Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 213 bits (542), Expect = 1e-59 Identities = 148/446 (33%), Positives = 231/446 (51%), Gaps = 20/446 (4%) Query: 42 VAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEELSVLESLDTGK 101 VA A + A+ AA KA P ++ ER AVL+ ER++EL+ ++ GK Sbjct: 35 VAVPDAKATEQAIAAAVKAAE-PMRQFKPWERQAVLQHCVQRFTERRDELAYALCVEAGK 93 Query: 102 PTWLSGSIDIPRAAYNFHFFSDYI-----RTITNEATQMDDVALNYAIRRPVGVIGLINP 156 P S ++ R F ++ TI E + + Y R P+G + I P Sbjct: 94 PIKDSAG-EVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTRRVPLGPVSFITP 152 Query: 157 WNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPN 216 +N PL L+ K+APA+AAG V+KPAE TP+ A ++ E+ + +P G ++++ G + Sbjct: 153 FNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKGAFSILNLDGKH 212 Query: 217 SAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIFADS--NLDE 274 ++ L E P +SFTG + G + A K+++ ELGG ++ AD LD Sbjct: 213 AS--PLVEDPRFKLLSFTG-SQIGWDLKTRAGH--KKVTLELGGNAACIVDADQLPRLDH 267 Query: 275 VIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALI 334 VIE + +F G+ C+ RIY Y+ ++ VA K L GDP +T +G +I Sbjct: 268 VIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKAGDPKKKETFLGPMI 327 Query: 335 SDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGP 394 + ER+ G+I+ A + GG +L GGKR KG LE T++ + D +V ++E+FGP Sbjct: 328 DEAAAERLHGWIEEARKGGGKVLCGGKR-----KGPMLEATLMENVRGDAKVNRQEVFGP 382 Query: 395 VVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVN-TWFLRDLR 453 + PF + +E + ND+ YGL A ++T+ L A R ++E G V VN R Sbjct: 383 FALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGVIVNDVPSFRVDN 442 Query: 454 TPFGGMKQSGIGREGGLHSFEFYSEL 479 P+GG+K SG GREG ++ E +E+ Sbjct: 443 MPYGGVKLSGAGREGVRYAIEDMTEI 468 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: 542 Number of extensions: 31 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: 486 Length of database: 476 Length adjustment: 34 Effective length of query: 452 Effective length of database: 442 Effective search space: 199784 Effective search space used: 199784 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: 51 (24.3 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