Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate CCNA_03696 CCNA_03696 acetyl-coenzyme A synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__Caulo:CCNA_03696 Length = 647 Score = 852 bits (2202), Expect = 0.0 Identities = 411/643 (63%), Positives = 493/643 (76%), Gaps = 2/643 (0%) Query: 1 MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60 +S ++PV ++A D A Y A + +P+G+WR+ A RLDWI P T +K S+ Sbjct: 2 VSDGQVFPVPADLARDAHIDAAAYDAALARVEADPEGYWRDIAARLDWITPPTKIKDVSY 61 Query: 61 DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120 I+W+ DG LNVS NC+DRHL + D +A+++EGD+P S +TY +LHEEVC+ Sbjct: 62 AKEDFRIRWYEDGVLNVSANCIDRHLPAKKDDVALVFEGDEPGTSSTLTYGQLHEEVCRM 121 Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180 AN L+ Q V +GD VTIY+PM+P A VAMLAC RIGA+HSVVFGGFSP+++AGRI DC S Sbjct: 122 ANVLKAQGVKKGDRVTIYLPMVPLAAVAMLACARIGAVHSVVFGGFSPDSIAGRIQDCAS 181 Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240 VITADEG R G+++PLKAN+D+AL + + KV++ + T ++ RDI ++D+ Sbjct: 182 HFVITADEGRRGGRRVPLKANIDEALKH--CPWVGKVLMIRWTGADVPLKAGRDIVWQDV 239 Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300 C P+ M AE+ LFILYTSGSTGKPKGV HTT GYL +A+ T VFDYKPGEV Sbjct: 240 RDTVSADCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLAWASWTFWAVFDYKPGEV 299 Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360 +WCTADVGWVTGHSY+VYGPLANG T+L+FEGVPNYP +R +VIDKH+VSI YTAPTA Sbjct: 300 FWCTADVGWVTGHSYVVYGPLANGGTSLIFEGVPNYPTPSRFWEVIDKHQVSIFYTAPTA 359 Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420 +RA+M G A V D SSLRLLGSVGEPINPEAW WY++ VGKE+ PIVDTWWQTETGG Sbjct: 360 LRALMREGDAHVTKNDLSSLRLLGSVGEPINPEAWLWYHRVVGKEKLPIVDTWWQTETGG 419 Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480 +LI+PLPGATALKPGSA++P GV P LVD G ++GA EGNLVI DSWPGQ RT+YGD Sbjct: 420 MLITPLPGATALKPGSASKPLPGVKPQLVDAEGKFLDGATEGNLVITDSWPGQMRTVYGD 479 Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540 H RF +TYF T+ G YFTGDG RRD DGYYWITGRVDDV+NVSGHR+GTAEIESA+VAH Sbjct: 480 HQRFFETYFSTYPGKYFTGDGCRRDADGYYWITGRVDDVINVSGHRLGTAEIESALVAHE 539 Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600 VAEAAVVG PHDIKGQG+Y YVTL AG E ++ALR +L WVR EIGP A+PDVIQWAP Sbjct: 540 TVAEAAVVGYPHDIKGQGVYAYVTLKAGIEATDALRKDLVLWVRHEIGPFAAPDVIQWAP 599 Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 GLPKTRSGKIMRRILRKIA E LGD STLADP VV L++ Sbjct: 600 GLPKTRSGKIMRRILRKIAENELGSLGDTSTLADPSVVDDLVK 642 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: 1483 Number of extensions: 66 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 CCNA_03696 CCNA_03696 (acetyl-coenzyme A synthetase)
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.14577.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-302 990.7 0.0 1.5e-302 990.5 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_03696 CCNA_03696 acetyl-coenzyme A syn Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_03696 CCNA_03696 acetyl-coenzyme A synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 990.5 0.0 1.5e-302 1.5e-302 4 628 .. 22 642 .. 19 643 .. 