Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF3171 PGA1_c32220 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase HpcC
Query= BRENDA::Q93YB2 (503 letters) >FitnessBrowser__Phaeo:GFF3171 Length = 503 Score = 343 bits (880), Expect = 8e-99 Identities = 188/458 (41%), Positives = 266/458 (58%), Gaps = 11/458 (2%) Query: 28 INPATQNIIGDIPAATKEDVDVAVAAAKTALTRNKGADWATASGAVRARYLRAIAAKVTE 87 I+P +++I D+ T D+D A AA+ A A+W R + L IA + Sbjct: 42 ISPVDKSVICDVAHGTAADIDAAAQAARQAF-----AEWRDLPAVQRKKILIRIAEGIEA 96 Query: 88 KKPELAKLESIDCGKPLDEAAWDIDDVAGCFEYYADLAEKLDARQKAPVSLPMDTFKSHV 147 + E+A E D G+ + A F Y+AD + + AR + P T + Sbjct: 97 RAEEIALCECWDTGQAYKFMSKAALRGAENFRYFAD--QVVQARDGQHLQSP--TLMNVT 152 Query: 148 LREPIGVVGLITPWNYPMLMATWKVAPALAAGCAAILKPSELASLTCLELGEICKEVGLP 207 R PIG VG+ITPWN P +++TWK+APALAAGC + KP+E + LT L EI +E GLP Sbjct: 153 TRVPIGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEASPLTARLLVEIAEEAGLP 212 Query: 208 PGVLNILTGLGPEAGAPLATHPDVDKVAFTGSSATGSKIMTAAAQLVKPVSLELGGKSPL 267 PGVLN + G G EAG L HP + +AF G S TGS I A +K LELGGK+P+ Sbjct: 213 PGVLNTVNGFGDEAGKALCEHPAIRAIAFVGESRTGSLITKQGADTLKRNHLELGGKNPV 272 Query: 268 VVFEDVDLDKAAEWAIFGCFWTNGQICSATSRLILHESIATEFLNRIVKWIKNIKISDPL 327 +VFED DL++A + IF + NG+ C+++SRL++ +SI +F R+++ I NIK+ PL Sbjct: 273 IVFEDADLERALDAVIFMIYSINGERCTSSSRLLIQDSIRDDFEARLIERINNIKVGHPL 332 Query: 328 EEGCRLGPVVSEGQYEKILKFVSNAKSEGATILTGGSRPEHLKKGFFIEPTIITDVTTNM 387 + +GP+VSE + K+ + A EGATI GG ++G+FI PT+ TD +M Sbjct: 333 DPTTEIGPLVSEEHFNKVTSYFDIATKEGATIAAGGEPVG--EEGYFIRPTLFTDARNDM 390 Query: 388 QIWREEVFGPVLCVKTFSTEEEAIDLANDTVYGLGAAVISNDLERCERVTKAFKAGIVWV 447 +I +EE+FGPVL F+TE EA+ LANDT YGL + +NDL R R T +AG++WV Sbjct: 391 RIAQEEIFGPVLTSIPFTTEAEALALANDTAYGLTGYLWTNDLTRALRFTDRLEAGMIWV 450 Query: 448 NCSQPCFTQAPWGGVKRSGFGRELGEWGLDNYLSVKQV 485 N P+GGVK SG GR+ G+W + Y+ K + Sbjct: 451 NSENVRHLPTPFGGVKASGIGRDGGDWSFEFYMEQKHI 488 Lambda K H 0.318 0.135 0.416 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: 653 Number of extensions: 26 Number of successful extensions: 3 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: 503 Length adjustment: 34 Effective length of query: 469 Effective length of database: 469 Effective search space: 219961 Effective search space used: 219961 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