Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_057507083.1 ABB28_RS02385 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_001431535.1:WP_057507083.1 Length = 647 Score = 879 bits (2271), Expect = 0.0 Identities = 423/644 (65%), Positives = 499/644 (77%), Gaps = 1/644 (0%) Query: 4 ASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDH 63 A LYPV P+ A + D+ TY+ YQ S+ PD FW E A+RL W K + +K S+D Sbjct: 2 ADLYPVDPQFAKNARIDKTTYQQQYQASIDAPDAFWGEAAQRLQWFKQPSIIKNVSYDLA 61 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDP-SESRNITYRELHEEVCKFAN 122 IKWF DG LN S NCLDR L +RG++ A+++E D P + ++++TYREL+E C+ N Sbjct: 62 DFRIKWFEDGELNASVNCLDRQLEKRGEKTALLFEPDSPDAPAQHVTYRELYERTCRLGN 121 Query: 123 ALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKV 182 ALR V +GD VTIY+PMI +A VAMLAC RIGAIHSVVFGGF+P ++A R+ DC SK+ Sbjct: 122 ALRNLGVKKGDRVTIYLPMIVDAAVAMLACARIGAIHSVVFGGFAPNSIADRVSDCASKL 181 Query: 183 VITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMK 242 +ITADEG+R GKKIPLKANVD AL P T++++ V+V + T G + RD W+ D++ Sbjct: 182 IITADEGLRGGKKIPLKANVDAALKLPGTNTVETVLVVRHTGGAVDMQAPRDRWFHDVVD 241 Query: 243 VAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYW 302 C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLLYAA THE VFD + ++YW Sbjct: 242 SQPAECEPERMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYAAYTHEAVFDLREDDIYW 301 Query: 303 CTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIR 362 CTADVGWVTGHSYIVYGPLANGAT+L+FEGVPNYPD +R VIDKHKVS+ YTAPTAIR Sbjct: 302 CTADVGWVTGHSYIVYGPLANGATSLMFEGVPNYPDTSRFWNVIDKHKVSLFYTAPTAIR 361 Query: 363 AMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVL 422 A+M G V+ +SLRLLGSVGEPINPEAW WYY+ VG RCPIVDTWWQTETGG+L Sbjct: 362 ALMREGEEPVKRTSRASLRLLGSVGEPINPEAWRWYYEVVGDSRCPIVDTWWQTETGGIL 421 Query: 423 ISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHD 482 ISPLPGA LKPGSA+ PFFGV PALV+ G + +GA EGNL+I DSWPGQ RT+YGD Sbjct: 422 ISPLPGAVDLKPGSASLPFFGVQPALVNADGEIKDGATEGNLIIRDSWPGQMRTVYGDDQ 481 Query: 483 RFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKV 542 RF+DTYF+T+ G YFTGDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+HPKV Sbjct: 482 RFIDTYFRTYPGAYFTGDGCRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKV 541 Query: 543 AEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGL 602 AEAAVVG PH++KGQGIY YVTL A E SE L EL WVRKEIGPIA+PD +QWAPGL Sbjct: 542 AEAAVVGFPHEVKGQGIYAYVTLIADEAPSEELHKELVAWVRKEIGPIATPDHLQWAPGL 601 Query: 603 PKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHK 646 PKTRSGKIMRRILRKIA D LGD STLADP VVA L++ K Sbjct: 602 PKTRSGKIMRRILRKIAENAPDQLGDTSTLADPSVVASLVDERK 645 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: 1394 Number of extensions: 53 Number of successful extensions: 2 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: 647 Length adjustment: 38 Effective length of query: 613 Effective length of database: 609 Effective search space: 373317 Effective search space used: 373317 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_057507083.1 ABB28_RS02385 (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.363.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-307 1005.7 0.0 4.4e-307 1005.4 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057507083.1 ABB28_RS02385 acetate--CoA ligas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057507083.1 ABB28_RS02385 acetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1005.4 0.0 4.4e-307 4.4e-307 4 627 .. 19 641 .. 