Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_099018876.1 CCS90_RS07185 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_002591915.1:WP_099018876.1 Length = 646 Score = 900 bits (2325), Expect = 0.0 Identities = 435/637 (68%), Positives = 495/637 (77%), Gaps = 2/637 (0%) Query: 7 YPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66 YPV PE A TL D Y +MYQQS+ N + FW KRLDWIKP+ +K SFD + Sbjct: 5 YPVHPEFATHTLCDNDKYLSMYQQSIENNEAFWGLHGKRLDWIKPYIQIKDVSFDQQDLH 64 Query: 67 IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALRG 126 IKWFADG LNVSYNC+DRHL + DQ AIIWEGD+P+ES+NI+Y ELH+EV +FAN L+ Sbjct: 65 IKWFADGQLNVSYNCIDRHLPTKADQTAIIWEGDNPAESKNISYAELHQEVGRFANTLKK 124 Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186 V +GD VT+YMPMIPEA AMLAC RIGAIHSVVFGGFSPEAL RII+CKSK+VITA Sbjct: 125 LGVIKGDRVTLYMPMIPEAAYAMLACARIGAIHSVVFGGFSPEALGDRIINCKSKLVITA 184 Query: 187 DEGVRAGKKIPLKANVDDALTNPETSS-IQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245 D GVR K I LKANVD A ++ V+V K + W H D WY ++ + Sbjct: 185 DRGVRGAKSIGLKANVDKATKKAGVKDYLESVLVIKTADHEVDWYDH-DHWYHEVSQSVD 243 Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305 T C P M AE+ LFILYTSGSTG+PKGV HT+ GYLLYA++THE VFD +PG+VYWCTA Sbjct: 244 TFCEPAIMNAEDPLFILYTSGSTGQPKGVLHTSGGYLLYASMTHEYVFDIQPGDVYWCTA 303 Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365 DVGW+TGHSY+VYGPLANG TTL+FEGVPNYPD +R ++ DKH+V+I YTAPTAIRA+M Sbjct: 304 DVGWITGHSYVVYGPLANGGTTLMFEGVPNYPDHSRFWQICDKHQVNICYTAPTAIRALM 363 Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425 G V+ SLR+LGSVGEPINPEAW WYY+ VG+ R PIVDTWWQTETGG++ISP Sbjct: 364 KEGDEPVKSTSRKSLRVLGSVGEPINPEAWKWYYEVVGEARSPIVDTWWQTETGGIMISP 423 Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485 LPGATALKPGSATRPFFG+ PAL+DN GN + G A GNLVI DSWPGQ RT+YGDH RF Sbjct: 424 LPGATALKPGSATRPFFGIKPALLDNEGNELNGVASGNLVITDSWPGQMRTVYGDHARFY 483 Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545 TYF F +Y TGDGA+RDEDGYYWITGR DDVLNVSGHRMGTAE+ESA+VAHP VAEA Sbjct: 484 TTYFAAFKNVYTTGDGAKRDEDGYYWITGRTDDVLNVSGHRMGTAEVESALVAHPAVAEA 543 Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605 AVVG PHDIKGQGIY YVTL G SE L EL NWVR EIGPIA+PD IQWAPGLPKT Sbjct: 544 AVVGYPHDIKGQGIYAYVTLVNGMAESETLLSELVNWVRSEIGPIATPDKIQWAPGLPKT 603 Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642 RSGKIMRRILRKIA E+ LGD STLA+P VV +LI Sbjct: 604 RSGKIMRRILRKIAANEHKNLGDTSTLAEPEVVVNLI 640 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: 1408 Number of extensions: 59 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: 646 Length adjustment: 38 Effective length of query: 613 Effective length of database: 608 Effective search space: 372704 Effective search space used: 372704 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_099018876.1 CCS90_RS07185 (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.2840434.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-306 1001.4 0.1 8.6e-306 1001.2 0.1 1.0 1 NCBI__GCF_002591915.1:WP_099018876.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002591915.1:WP_099018876.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1001.2 0.1 8.6e-306 8.6e-306 3 628 .. 18 641 .. 16 642 .. 