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_073038467.1 BUB04_RS07990 AMP-dependent synthetase
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_900129305.1:WP_073038467.1 Length = 546 Score = 248 bits (632), Expect = 6e-70 Identities = 170/562 (30%), Positives = 288/562 (51%), Gaps = 38/562 (6%) Query: 31 PQNFSNYESMKQDFKI-----EIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGE 85 P+N+ + M ++ + + P N A +LD+ + NPA ++D Sbjct: 5 PENYLPPKEMWPEYVVPEEFADTPMELNLADYLLDRHVREGRG----DNPAVKFMDKV-- 58 Query: 86 ELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGT 145 +++ +L + KF N L EA ++ DRV + L P+ + A + G + +P + Sbjct: 59 ---FTYAQLQQMVNKFGNALKEA-GVEPQDRVGIRLVNSPQALVTIFAIEKVGAIPVPTS 114 Query: 146 TQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSRE--GWGNL- 202 +++++ + + +++ K + + L V+ E +++ + E GNL Sbjct: 115 PLWSKEEVAFVVNNAEMKFFVVNAPLMGPVEEAKPDFEYGTKVIVIGGNPDEVKAQGNLV 174 Query: 203 -KEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLI 261 +EM++ S + V K D++ I +TSGTTG PK H + + ++ +L Sbjct: 175 FEEMLEKGSPNLDAVMLKADDIGVILYTSGTTGMPKGCVHFVRPIIIEARLVNKYVYNLK 234 Query: 262 ASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAP 321 DV+ + +A + P+ GA + +P+F +++ + K ITV P Sbjct: 235 PGDVLGGAAPVSFAAGFGTFTLIPFEGGAAI--SLIPKFAPADMMELIEKHKITVLTGLP 292 Query: 322 TAYRMLVQ-NDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETV-LIC 379 TAYR L++ D Y F+S++ C S G+ + E +E W K TG I+EG G TE + L+ Sbjct: 293 TAYRALMKFPDFKKYDFSSVRLCTSGGDALGAETLEAWTKLTGQPIWEGLGGTEMLHLLT 352 Query: 380 GNFKGMKIKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGL--FTHYVD 437 N + P S+GK P V+++D P + G + ++ P G + YVD Sbjct: 353 SNTMNPEPVPNSIGKALPGVQVRVVDPEWNDCKPNEVGSMIIK----GPSGTLYWKPYVD 408 Query: 438 NPSKTASTLRG---SFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEH 494 N S +G + GD YM EDG +FV+R DD+I SSGYRIGP EVE A+++H Sbjct: 409 NERLLKSQQKGVKNGWNQMGDAVYMREDGNIFFVSREDDMIKSSGYRIGPAEVEEAILKH 468 Query: 495 PSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQ--EQLKKEIQEHVKKTTAPYKYPRK 552 P++A++ VV PDP +G+V KAF+VL P Y+ D E+LK+ +++H+ A YK PR Sbjct: 469 PAVADAGVVGVPDPEKGQVTKAFVVLKPGYEGSDAFFEELKEFLKQHI----AVYKLPRL 524 Query: 553 VEFIEELPKTVSGKVKRNELRK 574 +E+++ LP+T +GK+ R +LRK Sbjct: 525 IEYVDALPRTPTGKLLRRKLRK 546 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: 792 Number of extensions: 44 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: 546 Length adjustment: 36 Effective length of query: 544 Effective length of database: 510 Effective search space: 277440 Effective search space used: 277440 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