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 Pf1N1B4_4784 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4784 Length = 554 Score = 276 bits (706), Expect = 2e-78 Identities = 181/512 (35%), Positives = 277/512 (54%), Gaps = 27/512 (5%) Query: 76 AFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACL 135 A +W +G ++F +L + +FAN L A +++GD+V +LP+ E + A Sbjct: 45 ALFWEGRDGASATYTFSDLQDKAARFANFLL-AQGVKKGDKVAGLLPRNIELLITVFATW 103 Query: 136 RTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHS 195 R G V P T K I +RL SS A ++TD P + A A C IV+ Sbjct: 104 RIGAVYQPLFTAFGPKAIEHRLNSSGAAVVVTDAVNRPKL-AEVADCPT-----IVTVGG 157 Query: 196 REGWGNLK-------EMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGL 248 +G G ++ E+ Y+S+ + T D + + FTSGTTGP K + + + Sbjct: 158 PKGQGIVRGDFSFWAELANYSSECEPVLLTGEDPFL-LMFTSGTTGPSKALSVPLKAI-V 215 Query: 249 GLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQT 308 R +DL D WN +D GWA + V P G + + P F S + Sbjct: 216 AFQSYTRDAVDLRPEDAFWNVADPGWAYGIYFGVTGPMAMGHPITFYDGP-FTLESTCRV 274 Query: 309 LSKFPITVFCSAPTAYRMLVQ--NDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDI 366 ++K+ IT +PTAYR+L+ ++ + L+ SAGEP+NPEV+ + G+ I Sbjct: 275 INKYGITNLTGSPTAYRLLIAGGDEFARSIKGKLRIVSSAGEPLNPEVIRWFADNLGVVI 334 Query: 367 YEGYGQTETVLICGNFKGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVL 424 ++ YGQTE ++ N G+ + G+ G SP + +LD+ L GQ G +A+ Sbjct: 335 HDHYGQTELGMVLCNHHGLDHPVHVGAAGFASPGHRIVVLDDEYKELGVGQPGILAID-R 393 Query: 425 PERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGP 484 + P F Y P+K G++Y++GD + DG FV RSDD+I +SGYR+GP Sbjct: 394 TQSPMCWFGGYEGAPTKA---FVGNYYLSGDTVEWNPDGSISFVGRSDDVITTSGYRVGP 450 Query: 485 FEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTT 544 F+VESALIEHP++ E+AV+ PDP R E+VKAF+VL+P Y++ + L +E+++HV+K Sbjct: 451 FDVESALIEHPAVVEAAVIGKPDPERTELVKAFVVLSPQYRA--EPALAEELRQHVRKRL 508 Query: 545 APYKYPRKVEFIEELPKTVSGKVKRNELRKKE 576 A + YPR++EF+ ELPKT SGK++R LR +E Sbjct: 509 AAHAYPREIEFVSELPKTPSGKLQRFILRNQE 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: 778 Number of extensions: 54 Number of successful extensions: 9 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: 554 Length adjustment: 36 Effective length of query: 544 Effective length of database: 518 Effective search space: 281792 Effective search space used: 281792 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