Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO356_16045 AO356_16045 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_16045 Length = 645 Score = 820 bits (2119), Expect = 0.0 Identities = 398/640 (62%), Positives = 479/640 (74%), Gaps = 5/640 (0%) Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63 S YP V + + YK +Y++S+ +P FW EQA R LDW+ P+ TV++ +D Sbjct: 5 SQYPHADAVRRAAQLSQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQR--YDLK 62 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123 + D WFA G LNVS NC+DRHL RG+Q+AIIWEGD+P+ES ITY++LH VC+ AN Sbjct: 63 NGDATWFAGGKLNVSANCIDRHLDTRGEQVAIIWEGDNPAESAQITYKKLHNHVCRLANV 122 Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183 L+ + V +GD V IYMPMIPEA AMLACTRIGA+HSVVFGGFSP++L RI+D + V Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTV 182 Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243 ITADEGVR G+ IPLK NVD AL + ++ V+V +RT G + W + RD+WY M Sbjct: 183 ITADEGVRGGRFIPLKRNVDKALES--CPNVSTVLVVERTQGEVGWVEGRDLWYHQAMHD 240 Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303 C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ EV+WC Sbjct: 241 MSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDNEVFWC 300 Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363 TADVGWVTGHSYIVYGPLANGATTL+FEGVP++P +R +VIDKH+V+I YTAPTA+RA Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSHPSSSRFWQVIDKHQVNIFYTAPTALRA 360 Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423 +M G ++ SLRLLGSVGEPINPEAW+WY+ VG++RCPIVDTWWQTETGG+++ Sbjct: 361 LMREGAGPLQETSRKSLRLLGSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGGIML 420 Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483 SPL A LKPG ATRP FGV P L+D +G I GA G L I SWPGQ R++YGDH R Sbjct: 421 SPLVSAPRLKPGCATRPMFGVQPVLLDEVGKEISGAGSGVLAIKSSWPGQIRSVYGDHQR 480 Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543 VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H +A Sbjct: 481 MVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDNIA 540 Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603 EAAVVG PHD+KGQGIY +VT G E ++ L+ EL V KEIG A P++IQWAP LP Sbjct: 541 EAAVVGYPHDLKGQGIYAFVTPMNGVEANDELKKELLAHVSKEIGSFAKPELIQWAPALP 600 Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 KTRSGKIMRRILRKIA E D LGD STLADP VV LI+ Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVEGLID 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: 1350 Number of extensions: 72 Number of successful extensions: 3 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: 645 Length adjustment: 38 Effective length of query: 613 Effective length of database: 607 Effective search space: 372091 Effective search space used: 372091 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 AO356_16045 AO356_16045 (acetyl-CoA 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.2012303.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 1027.5 0.0 0 1027.3 0.0 1.0 1 FitnessBrowser__pseudo5_N2C3_1:AO356_16045 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo5_N2C3_1:AO356_16045 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1027.3 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.99 Alignments for each domain: == domain 1 score: 1027.3 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhve 68 +++eyk+ly+e+ie+p++fwa++a++ l+w++p+++v++ +l++ +++Wf++g+lnvs+nc+drh+ FitnessBrowser__pseudo5_N2C3_1:AO356_16045 20 SQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQRYDLKNgDATWFAGGKLNVSANCIDRHLD 86 5799*************************************9999********************** PP TIGR02188 69 krkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlaca 135 +r ++vaiiwegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipea++amlac+ FitnessBrowser__pseudo5_N2C3_1:AO356_16045 87 TRGEQVAIIWEGDNPAE-SAQITYKKLHNHVCRLANVLKSRGVKKGDRVCIYMPMIPEAAYAMLACT 152 *************9996.************************************************* PP TIGR02188 136 RiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvk 202 RiGavhsvvf+Gfs+++l++Ri da++++vitadeg+Rgg+ i+lk++vd+ale+++ +v++vlvv+ FitnessBrowser__pseudo5_N2C3_1:AO356_16045 153 RIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGRFIPLKRNVDKALESCP-NVSTVLVVE 218 ********************************************************9.6******** PP TIGR02188 203 rtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaa 269 rt+ ev w+egrD+w+++++++ s++c+pe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa FitnessBrowser__pseudo5_N2C3_1:AO356_16045 219 RTQGEVG-WVEGRDLWYHQAMHD-MSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAA 283 *****76.**************7.******************************************* PP TIGR02188 270 ltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvti 336 +t+kyv d++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp++p++srfw+vi+k++v+i FitnessBrowser__pseudo5_N2C3_1:AO356_16045 284 MTFKYVLDYRDNEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPSHPSSSRFWQVIDKHQVNI 350 ******************************************************************* PP TIGR02188 337 fYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGg 403 fYtaPta+Ralm++g +++++++slr+lgsvGepinpeaweWy++vvG+++cpivdtwWqtetGg FitnessBrowser__pseudo5_N2C3_1:AO356_16045 351 FYTAPTALRALMREGAGPLQETSRKSLRLLGSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGG 417 ******************************************************************* PP TIGR02188 404 ilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfv 470 i+++pl + a lkpg+at+P+fG++++++de gke++ + gvL+ik++wP+++r++ygd++r+v FitnessBrowser__pseudo5_N2C3_1:AO356_16045 418 IMLSPLVS-APRLKPGCATRPMFGVQPVLLDEVGKEISGAGS-GVLAIKSSWPGQIRSVYGDHQRMV 482 ********.69**************************98777.8*********************** PP TIGR02188 471 etYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpd 537 +tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esalv h+++aeaavvg+p+ FitnessBrowser__pseudo5_N2C3_1:AO356_16045 483 DTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDNIAEAAVVGYPH 549 ******************************************************************* PP TIGR02188 538 eikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrki 604 ++kg+ i+afv+ ++gve+++e l+kel ++v+keig++akp+ i+++++lPktRsGkimRR+lrki FitnessBrowser__pseudo5_N2C3_1:AO356_16045 550 DLKGQGIYAFVTPMNGVEANDE-LKKELLAHVSKEIGSFAKPELIQWAPALPKTRSGKIMRRILRKI 615 ********************95.******************************************** PP TIGR02188 605 aege.ellgdvstledpsvveelke 628 a +e ++lgd+stl+dpsvve l++ FitnessBrowser__pseudo5_N2C3_1:AO356_16045 616 ACNElDSLGDTSTLADPSVVEGLID 640 *********************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (645 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: 00:00:00.02 # Mc/sec: 15.97 // [ok]
This GapMind analysis is from Apr 09 2024. 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