0.98 Alignments for each domain: == domain 1 score: 990.5 bits; conditional E-value: 1.5e-302 TIGR02188 4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 + +y + ++ ++dpe +w++ a +l+w++p +k++d s ++ +++W+edg lnvs+nc+drh+ ++kd lcl|FitnessBrowser__Caulo:CCNA_03696 22 AAAYDAALARVEADPEGYWRDIAA-RLDWITPPTKIKDVSYAKedfRIRWYEDGVLNVSANCIDRHLPAKKDD 93 56899999999************9.5************998877789************************** PP TIGR02188 74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146 va+++egde+g+ s +ltY +l++evcr+anvlk++Gvkkgdrv+iYlpm+p a++amlacaRiGavhsvvf+ lcl|FitnessBrowser__Caulo:CCNA_03696 94 VALVFEGDEPGT-SSTLTYGQLHEEVCRMANVLKAQGVKKGDRVTIYLPMVPLAAVAMLACARIGAVHSVVFG 165 ***********7.************************************************************ PP TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvww 219 Gfs++++a Ri+d+ +++vitadeg Rgg++++lk+++deal++++ v kvl+++ tg++v +k grD++w lcl|FitnessBrowser__Caulo:CCNA_03696 166 GFSPDSIAGRIQDCASHFVITADEGRRGGRRVPLKANIDEALKHCP-WVGKVLMIRWTGADVP-LKAGRDIVW 236 *********************************************9.7*************66.********* PP TIGR02188 220 eelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGW 292 +++ ++ +sa+c+pe++++edplfiLYtsGstGkPkGvlhttgGyl +a+ t+ vfd+k++++fwCtaDvGW lcl|FitnessBrowser__Caulo:CCNA_03696 237 QDVRDT-VSADCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLAWASWTFWAVFDYKPGEVFWCTADVGW 308 ***995.****************************************************************** PP TIGR02188 293 vtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrv 365 vtGhsY+vygPLanG t+l+fegvp+yp++srfwevi+k++v+ifYtaPta+Ralm++g+++v+k dlsslr+ lcl|FitnessBrowser__Caulo:CCNA_03696 309 VTGHSYVVYGPLANGGTSLIFEGVPNYPTPSRFWEVIDKHQVSIFYTAPTALRALMREGDAHVTKNDLSSLRL 381 ************************************************************************* PP TIGR02188 366 lgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegk 438 lgsvGepinpeaw Wy++vvGkek pivdtwWqtetGg+litplpg at+lkpgsa++Pl+G+++++vd egk lcl|FitnessBrowser__Caulo:CCNA_03696 382 LGSVGEPINPEAWLWYHRVVGKEKLPIVDTWWQTETGGMLITPLPG-ATALKPGSASKPLPGVKPQLVDAEGK 453 **********************************************.6************************* PP TIGR02188 439 eveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhr 511 ++ +e g Lvi+++wP+++rt+ygd++rf+etYf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr lcl|FitnessBrowser__Caulo:CCNA_03696 454 FLDGATE-GNLVITDSWPGQMRTVYGDHQRFFETYFSTYPGKYFTGDGCRRDADGYYWITGRVDDVINVSGHR 525 ***8777.79*************************************************************** PP TIGR02188 512 lgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilv 584 lgtaeiesalv+he+vaeaavvg+p++ikg+ ++a+v+lk+g+e+++ +l+k+l +vr+eigp+a+pd i++ lcl|FitnessBrowser__Caulo:CCNA_03696 526 LGTAEIESALVAHETVAEAAVVGYPHDIKGQGVYAYVTLKAGIEATD-ALRKDLVLWVRHEIGPFAAPDVIQW 597 ********************************************999.5************************ PP TIGR02188 585 veelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 ++ lPktRsGkimRR+lrkiae+e +lgd+stl+dpsvv++l + lcl|FitnessBrowser__Caulo:CCNA_03696 598 APGLPKTRSGKIMRRILRKIAENElGSLGDTSTLADPSVVDDLVK 642 *****************************************9876 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 9.36 // [ok]
This GapMind analysis is from Sep 17 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