Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Synpcc7942_1352 Synpcc7942_1352 acetyl-CoA synthetase
Query= SwissProt::P31638 (660 letters) >FitnessBrowser__SynE:Synpcc7942_1352 Length = 656 Score = 758 bits (1956), Expect = 0.0 Identities = 376/658 (57%), Positives = 480/658 (72%), Gaps = 12/658 (1%) Query: 4 IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63 IES++QE RVF P FAS A I + EAY+ALC +A D FW A + L W +P+ + Sbjct: 6 IESILQEKRVFPPSAEFASAARI-NPEAYEALCQKAAADPVAFWGELAAQELDWFEPWQQ 64 Query: 64 VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123 LD SN PF KWF G+LN S+NCLDR+L +K AI++E + G +TY +LH +V Sbjct: 65 TLDWSNPPFAKWFVGGKLNISHNCLDRHLTTWRKNKAAIIWEGEPGDSRTLTYAQLHREV 124 Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183 C+FAN LK+LGI+KGD V +YMPM E +AM ACAR+GA HSVVFGGFSA++L++RLVD Sbjct: 125 CQFANVLKSLGIQKGDVVGVYMPMIPEAAIAMLACARIGAVHSVVFGGFSAEALRDRLVD 184 Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243 A ++TAD R +PLK D AL C +V++V+V RT + GRD W Sbjct: 185 GQAKLVVTADGGWRKDAIVPLKDSVDQALEGNACPSVQHVLVVERTKQDIHMEPGRDHWW 244 Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303 ++ TC AEP+ +E LFVLYTSGSTGKPKGV H+TGGY L+A +T +WTFD++ Sbjct: 245 HELQQTVSATCPAEPMDSEDLLFVLYTSGSTGKPKGVVHTTGGYNLYAHITTQWTFDLQD 304 Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363 D++WCTAD+GW+TGH+YI YGPL+ GAT +++EG P N G FWD+I ++ V+ FYTA Sbjct: 305 TDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCFWDVIEKYGVTTFYTA 364 Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423 PTAIR+ IK E HP DLSSLRLLGTVGEPINPEAW+WY++ IG +RCPIVDT+ Sbjct: 365 PTAIRAFIKMGEQ----HPAARDLSSLRLLGTVGEPINPEAWIWYHRVIGGDRCPIVDTW 420 Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483 WQTETGGHMIT LPGA P PGS T P PGI+A +VD G VP+ GG LV++ PWP M Sbjct: 421 WQTETGGHMITSLPGAVPTKPGSATKPFPGILADVVDLDGRSVPDNEGGYLVIRHPWPGM 480 Query: 484 IRTIWGDPERFRKSYF---PEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540 +RT++GDP+RFR++Y+ P + G LY AGDG+ RD D GYF +MGR+DDV+NVSGHR+ Sbjct: 481 MRTVYGDPDRFRRTYWEHIPPQNGQYLYFAGDGARRDAD-GYFWVMGRVDDVINVSGHRL 539 Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600 GTMEIESALVS+P VAEAAVVGRPDD+ GE I AF+ L+ TG+E VK +L+ V Sbjct: 540 GTMEIESALVSHPAVAEAAVVGRPDDLKGEGIVAFITLESGIETGDELVK---DLKKHVA 596 Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658 +EIG IA+P +IRF + LPKTRSGKIMRRLLRSLA G+E++ DTSTLE+ ++L++L+Q Sbjct: 597 QEIGAIARPDEIRFSEALPKTRSGKIMRRLLRSLAAGQEVSGDTSTLEDRSVLDKLRQ 654 Lambda K H 0.319 0.136 0.422 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: 1408 Number of extensions: 67 Number of successful extensions: 6 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: 660 Length of database: 656 Length adjustment: 38 Effective length of query: 622 Effective length of database: 618 Effective search space: 384396 Effective search space used: 384396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
