Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate SMc00261 SMc00261 acyl-CoA synthetase
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Smeli:SMc00261 Length = 549 Score = 138 bits (348), Expect = 5e-37 Identities = 131/495 (26%), Positives = 217/495 (43%), Gaps = 47/495 (9%) Query: 66 GLQRGDRVLLFSGN-DLFFPVVFLGVIMAGGIFTGANPTFVARELAYQLQDSGATYLLCA 124 G+++GDR+L+ S N + F +F AG ++ N + E+AY + SGA ++ Sbjct: 65 GVRKGDRILVHSANCNQMFESMF-AAFRAGAVWVPTNFRQLPEEVAYLAESSGARLVIFQ 123 Query: 125 SNSLETGLEAAKQAKLPQSHIFAYDTSI----YDGVTNPQKGCAYWSDLLASEEEGAAFT 180 + + E EA + A +S YD + G + S + ++ + Sbjct: 124 A-AFEAHAEACRAAGEQIGSCIPIGSSRVGEDYDAIVARNLGRSV-SPVAVDRDDPCWYF 181 Query: 181 WDELSTPALSSTTLALNYSSGTTGRPKGVEISHRN--YVANMLQYCHTASLHPDYKARLE 238 Y+SGTTGRPK ++H +V N H L P A Sbjct: 182 -----------------YTSGTTGRPKAAVLTHGQMAFVINN----HIGDLFP---ATTH 217 Query: 239 RSRWLCFLPMYHAMAQNIFIAAALYRATPVYIMSKFDFVKMLEYTQRFRITDFILVPPVV 298 R R + P+ H + A T + K D + +++R+ + VP +V Sbjct: 218 RDRSIVVAPLSHGAGIHQLCQVARGATTILLPSEKLDIPQFWALVEKWRVNNLFAVPTIV 277 Query: 299 VALAKHPAVGQYDLSSVELVGSGAAPLGREVCEEVEKLWPPGKINIKQGWGMTEATCSVT 358 L + P+V +YD SS+ V AP+ R ++ + L G + + Q +G+ E T ++T Sbjct: 278 KLLIEDPSVDRYDHSSLRYVIYAGAPMYR--ADQKKALEKLGAVLV-QYFGLGEVTGAIT 334 Query: 359 GWNPA----EISTSASVGELN---ANCEAKIMFDGVEVKERNSRGELWVRAPNVMKGYWR 411 PA E A +G + +I + + GE+ V P V GY+R Sbjct: 335 VLPPAFHSSEDGPDARIGTCGFERTGMQLQIQDEDGNEVPAGATGEICVIGPAVFAGYYR 394 Query: 412 NEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELIKVKGNQVAPAELEALLLEHPA 471 N +A + +GW TGD+ VD G ++ R ++ G+ V P E+E LL HP Sbjct: 395 NPEANAKA-FRNGWFRTGDLGHVDAQGFLYITGRASDMYISGGSNVYPREIEEKLLMHPD 453 Query: 472 ISDVAVIGVVINN-DERPRAYVVLRPGQSATANEIAHYLDNKVSAFKRITGGVVFLEAIP 530 IS+ A++GV E A V R G + A + +LD K++ +K + +VF +P Sbjct: 454 ISEAAIVGVPDPVWGEVGIAVCVARGGATVGAAALREWLDGKIARYK-LPKKIVFWSEMP 512 Query: 531 KNPSGKILRMKLREQ 545 K+ GKI + +RE+ Sbjct: 513 KSAYGKITKKLIREE 527 Lambda K H 0.319 0.134 0.403 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: 656 Number of extensions: 35 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 549 Length adjustment: 36 Effective length of query: 520 Effective length of database: 513 Effective search space: 266760 Effective search space used: 266760 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