0.98 Alignments for each domain: == domain 1 score: 1001.2 bits; conditional E-value: 8.6e-306 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 ++++y ++y+++ie+ e+fw+ ++k +l+w+kp+ +++d s+++ ++kWf+dg+lnvsync+drh+ +++d NCBI__GCF_002591915.1:WP_099018876.1 18 DNDKYLSMYQQSIENNEAFWGLHGK-RLDWIKPYIQIKDVSFDQqdlHIKWFADGQLNVSYNCIDRHLPTKAD 89 5789********************9.5************999887789************************* PP TIGR02188 73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145 ++aiiwegd++ e s++++Yael++ev r+an+lk+lGv kgdrv++Y+pmipea++amlacaRiGa+hsvvf NCBI__GCF_002591915.1:WP_099018876.1 90 QTAIIWEGDNPAE-SKNISYAELHQEVGRFANTLKKLGVIKGDRVTLYMPMIPEAAYAMLACARIGAIHSVVF 161 *********9996.*********************************************************** PP TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee..svekvlvvkrtgeevaewkegrD 216 +Gfs+eal +Ri+++++klvitad g+Rg k+i lk++vd+a +ka +e+vlv+k +++ev w ++D NCBI__GCF_002591915.1:WP_099018876.1 162 GGFSPEALGDRIINCKSKLVITADRGVRGAKSIGLKANVDKATKKAGVkdYLESVLVIKTADHEVD-WY-DHD 232 ********************************************9987668*************76.87.79* PP TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289 +w++e+ ++ +++ cep+ +++edplfiLYtsGstG+PkGvlht+gGyll+a++t++yvfdi+++d++wCtaD NCBI__GCF_002591915.1:WP_099018876.1 233 HWYHEVSQS-VDTFCEPAIMNAEDPLFILYTSGSTGQPKGVLHTSGGYLLYASMTHEYVFDIQPGDVYWCTAD 304 ********5.*************************************************************** PP TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362 vGW+tGhsY+vygPLanG ttl+fegvp+ypd+srfw++++k++v+i YtaPtaiRalmk+g+e vk+++++s NCBI__GCF_002591915.1:WP_099018876.1 305 VGWITGHSYVVYGPLANGGTTLMFEGVPNYPDHSRFWQICDKHQVNICYTAPTAIRALMKEGDEPVKSTSRKS 377 ************************************************************************* PP TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435 lrvlgsvGepinpeaw+WyyevvG+ ++pivdtwWqtetGgi+i+plpg at+lkpgsat+P+fGi+++++d+ NCBI__GCF_002591915.1:WP_099018876.1 378 LRVLGSVGEPINPEAWKWYYEVVGEARSPIVDTWWQTETGGIMISPLPG-ATALKPGSATRPFFGIKPALLDN 449 *************************************************.6********************** PP TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508 eg+e++ ++ g Lvi+++wP+++rt+ygd+ rf +tYf ++k++y tGDga+rd+dGy+wi+GR+Ddv+nvs NCBI__GCF_002591915.1:WP_099018876.1 450 EGNELNGVAS-GNLVITDSWPGQMRTVYGDHARFYTTYFAAFKNVYTTGDGAKRDEDGYYWITGRTDDVLNVS 521 *****98777.89************************************************************ PP TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581 Ghr+gtae+esalv+h+avaeaavvg+p++ikg+ i+a+v+l +g++e+e +l +el ++vr+eigpia+pdk NCBI__GCF_002591915.1:WP_099018876.1 522 GHRMGTAEVESALVAHPAVAEAAVVGYPHDIKGQGIYAYVTLVNGMAESE-TLLSELVNWVRSEIGPIATPDK 593 ***********************************************999.5********************* PP TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 i++++ lPktRsGkimRR+lrkia++e ++lgd+stl++p+vv +l++ NCBI__GCF_002591915.1:WP_099018876.1 594 IQWAPGLPKTRSGKIMRRILRKIAANEhKNLGDTSTLAEPEVVVNLIN 641 ***************************99*************998875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (646 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: 28.65 // [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