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.12109.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 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 AO356_16045 acetyl-CoA synthetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 AO356_16045 acetyl-CoA synthetase # 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.kvkWfedgelnvsyncvd 64 +++eyk+ly+e+ie+p++fwa++a++ l+w++p+++v++ +l++ +++Wf++g+lnvs+nc+d lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 20 SQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQRYDLKNgDATWFAGGKLNVSANCID 82 5799*************************************9999****************** PP TIGR02188 65 rhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipea 127 rh+ +r ++vaiiwegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipea lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 83 RHLDTRGEQVAIIWEGDNPAE-SAQITYKKLHNHVCRLANVLKSRGVKKGDRVCIYMPMIPEA 144 *****************9996.***************************************** PP TIGR02188 128 viamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealek 190 ++amlac+RiGavhsvvf+Gfs+++l++Ri da++++vitadeg+Rgg+ i+lk++vd+ale+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 145 AYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGRFIPLKRNVDKALES 207 *************************************************************** PP TIGR02188 191 aeesvekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGk 253 ++ +v++vlvv+rt+ ev w+egrD+w+++++++ s++c+pe++d+edplfiLYtsGstGk lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 208 CP-NVSTVLVVERTQGEVG-WVEGRDLWYHQAMHD-MSDDCPPEPMDAEDPLFILYTSGSTGK 267 *9.6*************76.**************7.*************************** PP TIGR02188 254 PkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegv 316 PkGvlhttgGyll+aa+t+kyv d++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegv lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 268 PKGVLHTTGGYLLQAAMTFKYVLDYRDNEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGV 330 *************************************************************** PP TIGR02188 317 ptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeawe 379 p++p++srfw+vi+k++v+ifYtaPta+Ralm++g +++++++slr+lgsvGepinpeawe lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 331 PSHPSSSRFWQVIDKHQVNIFYTAPTALRALMREGAGPLQETSRKSLRLLGSVGEPINPEAWE 393 *************************************************************** PP TIGR02188 380 WyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkevee 442 Wy++vvG+++cpivdtwWqtetGgi+++pl + a lkpg+at+P+fG++++++de gke++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 394 WYFNVVGEQRCPIVDTWWQTETGGIMLSPLVS-APRLKPGCATRPMFGVQPVLLDEVGKEISG 455 ********************************.69**************************98 PP TIGR02188 443 eeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvi 505 + gvL+ik++wP+++r++ygd++r+v+tYfk ++g+yftGDgarrd+dG++wi+GR+Ddvi lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 456 AGS-GVLAIKSSWPGQIRSVYGDHQRMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVI 517 777.8********************************************************** PP TIGR02188 506 nvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkkl 568 nvsGhr+gtae+esalv h+++aeaavvg+p+++kg+ i+afv+ ++gve+++e l+kel ++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 518 NVSGHRIGTAEVESALVLHDNIAEAAVVGYPHDLKGQGIYAFVTPMNGVEANDE-LKKELLAH 579 ****************************************************95.******** PP TIGR02188 569 vrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 v+keig++akp+ i+++++lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvve l++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16045 580 VSKEIGSFAKPELIQWAPALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVEGLID 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 8.16 // [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