Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_043768008.1 U743_RS10390 acetate--CoA ligase
Query= reanno::pseudo3_N2E3:AO353_03060 (651 letters) >NCBI__GCF_000733765.1:WP_043768008.1 Length = 649 Score = 947 bits (2448), Expect = 0.0 Identities = 452/644 (70%), Positives = 527/644 (81%) Query: 3 AASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDD 62 +++++PV+PE D A Y+ MY SV +P+ FW E KR+DWIKPF+ VK +FD Sbjct: 2 SSNIHPVKPEWRQGAKVDAAGYEKMYADSVRDPETFWAEHGKRIDWIKPFSKVKDVNFDA 61 Query: 63 HHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKFAN 122 + I+WF DGTLNV+ NCLDRHLAERGDQ AIIWEGD+P + I+YRELHE+VC+ N Sbjct: 62 SDLHIRWFYDGTLNVAANCLDRHLAERGDQTAIIWEGDEPDQDARISYRELHEKVCRLGN 121 Query: 123 ALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKV 182 ALR V RGDVVTIYMPMIPEA VAMLAC RIGA+HSVVFGGFSPEALAGRI DC SK Sbjct: 122 ALRDMGVARGDVVTIYMPMIPEAAVAMLACARIGAVHSVVFGGFSPEALAGRIEDCGSKW 181 Query: 183 VITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMK 242 VITADEG+R GKKI LKANVD AL P +S++K +V +RTGG++ W++ RD WY+D+ + Sbjct: 182 VITADEGVRGGKKIPLKANVDTALGLPGGASVKKTVVVRRTGGDVDWSEGRDHWYQDITE 241 Query: 243 VAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYW 302 A + C P+EMGAE+ LFILYTSGSTGKPKGV HT GGYL++A++THE FDYR GEIYW Sbjct: 242 AASSDCPPEEMGAEDPLFILYTSGSTGKPKGVLHTQGGYLVHASMTHEYCFDYRDGEIYW 301 Query: 303 CTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIR 362 CTADVGWVTGH+YIVYGPLANGATTL+FEGVPNYPD+ R ++ DKH VNI YTAPTAIR Sbjct: 302 CTADVGWVTGHSYIVYGPLANGATTLMFEGVPNYPDMGRFWQVCDKHGVNIFYTAPTAIR 361 Query: 363 AMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATL 422 A+M +G V+ +LR+LG+VGEPINPEAWEWY++ VG SRCP++DTWWQTETG L Sbjct: 362 ALMREGEDPVKKHRRDTLRVLGTVGEPINPEAWEWYFRVVGDSRCPVIDTWWQTETGGIL 421 Query: 423 MSPLPGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGDHD 482 ++PLPGA LKPGSA PFFGV PALVDN G+I+EG A+GNLVILDSWPGQ RT+YGDH+ Sbjct: 422 IAPLPGATDLKPGSATTPFFGVQPALVDNEGHILEGEADGNLVILDSWPGQMRTVYGDHE 481 Query: 483 RFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKV 542 RFV TYF T+ G YF+GDGARRDADGY+WITGRVDDVLN+SGHRMGTAEIESA+VAH +V Sbjct: 482 RFVQTYFSTYPGRYFSGDGARRDADGYFWITGRVDDVLNISGHRMGTAEIESALVAHSQV 541 Query: 543 AEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAPGL 602 AEAAVVG PHD+KGQGIY YV+L G EPSEAL+ EL VRKEIG IASPD+I +APGL Sbjct: 542 AEAAVVGYPHDLKGQGIYCYVSLVVGAEPSEALKKELVQHVRKEIGAIASPDIIHFAPGL 601 Query: 603 PKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLIDTHK 646 PKTRSGKIMRRILRKIA GEY LGD STLADPGVV L+ K Sbjct: 602 PKTRSGKIMRRILRKIAEGEYSSLGDTSTLADPGVVDTLVTEAK 645 Lambda K H 0.319 0.136 0.425 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: 1549 Number of extensions: 64 Number of successful extensions: 1 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate WP_043768008.1 U743_RS10390 (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.1022325.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 1021.4 0.0 0 1021.1 0.0 1.0 1 NCBI__GCF_000733765.1:WP_043768008.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000733765.1:WP_043768008.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1021.1 0.0 0 0 5 627 .. 