Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AO353_23135 AO353_23135 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23135 Length = 498 Score = 330 bits (847), Expect = 5e-95 Identities = 182/470 (38%), Positives = 271/470 (57%), Gaps = 16/470 (3%) Query: 5 LLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPKV 62 + I GE G GE+ PATG+ + + AS E V+ AV A AF W Q P Sbjct: 9 ICIAGEWRLGRGERYATRYPATGEAVAWLNAASVEDVEDAVHGAHQAFLHSGWAQRKPHE 68 Query: 63 RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGL- 121 RA L ++A++I + + A+L+ ++ GKP++ + + F+FFA A L Sbjct: 69 RASVLYRIAELIRQRSEELAQLQRQDNGKPINET-RALVASAAGTFQFFAAACETLEETI 127 Query: 122 --AAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPL 179 + G+++ SM +P+GV+A+I PWN P+ A K+APALAAGN VV+KP+EITPL Sbjct: 128 TPSRGDFV----SMSVYEPMGVIAAITPWNSPIASEAQKVAPALAAGNAVVIKPAEITPL 183 Query: 180 TALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTAS 238 AL+LA + +D P G++++L G+G +GD LT HP V+ VS TG TG+HI A Sbjct: 184 MALQLARICEDAGLPKGLLSVLPGKGSLLGDALTRHPLVKRVSFTGGTKTGKHIAHIAAD 243 Query: 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 + +ELGGK+P IV DDAD++ V GV + ++G+ C A R++ + +Y+ + Sbjct: 244 KMMPVSLELGGKSPTIVLDDADLDHAVAGVLYGIFSSSGEACIAGSRLFVARALYEPFMA 303 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG--- 355 +L AA A L+ G P DE T++GPL S H E V + V A G +++ GG++ G Sbjct: 304 RLVAAAAELRVGDPADERTQMGPLISAGHRESVERYVALGLAEGG-RLLLGGQRPSGGVY 362 Query: 356 -NGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKD 414 GYYY PT+L G + Q+E+FGPV+ PFD+E Q++ ANDS Y LA+ +WT+D Sbjct: 363 DQGYYYPPTILEGLNNSQQVCQEEIFGPVLVAMPFDDEAQLIEQANDSLYALAAGIWTRD 422 Query: 415 VGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDY 464 RA + ++Q G W+NT+ P GG + SG G++ G+ Y Sbjct: 423 YKRAWALGRKIQAGTVWINTYKQFSISTPFGGWRDSGLGREKGRLGILQY 472 Lambda K H 0.317 0.134 0.397 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: 576 Number of extensions: 27 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: 474 Length of database: 498 Length adjustment: 34 Effective length of query: 440 Effective length of database: 464 Effective search space: 204160 Effective search space used: 204160 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