Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate AO356_25585 AO356_25585 2-hydroxymuconic semialdehyde dehydrogenase
Query= reanno::WCS417:GFF2142 (499 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25585 Length = 486 Score = 246 bits (629), Expect = 1e-69 Identities = 162/456 (35%), Positives = 246/456 (53%), Gaps = 8/456 (1%) Query: 5 IEHYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIR 64 I+H+I+ + V D + + +NPATGE G VA + V++AVAAA+ AF WA+TP Sbjct: 2 IKHWIDGREVESKDVFVN-YNPATGEAIGEVASGGAEEVAQAVAAAKEAFPKWANTPAKE 60 Query: 65 RARVLFEYLHLLRERKDDLARIIVAEHGKVFTDAQGE-VDRGIDILEFACGIPNLLKGEH 123 RAR++ + L+ + LA + + G + + R +F + + G H Sbjct: 61 RARLMRKLGELIEQNVPKLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDG-H 119 Query: 124 SDQVSRGMDNWTMRQPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASL 183 + V M N+T+ QP+GV A V+P+N P M W +A GNT +LK S P + Sbjct: 120 TYPVDDQMLNYTLYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTAN 179 Query: 184 FMAELLREAGLPKGVFNVVQGDKESV-DALIEHPDVKAVSFVGSTPIAQYIYETGARNGK 242 + L EAG+P GV NV+QG + DAL+ HPDV+A+SF G T + I +T K Sbjct: 180 ELGRLAVEAGIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAGLK-K 238 Query: 243 RVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAALT 302 LGG K+ +++ DAD+E+ +DA + + GERC A S + V + +A Sbjct: 239 YSMELGG-KSPVLIFEDADLERALDAALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFA 297 Query: 303 ERAKHLRITDGRDLKAEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEPG-LE 361 RAK L + D +D K ++G ++++A ++++GYI+ G++ GA LL G + P L Sbjct: 298 ARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGGLERPANLPAHLS 357 Query: 362 NGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDG 421 +G ++ T+F V +M I +EEIFGPV+ + D AEA++L N E+G +T+D Sbjct: 358 HGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQDI 417 Query: 422 NIAREFARRIEVGMVGINVPISVPMAWHGFGGWKKS 457 A A IE GMV IN +V FGG K S Sbjct: 418 GKAHRLAHGIEAGMVFINSQ-NVRDLRQPFGGVKGS 452 Lambda K H 0.320 0.136 0.407 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: 551 Number of extensions: 22 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: 499 Length of database: 486 Length adjustment: 34 Effective length of query: 465 Effective length of database: 452 Effective search space: 210180 Effective search space used: 210180 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 (21.8 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