16 643 .. 0.98 Alignments for each domain: == domain 1 score: 1005.4 bits; conditional E-value: 4.4e-307 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvek 69 ++y++ y+ +i+ p++fw++ a+ +l+w+k+ + +++ s + ++kWfedgeln+s+nc+dr++ek lcl|NCBI__GCF_001431535.1:WP_057507083.1 19 KTTYQQQYQASIDAPDAFWGEAAQ-RLQWFKQPSIIKNVSYDLadfRIKWFEDGELNASVNCLDRQLEK 86 678*****************9999.5******999998887655579********************** PP TIGR02188 70 rkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiG 138 r +k+a+ +e d+++ ++++tY+el++++crl n+l++lGvkkgdrv+iYlpmi++a++amlacaRiG lcl|NCBI__GCF_001431535.1:WP_057507083.1 87 RGEKTALLFEPDSPDAPAQHVTYRELYERTCRLGNALRNLGVKKGDRVTIYLPMIVDAAVAMLACARIG 155 ***************9***************************************************** PP TIGR02188 139 avhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtge 206 a+hsvvf+Gf+++++a+R+ d+ +kl+itadeglRggk+i+lk++vd+al+ + +ve+vlvv++tg lcl|NCBI__GCF_001431535.1:WP_057507083.1 156 AIHSVVFGGFAPNSIADRVSDCASKLIITADEGLRGGKKIPLKANVDAALKLPGTnTVETVLVVRHTGG 224 ***************************************************99888************* PP TIGR02188 207 evaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyv 275 v ++ rD w++++v++ ++aecepe++++edplfiLYtsGstGkPkGvlhttgGyll+aa+t++ v lcl|NCBI__GCF_001431535.1:WP_057507083.1 225 AVD-MQAPRDRWFHDVVDS-QPAECEPERMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYAAYTHEAV 291 *66.**************5.************************************************* PP TIGR02188 276 fdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtai 344 fd++++di+wCtaDvGWvtGhsYivygPLanGat+l+fegvp+ypd+srfw+vi+k+kv+ fYtaPtai lcl|NCBI__GCF_001431535.1:WP_057507083.1 292 FDLREDDIYWCTADVGWVTGHSYIVYGPLANGATSLMFEGVPNYPDTSRFWNVIDKHKVSLFYTAPTAI 360 ********************************************************************* PP TIGR02188 345 RalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgva 413 Ralm++gee vk++++ slr+lgsvGepinpeaw+WyyevvG+++cpivdtwWqtetGgili+plpg a lcl|NCBI__GCF_001431535.1:WP_057507083.1 361 RALMREGEEPVKRTSRASLRLLGSVGEPINPEAWRWYYEVVGDSRCPIVDTWWQTETGGILISPLPG-A 428 *******************************************************************.6 PP TIGR02188 414 telkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyf 482 ++lkpgsa+lP+fG+++++v+ +g+ + +e g L+i+++wP+++rt+ygd++rf++tYf++++g yf lcl|NCBI__GCF_001431535.1:WP_057507083.1 429 VDLKPGSASLPFFGVQPALVNADGEIKDGATE-GNLIIRDSWPGQMRTVYGDDQRFIDTYFRTYPGAYF 496 ************************98886666.89********************************** PP TIGR02188 483 tGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551 tGDg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalvsh++vaeaavvg+p+e+kg+ i+a+v+l lcl|NCBI__GCF_001431535.1:WP_057507083.1 497 TGDGCRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKVAEAAVVGFPHEVKGQGIYAYVTLI 565 ********************************************************************* PP TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstled 619 + ++++ee l+kel ++vrkeigpia+pd++++++ lPktRsGkimRR+lrkiae++ ++lgd+stl+d lcl|NCBI__GCF_001431535.1:WP_057507083.1 566 ADEAPSEE-LHKELVAWVRKEIGPIATPDHLQWAPGLPKTRSGKIMRRILRKIAENApDQLGDTSTLAD 633 *****995.************************************************************ PP TIGR02188 620 psvveelk 627 psvv++l lcl|NCBI__GCF_001431535.1:WP_057507083.1 634 PSVVASLV 641 ****9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (647 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 12.89 // [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