Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO353_14365 AO353_14365 acetyl-CoA synthetase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >FitnessBrowser__pseudo3_N2E3:AO353_14365 Length = 645 Score = 822 bits (2123), Expect = 0.0 Identities = 399/640 (62%), Positives = 482/640 (75%), Gaps = 5/640 (0%) Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63 S +P V + + Y+ +Y+QS+ PD FW EQAKR LDW P+ +V+ T+ Sbjct: 5 STFPKADAVRQAAQLSQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTG 64 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123 +WFA LNVSYNC+DRHLA+RG+Q AIIWEGDDP+ES +ITY++LH VC+ AN Sbjct: 65 AA--QWFAGAQLNVSYNCIDRHLAQRGEQTAIIWEGDDPAESLHITYQKLHHCVCRLANV 122 Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183 L+ + V +GD V IYMPMIPEA AMLAC RIGA+HSVVFGGFSP++L RI+D + V Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPDSLRDRILDADCRTV 182 Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243 ITADEGVR GK +PLK NVD AL + ++ V+V + T + W + RD+WY ++ Sbjct: 183 ITADEGVRGGKYVPLKQNVDKALLS--CPAVSTVVVVEHTQIEVNWVEGRDLWYHQALRD 240 Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303 C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + VFDY+ GEV+WC Sbjct: 241 VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVFDYRDGEVFWC 300 Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363 TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP+ +R +VIDKH+V+I YTAPTA+RA Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPNSSRFWQVIDKHQVNIFYTAPTALRA 360 Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423 +M G ++ + +SLRLLGSVGEPINPEAWDWY+ VG++RCPIVDTWWQTETGG+++ Sbjct: 361 LMREGLEPLKDSSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIML 420 Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483 SPL A +KPG ATRP FGV P L+D G I GA G L I SWPGQ R++YGD R Sbjct: 421 SPLVSAQRIKPGCATRPMFGVQPVLLDEHGKEISGAGSGVLAIKSSWPGQIRSVYGDPQR 480 Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543 +DTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H +A Sbjct: 481 MIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIA 540 Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603 EAAVVG PHD+KGQGIY +VT G E S+AL+ EL V +EIG A PD+IQWAP LP Sbjct: 541 EAAVVGYPHDLKGQGIYAFVTPMNGIEPSDALKKELLAHVSQEIGSFAKPDLIQWAPALP 600 Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 KTRSGKIMRRILRKIA E D LGD STLADP VVA LI+ Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVAGLID 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: 1340 Number of extensions: 69 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 AO353_14365 AO353_14365 (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.14295.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 1025.2 0.0 0 1025.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 AO353_14365 acetyl-CoA synthetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 AO353_14365 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1025.0 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.99 Alignments for each domain: == domain 1 score: 1025.0 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrh 66 ++++y++ly+++ie+p+ fwa++ak+ l+w +p+++v++++ ++ ++Wf++++lnvsync+drh lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 20 SQDDYQRLYRQSIEQPDVFWAEQAKRFLDWSTPWQSVQHTNIKTgAAQWFAGAQLNVSYNCIDRH 84 5789**************************************9999******************* PP TIGR02188 67 vekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviam 131 +++r +++aiiwegd++ e s ++tY++l++ vcrlanvlk+ Gvkkgdrv+iY+pmipea++am lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 85 LAQRGEQTAIIWEGDDPAE-SLHITYQKLHHCVCRLANVLKSRGVKKGDRVCIYMPMIPEAAYAM 148 *****************96.********************************************* PP TIGR02188 132 lacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesve 196 lacaRiGavhsvvf+Gfs+++l++Ri da++++vitadeg+Rggk ++lk++vd+al +++ +v+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 149 LACARIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGKYVPLKQNVDKALLSCP-AVS 212 ************************************************************9.7** PP TIGR02188 197 kvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhtt 261 +v+vv++t+ ev+ w+egrD+w+++++++ +s++c+pe++d+edplfiLYtsGstGkPkGvlhtt lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 213 TVVVVEHTQIEVN-WVEGRDLWYHQALRD-VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTT 275 ***********66.**************7.*********************************** PP TIGR02188 262 gGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfw 326 gGyll+aa+t+kyvfd++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp++srfw lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 276 GGYLLQAAMTFKYVFDYRDGEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPSYPNSSRFW 340 ***************************************************************** PP TIGR02188 327 eviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcp 391 +vi+k++v+ifYtaPta+Ralm++g e +k ++ slr+lgsvGepinpeaw+Wy++ vG+++cp lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 341 QVIDKHQVNIFYTAPTALRALMREGLEPLKDSSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCP 405 ***************************************************************** PP TIGR02188 392 ivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwP 456 ivdtwWqtetGgi+++pl + a +kpg+at+P+fG++++++de+gke++ + gvL+ik++wP lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 406 IVDTWWQTETGGIMLSPLVS-AQRIKPGCATRPMFGVQPVLLDEHGKEISGAGS-GVLAIKSSWP 468 ********************.6***************************98777.8********* PP TIGR02188 457 smlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesal 521 +++r++ygd++r+++tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esal lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 469 GQIRSVYGDPQRMIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESAL 533 ***************************************************************** PP TIGR02188 522 vsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvve 586 v h+++aeaavvg+p+++kg+ i+afv+ ++g+e+++ +l+kel ++v++eig++akpd i++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 534 VLHDSIAEAAVVGYPHDLKGQGIYAFVTPMNGIEPSD-ALKKELLAHVSQEIGSFAKPDLIQWAP 597 *************************************.5************************** PP TIGR02188 587 elPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 +lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvv+ l++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_14365 598 ALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVAGLID 640 **************************************98875 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 8.67 // [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