Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= BRENDA::A0A081YAY7 (498 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 181 bits (458), Expect = 7e-50 Identities = 139/458 (30%), Positives = 216/458 (47%), Gaps = 27/458 (5%) Query: 21 DVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRAQVLFRFKQLLEANEE 80 DV + +G+ +V + D + +QAI AA A R P +R VL Q + Sbjct: 22 DVLDKYSGKVATRVAVPDAKATEQAIAAAVKAAEPMRQFKPWERQAVLQHCVQRFTERRD 81 Query: 81 RIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGE-YSRNVGPNIDAWSDFQ-- 137 + + E GK I+D+AGE+ R IE A GE + + ++ + + Sbjct: 82 ELAYALCVEAGKPIKDSAGEVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTRR 141 Query: 138 -PIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIAELFHEAGLPKG 196 P+G V+ ITPFNFP + AIA G F+LKP+ER P L+I E+ E LPKG Sbjct: 142 VPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPKG 201 Query: 197 VLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQALGGAKNHAVLM 256 ++++ D L+E P K LSF GS + G K K LGG +A + Sbjct: 202 AFSILNLDGKHASPLVEDPRFKLLSFTGSQIGWDLKTRAGHK--KVTLELGG---NAACI 256 Query: 257 PDAD----LDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQIKGLKIGA 312 DAD LD+ + L+ A+ G+ C+++ + + + D L ++LV +KGLK G Sbjct: 257 VDADQLPRLDHVIERLVFGAFYQSGQSCISVQ-RIYAHESLYDELKKRLVAAVKGLKAGD 315 Query: 313 GTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFLGGTLFDRV 372 +GP++ AA +++ G+I+ G +++ G+ G L TL + V Sbjct: 316 PKKKETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGK-------RKGPMLEATLMENV 368 Query: 373 TPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVG 432 + + ++E+FGP + SL+EA+ + ND +YG IFT A +E+E G Sbjct: 369 RGDAKVNRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQG 428 Query: 433 MVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRF 470 V VN V +GG K L G +GVR+ Sbjct: 429 GVIVNDVPSFRVDNMPYGGVK------LSGAGREGVRY 460 Lambda K H 0.319 0.137 0.411 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: 568 Number of extensions: 29 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: 498 Length of database: 476 Length adjustment: 34 Effective length of query: 464 Effective length of database: 442 Effective search space: 205088 Effective search space used: 205088 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