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_011384660.1 AMB_RS11445 2-aminobenzoate-CoA ligase
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_000009985.1:WP_011384660.1 Length = 551 Score = 225 bits (573), Expect = 4e-63 Identities = 163/519 (31%), Positives = 253/519 (48%), Gaps = 49/519 (9%) Query: 73 SNPAFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANV 132 + P F + +G WS+ L + + A +LTE L G RV++ P + Sbjct: 64 AKPVFHYGEGT-----WSYAHLLDRAERIARVLTEDFWLVPGARVLLRSANTPMLVACWL 118 Query: 133 ACLRTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVS 192 A L+ G + + L K++ Y ++ ++ + + LA +D K L + Sbjct: 119 AVLKAGGICVTTMPLLRAKELSYIVEKARVSIALCELDLAEEMDLTRQKMAELRHVAYFT 178 Query: 193 Q--HSREGWGNLKEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGL 250 + +L + VDT D++ I FTSGTTG PK H H Sbjct: 179 PLCDGAKAEADLDRRAEAKPTGFANVDTAADDVALITFTSGTTGNPKGAMHFHR------ 232 Query: 251 SVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSP---WTQGACVFAHYLPRFESTS--- 304 D++AS W T + + SP +T G F Y R +T+ Sbjct: 233 --------DILASCDCWPRRHT--LEPDEVVIGSPSIAFTYGKAAFMMYPLRHRATAVLV 282 Query: 305 -------ILQTLSKFPITVFCSAPTAYRMLVQNDMSSYKFNSLKHCVSAGEPINPEVMEQ 357 IL+ + + T + PTA+ ++ + Y +SL+ SAGE + P++ + Sbjct: 283 PKPTPELILEGIQRHRATSLYAVPTAFNAML-GMVGKYDISSLRKASSAGEHLRPKLYDD 341 Query: 358 WRKKTGLDIYEGYGQTE--TVLICGNFKGMKIKPGSMGKPSPAFDVKILDENGATLPPGQ 415 W ++TG+ + G G TE T IC + KPG+ G P + ILD++ LP G Sbjct: 342 WLERTGVKLVNGIGMTEMLTHFICQSAD--VAKPGATGFPVDGYTACILDDDFNPLPVGS 399 Query: 416 EGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDII 475 +G +A++ P G Y+D+ ++ A+ +R + +TGD D +G+FW+V RSDD+I Sbjct: 400 KGRLAVR----GPTGC--RYLDDQARQAAFVRNGWNVTGDIMEQDAEGWFWYVDRSDDMI 453 Query: 476 LSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKE 535 +SSGY I EVE A++EHP +AE AV+ PD RG +V+A IVL D S E L +E Sbjct: 454 VSSGYNISAQEVERAVLEHPKVAECAVIGVPDEARGTIVRACIVL--DNPSQASELLAEE 511 Query: 536 IQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNELRK 574 IQ VK APYKYPR++ F++ LPKT +GK++R LR+ Sbjct: 512 IQNFVKANIAPYKYPREIRFVDFLPKTQTGKIQRFRLRE 550 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: 770 Number of extensions: 36 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: 551 Length adjustment: 36 Effective length of query: 544 Effective length of database: 515 Effective search space: 280160 Effective search space used: 280160 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 17 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