Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_106714004.1 CU102_RS26175 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_003010955.1:WP_106714004.1 Length = 649 Score = 897 bits (2317), Expect = 0.0 Identities = 428/649 (65%), Positives = 508/649 (78%), Gaps = 3/649 (0%) Query: 4 ASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDH 63 + +YPV L D TY Y+QS+ +P+ FW + KR+DW KP+T VK TSF+ Sbjct: 2 SEVYPVLASAKKDALIDNETYLNWYKQSIKDPEKFWAKHGKRIDWFKPYTKVKNTSFEGK 61 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123 V IKWF DG NVSYNC+DRHL +RGDQ+AIIWEGD+P + ITY EL+E+VC+ AN Sbjct: 62 -VAIKWFEDGVTNVSYNCIDRHLKKRGDQVAIIWEGDNPYLDKKITYNELYEQVCRLANV 120 Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183 L+ V +GD VTIYMPMIPEA AMLACTRIGAIHSVVFGGFSP+ALAGRI+DC+S V Sbjct: 121 LKKHGVKKGDRVTIYMPMIPEASYAMLACTRIGAIHSVVFGGFSPDALAGRIVDCESTFV 180 Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSI--QKVIVCKRTAGNIKWNQHRDIWYEDLM 241 IT+DEG+R GK IPLK N D A+ + + V+V +RT G W RD+WY + + Sbjct: 181 ITSDEGMRGGKPIPLKDNTDKAIDIAARHHVMVKNVLVVRRTGGKTGWAPGRDLWYHEEI 240 Query: 242 KVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVY 301 C P++M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY G++Y Sbjct: 241 ASVKPECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGDIY 300 Query: 302 WCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAI 361 WCTADVGWVTGHSYIVYGPLANGATTL+FEGVPNYP ++R VIDKHKV+I YTAPTAI Sbjct: 301 WCTADVGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWDVIDKHKVNIFYTAPTAI 360 Query: 362 RAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGV 421 RA+M++G V+ SLR+LGSVGEPINPEAW+WYY+ VG +R P+VDTWWQTETGG+ Sbjct: 361 RALMSAGDEPVKKTSRKSLRILGSVGEPINPEAWEWYYQVVGDKRSPVVDTWWQTETGGI 420 Query: 422 LISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDH 481 LI+PLPGATALKPGSATRPFFGV P LVDN G+++EG A+GNL I+DSWPGQ RT+YGDH Sbjct: 421 LITPLPGATALKPGSATRPFFGVQPQLVDNEGDVLEGGADGNLCIIDSWPGQMRTVYGDH 480 Query: 482 DRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPK 541 RF++TYF T+ G YFTGDG RRD+DGYYWITGRVDDVLNVSGHRMGTAE+ESA+V+H Sbjct: 481 KRFIETYFSTYKGKYFTGDGCRRDKDGYYWITGRVDDVLNVSGHRMGTAEVESALVSHDT 540 Query: 542 VAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPG 601 V+EAAVVG PHD+KGQGIY YVTL AG E ++ LR EL VRKEIGPIASPD IQ+AP Sbjct: 541 VSEAAVVGYPHDLKGQGIYCYVTLMAGLEGTDELRKELVTHVRKEIGPIASPDKIQFAPS 600 Query: 602 LPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNV 650 LPKTRSGKIMRRILRKIA ++ LGD STLADP VV +I + + Sbjct: 601 LPKTRSGKIMRRILRKIAEDDFGALGDTSTLADPTVVEDMIANRQNRRI 649 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: 1459 Number of extensions: 70 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: 649 Length adjustment: 38 Effective length of query: 613 Effective length of database: 611 Effective search space: 374543 Effective search space used: 374543 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_106714004.1 CU102_RS26175 (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.1896922.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 1050.9 0.2 0 1050.7 0.2 1.0 1 NCBI__GCF_003010955.1:WP_106714004.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106714004.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1050.7 0.2 0 0 3 627 .. 18 641 .. 16 643 .. 0.98 Alignments for each domain: == domain 1 score: 1050.7 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_106714004.1 18 DNETYLNWYKQSIKDPEKFWAKHGK-RIDWFKPYTKVKNTSFEGkvAIKWFEDGVTNVSYNCIDRHLKKRGDQ 89 6789*********************.5**************9987789************************* PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 vaiiwegd++ +k+tY+el+++vcrlanvlk++Gvkkgdrv+iY+pmipea +amlac+RiGa+hsvvf+ NCBI__GCF_003010955.1:WP_106714004.1 90 VAIIWEGDNPYL-DKKITYNELYEQVCRLANVLKKHGVKKGDRVTIYMPMIPEASYAMLACTRIGAIHSVVFG 161 ********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_106714004.1 162 GFSPDALAGRIVDCESTFVITSDEGMRGGKPIPLKDNTDKAIDIAARhhvMVKNVLVVRRTGGK-TGWAPGRD 233 *****************************************9877655579*************.56****** PP TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289 +w++e++++ ++ ec+pek+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++d+di+wCtaD NCBI__GCF_003010955.1:WP_106714004.1 234 LWYHEEIAS-VKPECKPEKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGDIYWCTAD 305 ********6.*************************************************************** PP TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362 vGWvtGhsYivygPLanGattl+fegvp+yp+ srfw+vi+k+kv+ifYtaPtaiRalm +g+e vkk++++s NCBI__GCF_003010955.1:WP_106714004.1 306 VGWVTGHSYIVYGPLANGATTLMFEGVPNYPSVSRFWDVIDKHKVNIFYTAPTAIRALMSAGDEPVKKTSRKS 378 ************************************************************************* PP TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435 lr+lgsvGepinpeaweWyy+vvG++++p+vdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd+ NCBI__GCF_003010955.1:WP_106714004.1 379 LRILGSVGEPINPEAWEWYYQVVGDKRSPVVDTWWQTETGGILITPLPG-ATALKPGSATRPFFGVQPQLVDN 450 *************************************************.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_106714004.1 451 EGDVLEGGAD-GNLCIIDSWPGQMRTVYGDHKRFIETYFSTYKGKYFTGDGCRRDKDGYYWITGRVDDVLNVS 522 ******9988.89************************************************************ PP TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581 Ghr+gtae+esalvsh++v+eaavvg+p+++kg+ i+++v+l++g e ++e l+kel ++vrkeigpia+pdk NCBI__GCF_003010955.1:WP_106714004.1 523 GHRMGTAEVESALVSHDTVSEAAVVGYPHDLKGQGIYCYVTLMAGLEGTDE-LRKELVTHVRKEIGPIASPDK 594 ***********************************************9995.********************* PP TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627 i+++++lPktRsGkimRR+lrkiae++ +lgd+stl+dp+vve+++ NCBI__GCF_003010955.1:WP_106714004.1 595 IQFAPSLPKTRSGKIMRRILRKIAEDDfGALGDTSTLADPTVVEDMI 641 ********************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (649 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: 33.77 // [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