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 WP_248635324.1 G491_RS0106115 AMP-binding protein
Query= SwissProt::Q53FZ2 (586 letters) >NCBI__GCF_000429905.1:WP_248635324.1 Length = 544 Score = 612 bits (1579), Expect = e-180 Identities = 289/545 (53%), Positives = 386/545 (70%), Gaps = 10/545 (1%) Query: 39 NFSNYESMKQDFKLGIPEYFNFAKDVLDQWTDKEKAGKKPSNPAFWWINRNGEEMRWSFE 98 N ++Y+ +FK +PEYFNFA DV+D+W + P A W++ +G E+R +F Sbjct: 7 NMTDYQKEYDEFKWEVPEYFNFAGDVIDKWA------QDPEKLAMLWVDDDGNEVRKTFA 60 Query: 99 ELGSLSRKFANILSEACSLQRGDRVILILPRVPEWWLANVACLRTGTVLIPGTTQLTQKD 158 +L + S+K AN+L+ + + +GD V+++LPR EWW AC+R G +L PGTTQLT KD Sbjct: 61 QLSAASKKLANLLT-SLGVGQGDVVMVVLPRNIEWWEVFTACIRMGALLAPGTTQLTSKD 119 Query: 159 ILYRLQSSKANCIITNDVLAPAVDAVASKCENLHSKLIVSENSREGWGNLKELMKHASDS 218 + +R ++A+CIITN LA D VA +C + SK+I++E RE W E ++ ASD Sbjct: 120 LQFRANKAEASCIITNPELAEKFDKVADECPTVKSKIIITE-PREDWTFYTEAVEAASDQ 178 Query: 219 HTCVKTKHNEIMAIFFTSGTSGYPKMTAHTHSSFGLGLSVNGRFWLDLTPSDVMWNTSDT 278 KTK ++ ++FTSGT G+PKM HTH+S+ +G V G++WLDL P D+ WN SDT Sbjct: 179 FETAKTKSSDNCLVYFTSGTVGFPKMALHTHASYPIGHQVTGKYWLDLKPEDMHWNVSDT 238 Query: 279 GWAKSAWSSVFSPWIQGACVFTHHLPRFEPTSILQTLSKYPITVFCSAPTVYRMLVQNDI 338 GWAK+AWSS F PW GA F HH RF+P L+ L++YPIT C APT+YRMLV D+ Sbjct: 239 GWAKAAWSSYFGPWNMGAAQFIHHTDRFDPIKTLELLAQYPITTMCGAPTIYRMLVLQDL 298 Query: 339 TSYKFKSLKHCVSAGEPITPDVTEKWRNKTGLDIYEGYGQTETVLICGNFKGMKIKPGSM 398 +KF +L+HCV AGEP+ P++ E W+ TG I +GYGQTETVL+ G+F ++ + GSM Sbjct: 299 AKFKFPTLRHCVGAGEPLNPEIIEVWKKATGCVIRDGYGQTETVLLAGSFPCIEPRFGSM 358 Query: 399 GKPSPAFDVKIVDVNGNVLPPGQEGDIGIQVLPNRPFGLFTHYVDNPSKTASTLRGNFYI 458 G+P+P ++K++D + N LPP EGDI I+V PNRP GLF Y P +TAS RG++Y+ Sbjct: 359 GRPTPGIELKVIDEDCNELPPNTEGDIAIKVKPNRPVGLFKEYWKEPDRTASVYRGDYYL 418 Query: 459 TGDRGYMDKDGYFWFVARADDVILSSGYRIGPFEVENALNEHPSVAESAVVSSPDPIRGE 518 TGDR Y+D+DGYFWFV RADDVIL+SGYRIGPFEVE+AL EHP+VAESAVVSSPD RGE Sbjct: 419 TGDRAYVDEDGYFWFVGRADDVILTSGYRIGPFEVESALIEHPAVAESAVVSSPDETRGE 478 Query: 519 VVKAFVVLNPDYKSHDQEQLIKEIQEHVKKTTAPYKYPRKVEFIQELPKTISGKTKRNEL 578 VVKAFV+L + + D +L KE+QEHVK TAPYKYPRK+EF+ LPKT+SGK +R +L Sbjct: 479 VVKAFVILAGGFTASD--ELAKELQEHVKNVTAPYKYPRKIEFVDVLPKTVSGKIRRVQL 536 Query: 579 RKKEW 583 R +EW Sbjct: 537 RNQEW 541 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: 927 Number of extensions: 39 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: 586 Length of database: 544 Length adjustment: 36 Effective length of query: 550 Effective length of database: 508 Effective search space: 279400 Effective search space used: 279400 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 Jul 25 2024. The underlying query database was built on Jul 25 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