Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate GFF2136 PS417_10895 AMP-dependent synthetase
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__WCS417:GFF2136 Length = 566 Score = 390 bits (1002), Expect = e-113 Identities = 214/546 (39%), Positives = 317/546 (58%), Gaps = 26/546 (4%) Query: 35 SNYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFEEL 94 ++Y + +DF+ FN+A D D A A W ++ +G E R+SF++L Sbjct: 17 TDYATAVRDFRWPQLGEFNWALDYFDAMAEGNPAD------ALWIVEEDGSEQRYSFQQL 70 Query: 95 GLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDIL 154 S + AN L A + RGDRV+++L W +A + G V+IP T L D+ Sbjct: 71 AARSNQVANHL-RALGVNRGDRVLLMLGNDVALWDTMLAAFKLGAVVIPATALLNPDDLR 129 Query: 155 YRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNLKEMMKYASDSHT 214 R++ + + ++ + +A C S++ V + GW +Y Sbjct: 130 DRIERGQVRHVVVGEAHVHKFAGLAQGC----SRICVGS-APAGWVAHNAAFEYPEQFEA 184 Query: 215 CVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIASDVMWNTSDTGW 274 T + M +YFTSGTT PKM+ H+H S+ +G ++ +W+ L D+ N S GW Sbjct: 185 QGRTLATDPMLLYFTSGTTSKPKMVLHSHQSYPVG-HLSTMYWIGLQPGDLHLNISSPGW 243 Query: 275 AKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLVQNDMSS 334 AK AWS +F+PW GAC+F H + RF + ++L L ++ +T C+ PT +RML+Q D++S Sbjct: 244 AKHAWSCLFAPWNAGACIFIHNVARFSAPALLSALERYGVTSLCAPPTVWRMLIQEDLAS 303 Query: 335 YKFN-SLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKGMKIKPGSMG 393 Y+ SL+ V AGEP+NPE++EQ ++ GL + +G+GQ+ET + GN G +KPGSMG Sbjct: 304 YRPRLSLRELVGAGEPLNPEIIEQIQQAWGLPLRDGFGQSETTALVGNTPGQLLKPGSMG 363 Query: 394 KPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYIT 453 +P P + V +LD +G PG EG++AL L RP GL Y D+P KTA +R +Y T Sbjct: 364 RPLPGYQVALLDPDGI---PGNEGEVALP-LDVRPLGLMLCYEDSPEKTAEVMRDGYYRT 419 Query: 454 GDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEV 513 GD +D DGY FV R+DD+ +S YRI PFE+ESALIEHP++ E AVV SPDP+R V Sbjct: 420 GDTAQIDADGYITFVGRADDVFKASDYRISPFELESALIEHPAVMEVAVVPSPDPLRLAV 479 Query: 514 VKAFIVLNPDYKSHDQ---EQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRN 570 KAF++L +HD+ L + I ++ APYK R++EF+ ELPKT+SGK++R Sbjct: 480 PKAFLIL-----AHDEPGSAALAQHILAFAREHLAPYKRVRRIEFVTELPKTISGKIRRV 534 Query: 571 ELRKKE 576 ELR+ E Sbjct: 535 ELRQME 540 Lambda K H 0.319 0.134 0.416 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: 876 Number of extensions: 48 Number of successful extensions: 7 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: 580 Length of database: 566 Length adjustment: 36 Effective length of query: 544 Effective length of database: 530 Effective search space: 288320 Effective search space used: 288320 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: 53 (25.0 bits)
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