Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate SMa0220 SMa0220 NAD-dependent aldehyde dehydrogenase
Query= reanno::WCS417:GFF5420 (497 letters) >FitnessBrowser__Smeli:SMa0220 Length = 504 Score = 359 bits (922), Expect = e-103 Identities = 207/493 (41%), Positives = 298/493 (60%), Gaps = 24/493 (4%) Query: 16 LKIEGRAYINGEYTAAVSGDTFECISPVD-GRLLATVASCDAADAQRAVENARATFNSGV 74 +K + ++G+ A SG T + +SP G ++ T A D ++AV AR F++G Sbjct: 17 IKSRYQMLVDGKSVDAASGSTIDRVSPGHAGEVVGTWPEASADDVRKAVAAARKAFDAGP 76 Query: 75 WSRLAPAKRKSAMLRFAALLKANAEELALLETLDMGKPISDS-------LNIDVPGAANA 127 W R++ A+R M + A L+ A EELAL+E+L++GKPI+ + ++ A A Sbjct: 77 WPRMSGAERSRLMFKVADLILARQEELALIESLEVGKPIAQARGEIGFCADLWSYAAGQA 136 Query: 128 LSWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNS 187 + G+ + I D D+LGLV REPVGVVG I PWNFP ++A ++ A+ +G + Sbjct: 137 RALEGQTHNNIGD-------DRLGLVLREPVGVVGIITPWNFPFIIASERVPWAIGSGCT 189 Query: 188 VILKPSEKSPLTAIRIAALAVEAGIPKGVFNVLPGYGHTVGNALALHMDVDTLVFTGSTK 247 V+LKPSE + T+IR+A LA EAGIP GVFNV+ GYG G LA +VD + FTGS + Sbjct: 190 VVLKPSEFTSGTSIRLAELAREAGIPDGVFNVVTGYGDPAGQVLAEDPNVDMVAFTGSVR 249 Query: 248 IAKQLLIRSGE---SNMKRVWLEAGGKSPNIVFADAPDLQAAAESAAGAIAFNQGEVCTA 304 + +L GE +KRV LE GGK P IVFADA DL AAA+ A + N G+ C + Sbjct: 250 VGTKL----GEIAARTVKRVGLELGGKGPQIVFADA-DLDAAADGIAYGVYHNAGQCCIS 304 Query: 305 GSRLLVERSIKDKFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHADG 364 GSRLLV+ I+D + +++ + G+PL+ T +GA++ V SY+ AG G Sbjct: 305 GSRLLVQEGIRDALMERLLDISRKVAFGDPLNERTKIGAMISEAHAEKVHSYVTAGITSG 364 Query: 365 AKLVAGGKRTLEETGGTYVEPTIFDGVTNAMKIAKEEIFGPVLSVITFDSAEEAVAIAND 424 A+L+ GG+R E G Y PT+F GVT M IA+EEIFGPVLS +TF +A+EAVA+AN Sbjct: 365 AELLLGGERIGREAG-LYYAPTVFAGVTPDMSIAREEIFGPVLSTLTFKTADEAVALANA 423 Query: 425 TIYGLAAAVWTADISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAF 484 T +GL+A+VW+ ++ A T + +RAG W+N G P GG+K+SG GR+ + F Sbjct: 424 TEFGLSASVWSTNLETALQTIRRIRAGRCWINSVIDGTPELPIGGYKKSGLGRELGRYGF 483 Query: 485 DKYTELKATWIKL 497 D+Y++ K + L Sbjct: 484 DEYSQFKGVHVTL 496 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: 562 Number of extensions: 26 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: 497 Length of database: 504 Length adjustment: 34 Effective length of query: 463 Effective length of database: 470 Effective search space: 217610 Effective search space used: 217610 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: 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