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_052473675.1 SUTH_RS14585 AMP-binding protein
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_000828635.1:WP_052473675.1 Length = 559 Score = 266 bits (680), Expect = 2e-75 Identities = 177/556 (31%), Positives = 287/556 (51%), Gaps = 29/556 (5%) Query: 36 NYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFEELG 95 ++++++ F+ ++P +N A+ +W + S A ++ D +G W+F ++ Sbjct: 12 DWQALRASFRWQVPARYNIAQACCGRWADDR------SRFALYYEDESGHTEAWTFWDVQ 65 Query: 96 LLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKDILY 155 + + +N+L A + GDRV ++LP+ PE +A++AC + G + +P + + Y Sbjct: 66 QAANRLSNVLG-AMGVMAGDRVAIMLPQRPETGIAHMACYQMGAIAVPISHLFGADALEY 124 Query: 156 RLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGW-GNLKEMMKYASDSHT 214 RL ++ A+ I DD + AV K L + V +RE W ++ A+ +T Sbjct: 125 RLSNAGARVAIIDDGGLEKLAAVRDKLPQLKHVIGVGG-AREAWVREWATLLPLAASRYT 183 Query: 215 CVDTKHDEMMAIYFTSGTTGPPK--MIGHTHSSFGL-GLSVNGRFWLDLIASDVMWNTSD 271 DT D+ I +TSGTTG PK +I L G + F+ D+ W+ +D Sbjct: 184 PRDTAADDPAMIIYTSGTTGNPKGALIAQRSLLGNLPGFVCSHDFYPR--RGDMFWSPAD 241 Query: 272 TGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLVQN- 330 W + ++ W G + Y RF+ L K+ I PTA +M+++ Sbjct: 242 WAWTGGLFDALLPTWNFGQPLLG-YRGRFDPEKAFWLLEKYGIRNAFLFPTALKMMMKAV 300 Query: 331 DMSSYKFNS-LKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKGMKI-K 388 K+N L+ +SAGE + V ++ G+ + E YGQTE I GN + K Sbjct: 301 PQPKEKYNLVLRSIMSAGETVGEAVCHWAQEALGVTVNEMYGQTEINYIVGNCAAVTSPK 360 Query: 389 PGSMGKPSPAFDVKILDENGATLPPGQEGDIALQ--VLPERPFGLFTHYVDNPSKTASTL 446 PG+MG+ P + +LD+ G + PG+ G++ +Q E Y NP TA Sbjct: 361 PGAMGRGYPGHQLAVLDDAGNPVAPGELGEVCVQRSCNGEMDPVFMLGYWKNPEATAEKF 420 Query: 447 RG-------SFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAE 499 G ++ TGD MDEDG W+ RSDD+ S+GYRIGP E+E+ L++HP++A Sbjct: 421 IGGGVDDPQAWGRTGDLAKMDEDGVLWYQGRSDDMFKSAGYRIGPGEIENCLVKHPAVAN 480 Query: 500 SAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEEL 559 +AV+ PDP+RG VVKAFIVL K +L+ +Q+HV++ APY+YP+ +EFI+ L Sbjct: 481 AAVIGEPDPVRGTVVKAFIVLQAGEK--PSAELEASLQQHVRQFLAPYEYPKIIEFIDAL 538 Query: 560 PKTVSGKVKRNELRKK 575 P T +GKV+R LR++ Sbjct: 539 PMTTTGKVQRRLLRQR 554 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: 881 Number of extensions: 41 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: 559 Length adjustment: 36 Effective length of query: 544 Effective length of database: 523 Effective search space: 284512 Effective search space used: 284512 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 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