Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_086512010.1 BZY95_RS21920 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_002151265.1:WP_086512010.1 Length = 649 Score = 954 bits (2467), Expect = 0.0 Identities = 446/638 (69%), Positives = 527/638 (82%) Query: 6 LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65 +YPVR ++AA+ D Y+AMYQQSV +P+GFW EQAKR+DW K T +K TSFD H+V Sbjct: 7 VYPVRDDIAANAWIDREKYQAMYQQSVDDPEGFWAEQAKRIDWFKAPTKIKHTSFDPHNV 66 Query: 66 DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125 DI+WF DGTLN S +CLDRHL +RGDQ AIIWEGDDP +S++++YRELH + C+ ANAL+ Sbjct: 67 DIRWFEDGTLNASVSCLDRHLEKRGDQTAIIWEGDDPKDSKHVSYRELHAKTCQLANALK 126 Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185 + +GDVVT+YMPMIPEA VAMLAC RIGA+HSVVFGGFSP+ALA RI+ S++VIT Sbjct: 127 ELGIGKGDVVTLYMPMIPEAAVAMLACARIGAVHSVVFGGFSPDALAQRIVGADSRLVIT 186 Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245 ADE VR GK +PLK NVD ALT T +KV+V KRT G+I+W + RD+WY DL+ Sbjct: 187 ADESVRGGKHVPLKDNVDAALTRKGTEVCEKVLVVKRTGGDIEWKEGRDVWYHDLVDKQS 246 Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305 C +EM AE+ LFILYTSGSTG PKG++HTT GYL+YA+LTH+ +FDY+ GEVYWCTA Sbjct: 247 ADCPAEEMNAEDPLFILYTSGSTGAPKGLKHTTGGYLVYASLTHQYIFDYQDGEVYWCTA 306 Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365 DVGWVTGHSYIVYGPLANGATTL+FEGVP+YP R+ +V+DKH V+ILYTAPTAIRA+M Sbjct: 307 DVGWVTGHSYIVYGPLANGATTLMFEGVPSYPSHGRMGEVVDKHNVAILYTAPTAIRALM 366 Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425 A G ++ + SLRLLGSVGEPINPEAW+WY++ +G +CPIVDTWWQTETGG++I+P Sbjct: 367 AHGDGVMDSSKRDSLRLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGIMIAP 426 Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485 LPGA LKPGSAT PFFGV PAL+D+ GN ++GA +GNLVI DSWPGQAR+++GDHDRF+ Sbjct: 427 LPGAMDLKPGSATLPFFGVQPALLDSEGNELQGAVDGNLVISDSWPGQARSIWGDHDRFI 486 Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545 TYF T+ G YFTGDG RRDEDGYYWITGRVDDVLNVSGHRMGTAEIES++VAH VAEA Sbjct: 487 QTYFSTYKGYYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRMGTAEIESSLVAHEAVAEA 546 Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605 AVVG PHDIKGQGIY+YVTL G E ++ L+ EL WVRK+IGPIASPDVIQWAPGLPKT Sbjct: 547 AVVGFPHDIKGQGIYIYVTLGDGVEPTDELKKELTQWVRKDIGPIASPDVIQWAPGLPKT 606 Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 RSGKIMRRILRKIA E DGLGD STLADP VV LIE Sbjct: 607 RSGKIMRRILRKIAANETDGLGDTSTLADPSVVDDLIE 644 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: 1464 Number of extensions: 52 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate WP_086512010.1 BZY95_RS21920 (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.5019.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 1022.5 0.0 0 1022.3 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086512010.1 BZY95_RS21920 acetate--CoA ligas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086512010.1 BZY95_RS21920 acetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1022.3 0.0 0 0 3 628 .. 21 644 .. 19 645 .. 0.98 Alignments for each domain: == domain 1 score: 1022.3 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhve 68 + e+y+++y+++++dpe fwa++ak+ ++w+k +k++++s++p +++Wfedg+ln+s+ c+drh+e lcl|NCBI__GCF_002151265.1:WP_086512010.1 21 DREKYQAMYQQSVDDPEGFWAEQAKR-IDWFKAPTKIKHTSFDPhnvDIRWFEDGTLNASVSCLDRHLE 88 5689*********************5.