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 BPHYT_RS28035 BPHYT_RS28035 AMP-dependent synthetase
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__BFirm:BPHYT_RS28035 Length = 563 Score = 353 bits (906), Expect = e-101 Identities = 205/553 (37%), Positives = 303/553 (54%), Gaps = 22/553 (3%) Query: 25 DYRTATPQNFSNYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNG 84 D R ++ ++Y+ ++F FN+A D D + NPA W +D Sbjct: 9 DARDLLLRHRTDYDRAYREFAWPPLGEFNWALDYFDV------IARDNDNPALWIVDDPA 62 Query: 85 EE-LRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIP 143 + LR S+ ++ S + AN L + RGDR++++LP E W +A ++ G +++P Sbjct: 63 TDGLRLSYAQMSERSARMANFL-RGVGVGRGDRLLLMLPNRVELWDVMLAAMKLGAIVLP 121 Query: 144 GTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNLK 203 TTQL+ D+ R+Q A + D DA+ A L R+GW +L Sbjct: 122 ATTQLSADDVRDRVQIGGANFAVVDSAELAKFDALEAPLTRLSVGA-----PRDGWIDLA 176 Query: 204 EMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIAS 263 + T + M +YFTSGTT PK++ HTH S+ +G ++ +W+ L + Sbjct: 177 AAYDASPQFTPEGITLATDPMLLYFTSGTTSKPKLVEHTHQSYPVG-HLSTMYWIGLQPN 235 Query: 264 DVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAPTA 323 D+ WN S GWAK AWS F+PW ACVF RF L L +F IT C+ PT Sbjct: 236 DIHWNISSPGWAKHAWSCFFAPWNAQACVFVFNFARFVPKDTLNALVRFNITTLCAPPTV 295 Query: 324 YRMLVQNDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFK 383 +RMLVQ +S Y L+ V AGEP+NPEV+E+ + G+ I +GYGQTET GN Sbjct: 296 WRMLVQEHLSDYPVK-LREIVGAGEPLNPEVIERVKHAWGITIRDGYGQTETTCQIGNSP 354 Query: 384 GMKIKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTA 443 G + GSMG+P P + ++++D + P EG+I+L L +RP GL T Y +N TA Sbjct: 355 GQPVVAGSMGRPLPGYTIELIDADDQ---PVTEGEISLP-LAQRPLGLMTGYANNAKATA 410 Query: 444 STLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVV 503 +R FY T D +DGY+ +V R+DD+ SS YR+ PFE+ES LIEH +I E+AVV Sbjct: 411 QAMRNGFYRTSDVALRRDDGYYVYVGRADDVFKSSDYRLSPFELESVLIEHEAIGEAAVV 470 Query: 504 SSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTV 563 S D +R V KAF+ + Y++ +L + + ++ APYK R+++F ELPKT+ Sbjct: 471 PSADALRLSVPKAFVTVRQGYEA--GPELARAVFAFSREKLAPYKRIRRLQF-SELPKTI 527 Query: 564 SGKVKRNELRKKE 576 SGK++R ELR++E Sbjct: 528 SGKIRRVELRRRE 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: 849 Number of extensions: 49 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: 563 Length adjustment: 36 Effective length of query: 544 Effective length of database: 527 Effective search space: 286688 Effective search space used: 286688 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