21 641 .. 17 643 .. 0.98 Alignments for each domain: == domain 1 score: 1021.1 bits; conditional E-value: 0 TIGR02188 5 eeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkv 74 y+++y+++++dpe+fwa+++k +++w+kpf+kv+d ++++ +++Wf dg+lnv++nc+drh+++r d++ NCBI__GCF_000733765.1:WP_043768008.1 21 AGYEKMYADSVRDPETFWAEHGK-RIDWIKPFSKVKDVNFDAsdlHIRWFYDGTLNVAANCLDRHLAERGDQT 92 679********************.5************999887789*************************** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 aiiwegde+++ +++Y+el+++vcrl n+l+++Gv +gd v+iY+pmipea++amlacaRiGavhsvvf+G NCBI__GCF_000733765.1:WP_043768008.1 93 AIIWEGDEPDQ-DARISYRELHEKVCRLGNALRDMGVARGDVVTIYMPMIPEAAVAMLACARIGAVHSVVFGG 164 *********97.899********************************************************** PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvww 219 fs+eala Ri+d+ +k vitadeg+Rggk+i+lk++vd al sv+k++vv+rtg +v w+egrD+w+ NCBI__GCF_000733765.1:WP_043768008.1 165 FSPEALAGRIEDCGSKWVITADEGVRGGKKIPLKANVDTALGLPGGaSVKKTVVVRRTGGDVD-WSEGRDHWY 236 *****************************************988777**************66.********* PP TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292 ++++e as++c+pe++++edplfiLYtsGstGkPkGvlht+gGyl++a++t++y fd++d++i+wCtaDvGW NCBI__GCF_000733765.1:WP_043768008.1 237 QDITEA-ASSDCPPEEMGAEDPLFILYTSGSTGKPKGVLHTQGGYLVHASMTHEYCFDYRDGEIYWCTADVGW 308 *****5.****************************************************************** PP TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365 vtGhsYivygPLanGattl+fegvp+ypd++rfw+v++k++v+ifYtaPtaiRalm++ge+ vkkh +++lrv NCBI__GCF_000733765.1:WP_043768008.1 309 VTGHSYIVYGPLANGATTLMFEGVPNYPDMGRFWQVCDKHGVNIFYTAPTAIRALMREGEDPVKKHRRDTLRV 381 ************************************************************************* PP TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438 lg+vGepinpeaweWy++vvG+++cp++dtwWqtetGgili+plpg at+lkpgsat+P+fG+++++vd+eg+ NCBI__GCF_000733765.1:WP_043768008.1 382 LGTVGEPINPEAWEWYFRVVGDSRCPVIDTWWQTETGGILIAPLPG-ATDLKPGSATTPFFGVQPALVDNEGH 453 **********************************************.6************************* PP TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511 +e e++ g Lvi ++wP+++rt+ygd+erfv+tYf++++g yf+GDgarrd+dGy+wi+GRvDdv+n+sGhr NCBI__GCF_000733765.1:WP_043768008.1 454 ILEGEAD-GNLVILDSWPGQMRTVYGDHERFVQTYFSTYPGRYFSGDGARRDADGYFWITGRVDDVLNISGHR 525 **98777.89*************************************************************** PP TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilv 584 +gtaeiesalv+h++vaeaavvg+p+++kg+ i+++v l g+e++e +l+kel ++vrkeig+ia+pd i++ NCBI__GCF_000733765.1:WP_043768008.1 526 MGTAEIESALVAHSQVAEAAVVGYPHDLKGQGIYCYVSLVVGAEPSE-ALKKELVQHVRKEIGAIASPDIIHF 597 **********************************************9.5************************ PP TIGR02188 585 veelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627 ++ lPktRsGkimRR+lrkiaege ++lgd+stl+dp vv++l NCBI__GCF_000733765.1:WP_043768008.1 598 APGLPKTRSGKIMRRILRKIAEGEySSLGDTSTLADPGVVDTLV 641 *****************************************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 21.20 // [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