***************9988899******************** PP TIGR02188 69 krkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRi 137 kr d++aiiwegd+++ ds++++Y+el++++c+lan+lkelG+ kgd v++Y+pmipea++amlacaRi lcl|NCBI__GCF_002151265.1:WP_086512010.1 89 KRGDQTAIIWEGDDPK-DSKHVSYRELHAKTCQLANALKELGIGKGDVVTLYMPMIPEAAVAMLACARI 156 ***************9.5*************************************************** PP TIGR02188 138 GavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtg 205 Gavhsvvf+Gfs++ala+Riv a+++lvitade++Rggk+++lk++vd+al+++ + ekvlvvkrtg lcl|NCBI__GCF_002151265.1:WP_086512010.1 157 GAVHSVVFGGFSPDALAQRIVGADSRLVITADESVRGGKHVPLKDNVDAALTRKGTeVCEKVLVVKRTG 225 ****************************************************99995679********* PP TIGR02188 206 eevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvky 274 +++ wkegrDvw+++lv+k +sa+c++e++++edplfiLYtsGstG PkG+ httgGyl++a+lt++y lcl|NCBI__GCF_002151265.1:WP_086512010.1 226 GDIE-WKEGRDVWYHDLVDK-QSADCPAEEMNAEDPLFILYTSGSTGAPKGLKHTTGGYLVYASLTHQY 292 **66.**************7.************************************************ PP TIGR02188 275 vfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPta 343 +fd++d++++wCtaDvGWvtGhsYivygPLanGattl+fegvp+yp+++r+ ev++k++v+i+YtaPta lcl|NCBI__GCF_002151265.1:WP_086512010.1 293 IFDYQDGEVYWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPSYPSHGRMGEVVDKHNVAILYTAPTA 361 ********************************************************************* PP TIGR02188 344 iRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgv 412 iRalm+ g+ ++++ +++slr+lgsvGepinpeaweWy++v+G++kcpivdtwWqtetGgi+i+plpg lcl|NCBI__GCF_002151265.1:WP_086512010.1 362 IRALMAHGDGVMDSSKRDSLRLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGIMIAPLPG- 429 ********************************************************************. PP TIGR02188 413 atelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkgly 481 a++lkpgsatlP+fG++++++d+eg+e++ + g Lvi+++wP+++r+i+gd++rf++tYf+++kg+y lcl|NCBI__GCF_002151265.1:WP_086512010.1 430 AMDLKPGSATLPFFGVQPALLDSEGNELQGAVD-GNLVISDSWPGQARSIWGDHDRFIQTYFSTYKGYY 497 6****************************8888.89********************************* PP TIGR02188 482 ftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvl 550 ftGDg+rrd+dGy+wi+GRvDdv+nvsGhr+gtaeies+lv+heavaeaavvg+p++ikg+ i+++v+l lcl|NCBI__GCF_002151265.1:WP_086512010.1 498 FTGDGCRRDEDGYYWITGRVDDVLNVSGHRMGTAEIESSLVAHEAVAEAAVVGFPHDIKGQGIYIYVTL 566 ********************************************************************* PP TIGR02188 551 kegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstle 618 +gve+++e l+kel+++vrk igpia+pd i++++ lPktRsGkimRR+lrkia++e + lgd+stl+ lcl|NCBI__GCF_002151265.1:WP_086512010.1 567 GDGVEPTDE-LKKELTQWVRKDIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAANEtDGLGDTSTLA 634 ********5.************************************************999******** PP TIGR02188 619 dpsvveelke 628 dpsvv++l+e lcl|NCBI__GCF_002151265.1:WP_086512010.1 635 DPSVVDDLIE 644 ******9987 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 8.52 // [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