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 8499218 DvMF_0003 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__Miya:8499218 Length = 557 Score = 444 bits (1143), Expect = e-129 Identities = 226/548 (41%), Positives = 335/548 (61%), Gaps = 16/548 (2%) Query: 36 NYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFEELG 95 +Y+ F+I+ P+ FNFA DVLD + +++ +D G ++F + Sbjct: 11 DYKEFCATFRIDAPDTFNFAFDVLDPIAAADPGRLCIAH-----VDDAGVRRDYTFAWMA 65 Query: 96 LLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDILY 155 S K AN L +++GDRVM++L + E+W++ +A R G V IP QLT KDI++ Sbjct: 66 EASAKLANAL-RLRGIRKGDRVMLVLYRRIEFWVSMLALHRLGAVAIPAPAQLTPKDIVF 124 Query: 156 RLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSR-EGWGNLKEMMKYASDSHT 214 R++ +K +C+I D ++ V+A C L + V + GW + + A Sbjct: 125 RVERAKTRCVIVDHSITERVEAARPDCPGLAVCVQVGGDALPRGWVDYDTIFTPAEARFP 184 Query: 215 CVDTK-----HDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIASDVMWNT 269 ++ ++ + I+F+SGTTG PKM+ H H+ + LG + G +W DL+ D+ Sbjct: 185 RPESPLEFAGGEDPLLIFFSSGTTGMPKMVEHVHT-YPLGHLLTGMYWHDLVPGDLHLTL 243 Query: 270 SDTGWAKSAWSSVFSPWTQGACVFAH-YLPRFESTSILQTLSKFPITVFCSAPTAYRMLV 328 +DTGW K+ W + W GA VF + + +FE ++L L+ +T FC+ PT YR LV Sbjct: 244 ADTGWGKAVWGKFYGQWMAGASVFVYDFRGKFEPAALLDVLAAHAVTTFCAPPTVYRFLV 303 Query: 329 QNDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKGMKIK 388 + D+S+Y + L+HC +AGE +N V W+ TGL+I+EGYGQTET L M K Sbjct: 304 RQDLSAYDLSKLRHCTTAGELLNDSVFHDWKAATGLEIHEGYGQTETTLQIATLPCMTPK 363 Query: 389 PGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRG 448 GS+G+P P +DV + D G PPG+EG+I ++V P GLF Y++ P KTAS + G Sbjct: 364 AGSIGRPMPGWDVVLQDAAGNICPPGEEGEICVRVAEGLPVGLFRGYLEEPEKTASVMFG 423 Query: 449 SFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDP 508 +Y TGD+ +MDEDGY+WF+ R DD+I SSGYRIGPFEVESAL+ HP++ E+AV PDP Sbjct: 424 GYYHTGDKAWMDEDGYYWFLGRVDDLIKSSGYRIGPFEVESALVAHPAVVEAAVTGVPDP 483 Query: 509 IRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVK 568 +RG+ VKA +VL Y + D L KE+Q+HVKK TAPYKYPR ++++ ELPKT+SGK+K Sbjct: 484 LRGQAVKATVVLAAGYTASD--ALTKELQDHVKKVTAPYKYPRIIDYVAELPKTISGKIK 541 Query: 569 RNELRKKE 576 R E+R+++ Sbjct: 542 RAEIRERD 549 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: 892 Number of extensions: 29 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: 580 Length of database: 557 Length adjustment: 36 Effective length of query: 544 Effective length of database: 521 Effective search space: 283424 Effective search space used: 283424 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