Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= reanno::WCS417:GFF5420 (497 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 230 bits (587), Expect = 7e-65 Identities = 141/457 (30%), Positives = 236/457 (51%), Gaps = 9/457 (1%) Query: 40 ISPVDGRLLATVASCDAADAQRAVENARATFNSGVWSRLAPAKRKSAMLRFAALLKANAE 99 I+P G LL + A++ + + S W L ++R M + +L+ N + Sbjct: 4 INPYTGELLEEFTDHTEQQVEAAIQKGQEAYLS--WRELPISQRADLMKKAGQVLRDNTD 61 Query: 100 ELALLETLDMGKPISDSLNIDVPGAANALSWSGE-AIDKIYDEVAATPHDQLGLVTREPV 158 + + +L+MGK I++S + +V A + E A + + D A P + V P+ Sbjct: 62 KYGKIISLEMGKVITESKS-EVEKCAWVCEYYAENAEEMLADAPIALPDGKEAKVVYNPL 120 Query: 159 GVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIRIAALAVEAGIPKGVFN 218 G+V A++PWNFP P L+ GN +LK + P A+ I + +AG P+GVF Sbjct: 121 GIVLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVFQ 180 Query: 219 VLPGYGHTVGNALALHMDVDTLVFTGSTKIAKQLLIRSGESNMKRVWLEAGGKSPNIVFA 278 L V N +A H DV TGS K +++ ++GE +K+ LE GG P IV Sbjct: 181 SLLIGSDKVANIIA-HPDVKAATLTGSEKAGQKIAAQAGEQ-IKKTVLELGGSDPFIVLK 238 Query: 279 DAPDLQAAAESAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPA 338 DA D++ AA++AA N G+ C A R ++E+ + D+F+ A++ + PG+PLD Sbjct: 239 DA-DVKEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEK 297 Query: 339 TNVGALVDTQQMNTVLSYIEAGHADGAKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIA 398 + + +EA GA+++ G T E G +++P I +T M Sbjct: 298 AGYACMARPDLAMELYEQVEASIQKGAEVILEG--TKPEKGKAFIKPYILGKLTPDMPAY 355 Query: 399 KEEIFGPVLSVITFDSAEEAVAIANDTIYGLAAAVWTADISKAHLTAKALRAGSVWVNQY 458 +EE+FGPV SV + +EA+AIAND+ +GL A++WT D KA + ++ + +G+V++N Sbjct: 356 REELFGPVASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSM 415 Query: 459 DGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWI 495 + PFGG K+SG GR+ + + ++ +K ++ Sbjct: 416 VASNPYLPFGGIKKSGYGRELAENGIKEFMNIKTVYL 452 Lambda K H 0.316 0.132 0.386 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: 478 Number of extensions: 18 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: 497 Length of database: 453 Length adjustment: 33 Effective length of query: 464 Effective length of database: 420 Effective search space: 194880 Effective search space used: 194880 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 Apr 09 2024. 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