Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q8VWZ1 (503 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 246 bits (629), Expect = 9e-70 Identities = 146/463 (31%), Positives = 249/463 (53%), Gaps = 19/463 (4%) Query: 27 NINPSTENIIGDIPAATKEDVDLAVDAAKRAISRKNGRDWSAASGSLRARYLRAIAAKIK 86 +INP T ++ + T++ V+ A+ + A W S RA ++ ++ Sbjct: 3 SINPYTGELLEEFTDHTEQQVEAAIQKGQEAYL-----SWRELPISQRADLMKKAGQVLR 57 Query: 87 EKKDELGKLESIDCGKPLEEALADLDDVVACFEYYAGLAEELDSKQKAPISLPMDTFKSY 146 + D+ GK+ S++ GK + E+ ++++ EYYA AEE+ + API+LP D ++ Sbjct: 58 DNTDKYGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLAD--APIALP-DGKEAK 114 Query: 147 ILKEPIGVVALITPWNYPFLMATWKIAPALAAGCAAILKPSELASVTCLELGEICKEVGL 206 ++ P+G+V + PWN+PF AP L AG +LK + L + E+ + G Sbjct: 115 VVYNPLGIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGF 174 Query: 207 PRGVLNIVTGLGHEAGASLASHPDVDKISFTGSSATGSKIMTTAAQLVKPVSLELGGKSP 266 P GV + +G + A++ +HPDV + TGS G KI A + +K LELGG P Sbjct: 175 PEGVFQSLL-IGSDKVANIIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDP 233 Query: 267 IVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRLIVHESIAVEFVDKLVKWAENIKISDP 326 +V +D D+ + A+ G GQ C A R I+ + + EF+ E+ DP Sbjct: 234 FIVLKDADVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDP 293 Query: 327 LEE----GCRLGPIVSEAQYKKVLNCISSAKSEGATILTGGRRPEHLKKGYFVEPTIITD 382 L+E C P ++ Y++V ++ +GA ++ G +PE K F++P I+ Sbjct: 294 LDEKAGYACMARPDLAMELYEQV----EASIQKGAEVILEGTKPEKGKA--FIKPYILGK 347 Query: 383 VTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTHYGLGSAVMSNDLERCERLSKALQA 442 +T M +REE+FGPV +V + +EAI +AND+ +GLG+++ + D ++ + LS+ +++ Sbjct: 348 LTPDMPAYREELFGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIES 407 Query: 443 GIVWINCAQPSFIQAPWGGIKRSGFGRELGEWGLENYLSVKQV 485 G V+IN S P+GGIK+SG+GREL E G++ ++++K V Sbjct: 408 GAVFINSMVASNPYLPFGGIKKSGYGRELAENGIKEFMNIKTV 450 Lambda K H 0.317 0.134 0.402 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: 507 Number of extensions: 19 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: 503 Length of database: 453 Length adjustment: 34 Effective length of query: 469 Effective length of database: 419 Effective search space: 196511 Effective search space used: 196511 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 (21.6 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