Align candidate Synpcc7942_1352 Synpcc7942_1352 (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.2315.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 1022.8 0.0 0 1022.5 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1352 Synpcc7942_1352 acetyl-CoA synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1352 Synpcc7942_1352 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1022.5 0.0 0 0 3 628 .. 29 654 .. 27 655 .. 0.98 Alignments for each domain: == domain 1 score: 1022.5 bits; conditional E-value: 0 TIGR02188 3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 + e+y++l+++a++dp +fw++la +el+w++p++++ld+s++p++kWf++g+ln+s nc+drh+++ r lcl|FitnessBrowser__SynE:Synpcc7942_1352 29 NPEAYEALCQKAAADPVAFWGELAAQELDWFEPWQQTLDWSNPPFAKWFVGGKLNISHNCLDRHLTTwR 97 6789***************************************************************** PP TIGR02188 71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139 k+k+aiiweg+ +g dsr+ltYa+l+revc++anvlk+lG++kgd v +Y+pmipea+iamlacaRiGa lcl|FitnessBrowser__SynE:Synpcc7942_1352 98 KNKAAIIWEGE-PG-DSRTLTYAQLHREVCQFANVLKSLGIQKGDVVGVYMPMIPEAAIAMLACARIGA 164 ***********.77.59**************************************************** PP TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgee 207 vhsvvf+Gfsaeal++R+vd +aklv+tad+g+R++ +++lk+ vd+ale + sv++vlvv+rt+++ lcl|FitnessBrowser__SynE:Synpcc7942_1352 165 VHSVVFGGFSAEALRDRLVDGQAKLVVTADGGWRKDAIVPLKDSVDQALEGNACpSVQHVLVVERTKQD 233 **************************************************99888************** PP TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276 ++ ++ grD+ww+el ++ +sa+c++e++dsed+lf+LYtsGstGkPkGv+httgGy l+a++t++++f lcl|FitnessBrowser__SynE:Synpcc7942_1352 234 IH-MEPGRDHWWHELQQT-VSATCPAEPMDSEDLLFVLYTSGSTGKPKGVVHTTGGYNLYAHITTQWTF 300 76.**************6.************************************************** PP TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345 d++d+d++wCtaDvGW+tGhsYivygPL+nGattl++eg+p+ +++++fw+vieky+vt+fYtaPtaiR lcl|FitnessBrowser__SynE:Synpcc7942_1352 301 DLQDTDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCFWDVIEKYGVTTFYTAPTAIR 369 ********************************************************************* PP TIGR02188 346 almklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvat 414 a++k+ge++++++dlsslr+lg+vGepinpeaw Wy++v+G ++cpivdtwWqtetGg++it+lpg a+ lcl|FitnessBrowser__SynE:Synpcc7942_1352 370 AFIKMGEQHPAARDLSSLRLLGTVGEPINPEAWIWYHRVIGGDRCPIVDTWWQTETGGHMITSLPG-AV 437 ******************************************************************.6* PP TIGR02188 415 elkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.... 479 ++kpgsat+P++Gi a+vvd +g++v ++e+ g+Lvi++pwP+m+rt+ygd++rf +tY+++++ lcl|FitnessBrowser__SynE:Synpcc7942_1352 438 PTKPGSATKPFPGILADVVDLDGRSVPDNEG-GYLVIRHPWPGMMRTVYGDPDRFRRTYWEHIPPqngq 505 ***************************9999.8*****************************9877888 PP TIGR02188 480 .lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivaf 547 lyf+GDgarrd+dGy+w++GRvDdvinvsGhrlgt+eiesalvsh+avaeaavvg+pd++kge ivaf lcl|FitnessBrowser__SynE:Synpcc7942_1352 506 yLYFAGDGARRDADGYFWVMGRVDDVINVSGHRLGTMEIESALVSHPAVAEAAVVGRPDDLKGEGIVAF 574 89******************************************************************* PP TIGR02188 548 vvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvst 616 ++l++g+e+ +e l k+lkk+v++eig+ia+pd+i++ e+lPktRsGkimRRllr++a+g+e+ gd+st lcl|FitnessBrowser__SynE:Synpcc7942_1352 575 ITLESGIETGDE-LVKDLKKHVAQEIGAIARPDEIRFSEALPKTRSGKIMRRLLRSLAAGQEVSGDTST 642 **********95.******************************************************** PP TIGR02188 617 ledpsvveelke 628 led+sv+++l++ lcl|FitnessBrowser__SynE:Synpcc7942_1352 643 LEDRSVLDKLRQ 654 ********9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (629 nodes) Target sequences: 1 (656 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: 00:00:00.05 # Mc/sec: 7.67 // [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