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 353281 BT3755 acetyl-coenzyme A synthetase (NCBI ptt file)
Query= SwissProt::Q53FZ2 (586 letters) >FitnessBrowser__Btheta:353281 Length = 551 Score = 436 bits (1121), Expect = e-126 Identities = 220/552 (39%), Positives = 330/552 (59%), Gaps = 16/552 (2%) Query: 39 NFSNYESMKQDFKLGIPEYFNFAKDVLDQWTDKEKAGKKPSNPAFWWINRNGEEMRWSFE 98 +F++ E ++ K+ +PE FNF DV+D W A ++P A W N GE ++SF Sbjct: 10 SFASQEDFIKNLKINVPENFNFGYDVVDAW-----AAEQPDKNALLWTNDQGESRQFSFA 64 Query: 99 ELGSLSRKFANILSEACSLQRGDRVILILPRVPEWWLANVACLRTGTVLIPGTTQLTQKD 158 ++ + A+ ++ + RGD V+LIL R E+W + +A + G +IP T LT+KD Sbjct: 65 DMKRYTDMTASYF-QSLGIGRGDMVMLILKRRYEFWYSTIALHKLGATVIPATHLLTKKD 123 Query: 159 ILYRLQSSKANCIIT--NDVLAPAVDAVASKCENLHSKLIVSENSREGWGNLKELMKHAS 216 I+YR ++ I+ ++ + +C ++ + V EG+ + + + +A+ Sbjct: 124 IIYRCNAADIKMIVAAGEGIILQHIKDALPECPSVEKLVSVGPEVPEGFEDFHQGIDNAA 183 Query: 217 DSHTCVKTKH----NEIMAIFFTSGTSGYPKMTAHTHSSFGLGLSVNGRFWLDLTPSDVM 272 ++ +H ++I ++FTSGT+G PKM AH + + LG V G FW +L + + Sbjct: 184 PF---IRPRHANTNDDISLMYFTSGTTGEPKMVAHDFT-YPLGHIVTGSFWHNLDENSLH 239 Query: 273 WNTSDTGWAKSAWSSVFSPWIQGACVFTHHLPRFEPTSILQTLSKYPITVFCSAPTVYRM 332 +DTGW K+ W ++ WI GA +F + +F P +IL+ + +Y +T C+ PT++R Sbjct: 240 LTIADTGWGKAVWGKLYGQWIAGANIFVYDHEKFTPAAILEKIQEYQVTSLCAPPTIFRF 299 Query: 333 LVQNDITSYKFKSLKHCVSAGEPITPDVTEKWRNKTGLDIYEGYGQTETVLICGNFKGMK 392 L+ D+T Y SL++C AGE + P V E ++ TG+ + EG+GQTET L M+ Sbjct: 300 LIHEDLTKYDLSSLRYCTIAGEALNPAVFETFKKLTGIKLMEGFGQTETTLTVATMPWME 359 Query: 393 IKPGSMGKPSPAFDVKIVDVNGNVLPPGQEGDIGIQVLPNRPFGLFTHYVDNPSKTASTL 452 KPGSMG P+P +DV ++D G + G++G I I+ +P GLF Y + +T Sbjct: 360 PKPGSMGLPNPQYDVDLIDSEGRSVEAGEQGQIVIRTSKGKPLGLFKEYYRDAERTHEAW 419 Query: 453 RGNFYITGDRGYMDKDGYFWFVARADDVILSSGYRIGPFEVENALNEHPSVAESAVVSSP 512 Y TGD + D+DGY WFV RADDVI SSGYRIGPFEVE+AL HP+V E A+ P Sbjct: 420 HDGIYYTGDVAWKDEDGYLWFVGRADDVIKSSGYRIGPFEVESALMTHPAVIECAITGVP 479 Query: 513 DPIRGEVVKAFVVLNPDYKSHDQEQLIKEIQEHVKKTTAPYKYPRKVEFIQELPKTISGK 572 D IRG+VVKA +VL+ DYK+ E+LIKE+Q HVKK TAPYKYPR +EF+ ELPKTISGK Sbjct: 480 DEIRGQVVKATIVLSKDYKARAGEELIKELQNHVKKVTAPYKYPRVIEFVDELPKTISGK 539 Query: 573 TKRNELRKKEWK 584 +R E+R+ + K Sbjct: 540 IRRVEIRENDEK 551 Lambda K H 0.318 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: 832 Number of extensions: 39 Number of successful extensions: 5 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: 586 Length of database: 551 Length adjustment: 36 Effective length of query: 550 Effective length of database: 515 Effective search space: 283250 Effective search space used: 283250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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