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_109940824.1 DLD82_RS09165 AMP-binding protein
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_003173335.1:WP_109940824.1 Length = 616 Score = 528 bits (1359), Expect = e-154 Identities = 261/552 (47%), Positives = 368/552 (66%), Gaps = 19/552 (3%) Query: 33 NFSNYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFE 92 N +Y+ ++F+IE+PEYFNF DV+D W ++ + A W + GEE ++F Sbjct: 60 NMQSYDETYRNFRIEVPEYFNFGFDVVDAWAKKDR-----NKIAMVWTNQKGEEKFFTFR 114 Query: 93 ELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKD 152 ++ S + N++ + + +GDRV+++L ++PEWW VA ++ G + IP T LT KD Sbjct: 115 DISRRSNEIVNMMIKY-KIGKGDRVLIMLHRVPEWWFMTVALIKIGAIYIPAPTMLTPKD 173 Query: 153 ILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGW-GNLKEMMKYASD 211 I YR+ +++AK +ITD A VD + C L +K++V +GW +E+M A Sbjct: 174 IAYRVNTAEAKMVITDMENAHKVDEIVGDCPTLVTKMVVDGEC-DGWLSYTRELMYPAPV 232 Query: 212 SHTCVD------TKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIASDV 265 S ++ TK E M I+F+SGTTG PKM+ H+HS + LG V RFW D+ +D+ Sbjct: 233 SSRIINLKGMRKTKSSEPMVIFFSSGTTGEPKMVQHSHS-YPLGHIVTARFWHDVRNNDL 291 Query: 266 MWNTSDTGWAKSAWSSVFSPWTQGACVFAH-YLPRFESTSILQTLSKFPITVFCSAPTAY 324 + SDTGWAKSAW +F W +GA +F + Y RF +T +L + K+ IT FC+ PT Y Sbjct: 292 HFTVSDTGWAKSAWGKLFGQWIEGAAIFVYDYRSRFNATELLPLIEKYGITTFCAPPTIY 351 Query: 325 RMLVQNDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKG 384 RML+ D+ + F+ L+HCVSAGE INPEV++ W+ TGL+IYEGYGQTETVL G F Sbjct: 352 RMLIMADLRKWDFSELRHCVSAGELINPEVIKAWKDATGLEIYEGYGQTETVLCVGTFPC 411 Query: 385 MKIKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTAS 444 M+ K GSMGKPSP +++++ DE+G + PG+EG IA++ P RP G F Y N A+ Sbjct: 412 MEPKYGSMGKPSPGWEIELHDEDGNQVKPGEEGSIAIKTEP-RPVGFFMEYWGNEEANAN 470 Query: 445 TLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVS 504 + +G +Y TGDR D DGYFWFV R DD+I +SGYRIGPFEVESA+IEHP++ E+AVV Sbjct: 471 SFKGGYYYTGDRAMKDNDGYFWFVGRDDDVIKASGYRIGPFEVESAIIEHPAVQEAAVVG 530 Query: 505 SPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVS 564 SPD IRG +VKAF+VL ++ E++ ++IQE+VK +TAPYKYPRK+EFI+ELPKT+S Sbjct: 531 SPDIIRGFIVKAFVVLKAGFE--PSEKISRDIQEYVKNSTAPYKYPRKIEFIKELPKTIS 588 Query: 565 GKVKRNELRKKE 576 GK+KR +LR+ E Sbjct: 589 GKIKRKDLRELE 600 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: 1007 Number of extensions: 46 Number of successful extensions: 8 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: 616 Length adjustment: 37 Effective length of query: 543 Effective length of database: 579 Effective search space: 314397 Effective search space used: 314397 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 24 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