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 SMa0150 SMa0150 malonyl-CoA synthase
Query= SwissProt::Q3UNX5 (580 letters) >FitnessBrowser__Smeli:SMa0150 Length = 508 Score = 189 bits (479), Expect = 3e-52 Identities = 145/490 (29%), Positives = 239/490 (48%), Gaps = 26/490 (5%) Query: 89 WSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQL 148 W++ ++ S + A++L +A ++ GDRV V + K PE + +ACLRTG V +P T Sbjct: 28 WTYGDMLEHSGRIASVL-DALGVRPGDRVAVQVEKSPEALMLYLACLRTGAVYLPLNTAY 86 Query: 149 TQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNLKEMMKY 208 T ++ Y ++ + I+ + AA C V +G G+L ++ + Sbjct: 87 TLAELDYFFGDAEPRLIVCAPGAKEGIAKHAADCG-----AEVETLDEKGGGSLIDLARG 141 Query: 209 ASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIASDVMWN 268 + D D++ AI +TSGTTG K TH + + +W A D + + Sbjct: 142 KAPDFPDADRGPDDLAAILYTSGTTGRSKGAMLTHDNLLSNATTLREYWR-FTADDRLIH 200 Query: 269 TSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLV 328 + + GA +F +LP+F++ +L+ + + T PT Y LV Sbjct: 201 ALPIFHTHGLFVASNVILLAGASMF--FLPKFDANEVLRLMPQS--TSMMGVPTFYVRLV 256 Query: 329 QNDMSSYKFNS-LKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGN-FKGMK 386 QN +++ + ++ VS P+ E + + TG I E YG TET + N + G + Sbjct: 257 QNPGLTHEATAGMRLFVSGSAPLLAETHRTFAQMTGHAILERYGMTETNMNTSNPYDGER 316 Query: 387 IKPGSMGKPSPAFDVKILD-ENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTAST 445 I G++G P P +++ D E+G LP G+ G I + + +F Y P KT Sbjct: 317 IA-GTVGFPLPGVSLRVADPESGRPLPKGETGMIEV-----KGPNVFKGYWRMPEKTQGE 370 Query: 446 LRGS-FYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVS 504 R F+ITGD G +DE GY V R D+++S GY I P EVE+ + + P + E+AV+ Sbjct: 371 FRADGFFITGDLGRIDERGYVHIVGRGKDLVISGGYNIYPKEVETEIDQMPGVVETAVIG 430 Query: 505 SPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVS 564 P P GE V A +V P + + I + ++ A YK P++V F+++LP+ Sbjct: 431 LPHPDFGEGVTAVVVRKPGAAIDE-----RAILDGLEGRLARYKQPKRVIFVDDLPRNTM 485 Query: 565 GKVKRNELRK 574 GKV++N LR+ Sbjct: 486 GKVQKNVLRE 495 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: 660 Number of extensions: 42 Number of successful extensions: 5 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: 508 Length adjustment: 35 Effective length of query: 545 Effective length of database: 473 Effective search space: 257785 Effective search space used: 257785 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: 52 (24.6 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