GFSPEALAGRIVDCESTFVITCDEGVRGGKPVPLKDNTDTAIHIAARqhvNVSKVLVVRRTGGK-TGWAPGRD 234 *****************************************98765555799************.56****** PP TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289 +w++++v++ ++aec+p k+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++++di+wCtaD NCBI__GCF_000092045.1:WP_011427293.1 235 LWYHQEVAT-VKAECPPVKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHEYVFDYHHGDIYWCTAD 306 ********6.*************************************************************** PP TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362 vGWvtGhsYivygPL+n attl+fegvp++pd++rfwevi+k+kv+ifYtaPtaiR+lm +g+++v++ ++ss NCBI__GCF_000092045.1:WP_011427293.1 307 VGWVTGHSYIVYGPLSNCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRSLMGAGDDFVTRSSRSS 379 ************************************************************************* PP TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435 lr+lg+vGepinpeaweWyy+vvG+++cp++dtwWqtetGg++itplpg a++lkpgsat+P+fG+++e+vd+ NCBI__GCF_000092045.1:WP_011427293.1 380 LRLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMITPLPG-AIDLKPGSATVPFFGVKPELVDN 451 *************************************************.6********************** PP TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508 egk +e ++ g L+i ++wP+++rt+ygd+erf++tYf+++kg yftGDg+rrd+dGy+wi+GRvDdv+nvs NCBI__GCF_000092045.1:WP_011427293.1 452 EGKVLEGAAD-GNLCIADSWPGQMRTVYGDHERFIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVS 523 *****98777.79************************************************************ PP TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581 Ghrlgtae+esalvsh+ v+eaavvg+p+ ikg+ i+++v+l++g+e ++ +l++el k+vr+eigpia+pdk NCBI__GCF_000092045.1:WP_011427293.1 524 GHRLGTAEVESALVSHNLVSEAAVVGYPHAIKGQGIYCYVTLMAGHEGTD-TLRQELVKHVRAEIGPIASPDK 595 ***********************************************999.5********************* PP TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 i++++ lPktRsGkimRR+lrkiae++ +lgd+stl+dp+vv++l++ NCBI__GCF_000092045.1:WP_011427293.1 596 IQFAPGLPKTRSGKIMRRILRKIAEDDfGALGDTSTLADPAVVDDLIA 643 ********************************************9975 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 34.14 // [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