Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate H281DRAFT_02499 H281DRAFT_02499 Acyl-CoA reductase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Burk376:H281DRAFT_02499 Length = 503 Score = 369 bits (948), Expect = e-106 Identities = 189/470 (40%), Positives = 290/470 (61%), Gaps = 3/470 (0%) Query: 10 DCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNG-PWKKM 68 D I G++ + DG+T D +NPAT E +G +A A ++D AVQA +A G W+ M Sbjct: 10 DAQLLIGGEWTDAEDGRTLDIVNPATGEVIGALASASARDVDRAVQAGHRAFEGGAWRDM 69 Query: 69 TANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTI 128 + +R +L + DL E+ LE+L+ G+P I R + +F+ T Sbjct: 70 SIQQRARILNRFADLFEADLEQFYKLETLNNGRPI-AETRAQISRLPQFYRYFAALALTR 128 Query: 129 TNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPM 188 ++ ++ L Y R P+GV+ L+ +N PL++++ LAPALA GN+VV+K +E TP+ Sbjct: 129 RSDVIPIEGPYLCYTQRVPLGVVALMTSFNHPLMILSKSLAPALATGNSVVIKASEQTPL 188 Query: 189 TATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAA 248 T L ++ +DAGVP GVVN+V+G G AGAAL +HP + + FTG T G+ I +AA Sbjct: 189 TTVRLVKLLQDAGVPKGVVNVVNGEG-RVAGAALAQHPLIRKVVFTGGTEVGRSIGEAAA 247 Query: 249 KTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFL 308 + + ELGGK ++F D +++ + ++FI G+ C+CG+RI V++ Y AFL Sbjct: 248 RNFALTTLELGGKGAVILFDDFDIERAVNGASFAAFIGAGQTCVCGARILVQKSMYAAFL 307 Query: 309 EKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEK 368 E+F AK + + VGDP DAKT++G +IS+ +R+ ++ A + G +LTGG+ P+ L Sbjct: 308 ERFRAKVERIRVGDPTDAKTQLGPVISERSRQRILAMLERAQQAGAKLLTGGRVPQELTS 367 Query: 369 GYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLR 428 GYFLEPT++ + ++E+FGPV V+PF+ E + + NDT +GL+AS+WT D+ Sbjct: 368 GYFLEPTVVYDADPHSEIGQDEVFGPVTVVMPFEDEADAIRIANDTSFGLAASIWTQDVA 427 Query: 429 RAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 RAHRVAG++E G+VWVN D +P+GG K SG+GRE G+ SF+ +SE Sbjct: 428 RAHRVAGRLEFGMVWVNDHHRLDPASPWGGFKNSGVGRETGIESFDQFSE 477 Lambda K H 0.318 0.136 0.404 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: 603 Number of extensions: 15 Number of successful extensions: 4 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: 486 Length of database: 503 Length adjustment: 34 Effective length of query: 452 Effective length of database: 469 Effective search space: 211988 Effective search space used: 211988 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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