Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_100847194.1 C0J26_RS06710 acetate--CoA ligase
Query= reanno::pseudo5_N2C3_1:AO356_18695 (651 letters) >NCBI__GCF_003031005.1:WP_100847194.1 Length = 645 Score = 823 bits (2126), Expect = 0.0 Identities = 398/640 (62%), Positives = 480/640 (75%), Gaps = 5/640 (0%) Query: 5 SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63 S +P V + + Y+ +Y++S+ +P FW EQA R LDW P+ TV++ +D Sbjct: 5 STFPKADAVRRAAQLSQDDYQRLYRESIEHPSAFWAEQALRFLDWSTPWQTVQR--YDLK 62 Query: 64 HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123 + WFA G LNVSYNC+DRHL +RGDQ A++WEGDDP+ES ITY++LH VC+ AN Sbjct: 63 AGEAAWFAGGKLNVSYNCIDRHLEQRGDQTALLWEGDDPAESAQITYKKLHHHVCRLANV 122 Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183 L+ + V +GD V IYMPMIPEAV AMLAC RIGAIHSVVFGGFSP++L RI+D + V Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAVYAMLACARIGAIHSVVFGGFSPDSLRDRILDADCRTV 182 Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243 ITADEGVR GK +PLK NVD AL N ++ V+V +RT GN+ W + RD+WY ++ Sbjct: 183 ITADEGVRGGKFVPLKQNVDKALQN--CPAVSTVVVVERTQGNVDWVEGRDLWYHQAVRD 240 Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303 C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ GEV+WC Sbjct: 241 VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWC 300 Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363 TADVGWVTGHSYIVYGPLANGATTL+FEGVP+YP+ +R +VIDKHKV+I YTAPTA+RA Sbjct: 301 TADVGWVTGHSYIVYGPLANGATTLMFEGVPSYPNSSRFWQVIDKHKVNIFYTAPTALRA 360 Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423 +M G ++ SLRLLGSVGEPINPEAW+WY+ VG++RCPIVDTWWQTETGG+++ Sbjct: 361 LMREGAEPLKETSRQSLRLLGSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGGIML 420 Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483 SPL A +KPG AT+P FGV P L+D G I+GA G L I SWP Q R++YGD R Sbjct: 421 SPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEIKGAGSGVLAIKSSWPAQIRSVYGDPQR 480 Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543 VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H +A Sbjct: 481 MVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSIA 540 Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603 EAAVVG PHD+KGQGIY +VT G E ++ L+ EL V KEIG A PD+IQWAP LP Sbjct: 541 EAAVVGYPHDVKGQGIYAFVTPMNGTEPNDELKKELLAHVSKEIGSFAKPDLIQWAPALP 600 Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643 KTRSGKIMRRILRKIA E D LGD STLADP VV LI+ Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVQGLID 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: 1352 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 WP_100847194.1 C0J26_RS06710 (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.4134534.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 1035.1 0.0 0 1034.9 0.0 1.0 1 NCBI__GCF_003031005.1:WP_100847194.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003031005.1:WP_100847194.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1034.9 0.0 0 0 3 628 .. 20 640 .. 18 641 .. 0.99 Alignments for each domain: == domain 1 score: 1034.9 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkv 74 ++++y++ly+e+ie+p++fwa++a + l+w +p+++v++ +l++ +++Wf++g+lnvsync+drh+e+r d++ NCBI__GCF_003031005.1:WP_100847194.1 20 SQDDYQRLYRESIEHPSAFWAEQALRFLDWSTPWQTVQRYDLKAgEAAWFAGGKLNVSYNCIDRHLEQRGDQT 92 5789*************************************9999**************************** PP TIGR02188 75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaG 147 a+ wegd++ e s ++tY++l+++vcrlanvlk+ Gvkkgdrv+iY+pmipeav+amlacaRiGa+hsvvf+G NCBI__GCF_003031005.1:WP_100847194.1 93 ALLWEGDDPAE-SAQITYKKLHHHVCRLANVLKSRGVKKGDRVCIYMPMIPEAVYAMLACARIGAIHSVVFGG 164 *********96.************************************************************* PP TIGR02188 148 fsaealaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwe 220 fs+++l++Ri da++++vitadeg+Rggk ++lk++vd+al++++ +v++v+vv+rt+ +v w+egrD+w++ NCBI__GCF_003031005.1:WP_100847194.1 165 FSPDSLRDRILDADCRTVITADEGVRGGKFVPLKQNVDKALQNCP-AVSTVVVVERTQGNVD-WVEGRDLWYH 235 ********************************************9.7*************66.********** PP TIGR02188 221 elvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWv 293 ++v++ +s++c+pe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyv d++d+++fwCtaDvGWv NCBI__GCF_003031005.1:WP_100847194.1 236 QAVRD-VSDDCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWCTADVGWV 307 ****7.******************************************************************* PP TIGR02188 294 tGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvl 366 tGhsYivygPLanGattl+fegvp+yp++srfw+vi+k+kv+ifYtaPta+Ralm++g e +k+++++slr+l NCBI__GCF_003031005.1:WP_100847194.1 308 TGHSYIVYGPLANGATTLMFEGVPSYPNSSRFWQVIDKHKVNIFYTAPTALRALMREGAEPLKETSRQSLRLL 380 ************************************************************************* PP TIGR02188 367 gsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439 gsvGepinpeaweWy++vvG+++cpivdtwWqtetGgi+++pl + a +kpg+at+P+fG++++++de+gke NCBI__GCF_003031005.1:WP_100847194.1 381 GSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGGIMLSPLVS-AQRIKPGCATQPMFGVQPVLLDEQGKE 452 *********************************************.6************************** PP TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrl 512 ++ + gvL+ik++wP+++r++ygd++r+v+tYfk ++g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+ NCBI__GCF_003031005.1:WP_100847194.1 453 IKGAGS-GVLAIKSSWPAQIRSVYGDPQRMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRI 524 *98777.8***************************************************************** PP TIGR02188 513 gtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvv 585 gtae+esalv h+++aeaavvg+p+++kg+ i+afv+ ++g+e+++e l+kel ++v+keig++akpd i+++ NCBI__GCF_003031005.1:WP_100847194.1 525 GTAEVESALVLHDSIAEAAVVGYPHDVKGQGIYAFVTPMNGTEPNDE-LKKELLAHVSKEIGSFAKPDLIQWA 596 **********************************************5.************************* PP TIGR02188 586 eelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628 ++lPktRsGkimRR+lrkia +e ++lgd+stl+dpsvv+ l++ NCBI__GCF_003031005.1:WP_100847194.1 597 PALPKTRSGKIMRRILRKIACNElDSLGDTSTLADPSVVQGLID 640 ***************************************99875 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 40.97 // [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