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_057508577.1 ABB28_RS10145 AMP-binding protein
Query= SwissProt::Q3UNX5 (580 letters) >NCBI__GCF_001431535.1:WP_057508577.1 Length = 555 Score = 248 bits (634), Expect = 4e-70 Identities = 167/508 (32%), Positives = 260/508 (51%), Gaps = 19/508 (3%) Query: 76 AFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACL 135 A WI +G ++FE+L S + A++LT A + RGD V +LP+ PE + Sbjct: 53 ALRWISTDGGLHLYTFEDLRAASTRVAHVLT-AQGIGRGDVVAGMLPRTPELLATILGTW 111 Query: 136 RTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHS 195 R G V P T K I RL++ + + ++TD +D V C + + L Q + Sbjct: 112 RVGAVYQPLFTAFGAKAIESRLRTGRTRLVVTDHANRHKLDDVE-DCPPVATILPAGQPA 170 Query: 196 REGWGNLKEMMKYASDS-HTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNG 254 + + + A + V + DE+M + TSGTTG PK + + + + Sbjct: 171 DAADIDWRVRIAAAGAAPFEPVLLRGDELMVLLSTSGTTGAPKGVPVPLRAL-MSFASYM 229 Query: 255 RFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPI 314 + +DL DV WN +D GWA + +V P G + P F + + + + + Sbjct: 230 QLAVDLRPGDVFWNIADPGWAYGLYYAVIGPLMLGEATTFNEAP-FTVQGLHEVIERLGV 288 Query: 315 TVFCSAPTAYRMLVQNDMSSYK--FNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQ 372 T +PTAYR ++ +S L+ SAGEP+N E+ + + + YGQ Sbjct: 289 TNLAGSPTAYRQIIAAGEASAARVAGQLRAVSSAGEPLNAEIARWFAAHLSTTVLDHYGQ 348 Query: 373 TETVLICGNFKGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFG 430 TET ++ N + ++ GS G P + V +LD++G LP G +A+ + P Sbjct: 349 TETGMVVNNHHALHHAVRTGSSGFAMPGYRVAVLDDDGHELPARTPGILAIDIA-RSPLM 407 Query: 431 LFTHY--VDNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVE 488 FT Y D P+ + +Y+TGD ++DG F+ RSDD+I SSGYRIGPF+VE Sbjct: 408 WFTGYYGADTPA-----IGDGYYLTGDTVECEDDGSISFIGRSDDVITSSGYRIGPFDVE 462 Query: 489 SALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYK 548 SAL+EHP++AE+ V+ PDP R E+VKAF++ + + L ++Q++VK + + Sbjct: 463 SALLEHPAVAEAVVIGVPDPQRTEIVKAFVITSTGIEG--DAALAAQLQQYVKTRLSAHA 520 Query: 549 YPRKVEFIEELPKTVSGKVKRNELRKKE 576 YPR VEF+ E+PKT SGKV+R LR E Sbjct: 521 YPRLVEFVSEVPKTPSGKVQRFVLRAAE 548 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: 757 Number of extensions: 38 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: 555 Length adjustment: 36 Effective length of query: 544 Effective length of database: 519 Effective search space: 282336 Effective search space used: 282336 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