Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate WP_092345688.1 BLU87_RS05845 aldehyde dehydrogenase family protein
Query= SwissProt::Q64057 (539 letters) >NCBI__GCF_900107645.1:WP_092345688.1 Length = 477 Score = 225 bits (573), Expect = 3e-63 Identities = 147/480 (30%), Positives = 239/480 (49%), Gaps = 13/480 (2%) Query: 51 NEGVFNGSWGGRGEVITTYCPAN-NEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPK 109 N+ NG W +V P++ N+ I +A + + I AK A N+W D+ + Sbjct: 4 NKNYINGEWVESNDVNLDINPSDTNDIIGEYARADEQQTNDAIQAAKAARNVWRDVCVNE 63 Query: 110 RGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTL 169 + I+ IG + + L L++ E GK L E GEV + + +G + + G L Sbjct: 64 KSIILDNIGSEILARKTELATLLAREEGKTLPEATGEVVRAGMIFKFFSGEAVRLTGDIL 123 Query: 170 PSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIA 229 S RPG + P+G++G+I+ +NFP+A+ W A AL GN + K A + A Sbjct: 124 ASTRPGLNVEITREPVGVIGVISPWNFPIAIPAWKIAPALAFGNTVVLKSADLVPASAWA 183 Query: 230 VTKIIAKVLEDNLLPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQER 289 + +II++ L GA + G+ +G + ++ ++FTGS +G + V R Sbjct: 184 LAEIISRA---GLPAGAFNLVMGSGSKVGDTIVNSPDIDAVTFTGSDAIGNGIRGKVAGR 240 Query: 290 FGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDR 349 K LE+GG N ++ +DADL + +A+ A GQRCT RL + E IHD V Sbjct: 241 GAKVQLEMGGKNPLVVLDDADLDTAINAAVDGAFFGTGQRCTASSRLIVTEGIHDAFVAG 300 Query: 350 LKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVM--DHPGN 407 + +R G+ D GP+ ++ + ++ + K+EG + YGG+++ D PG Sbjct: 301 VIERLQGLRTGHALDSKSQIGPVSSQAQLQTDLEYISIGKEEGAHLAYGGELLQRDTPGY 360 Query: 408 YVEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDL--G 465 Y+ P + T +D + +E F P+ V + KN EE E N+ + GL+S I T L Sbjct: 361 YLSPALFTETDNDMRLNREEVFGPVATVIRAKNYEEALELANDTRFGLTSGICTTSLESS 420 Query: 466 RIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTG-GGRESGSDAWKQYMRRSTCTI 524 + F+ + S+ G+V VN+PT+G + FGG K++ G RE GS A + + TC I Sbjct: 421 KDFK----RNSEAGMVMVNLPTAGIDYHVPFGGRKNSSYGSREQGSYAREFFTIVKTCYI 476 Lambda K H 0.319 0.137 0.417 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: 654 Number of extensions: 32 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: 539 Length of database: 477 Length adjustment: 34 Effective length of query: 505 Effective length of database: 443 Effective search space: 223715 Effective search space used: 223715 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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