Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate PP_3646 PP_3646 Aldehyde dehydrogenase family protein
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__Putida:PP_3646 Length = 493 Score = 324 bits (830), Expect = 5e-93 Identities = 182/483 (37%), Positives = 272/483 (56%), Gaps = 10/483 (2%) Query: 7 LLMLENFIDGKFLPCSS--YIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPS--WS 62 L+ + IDG++ S DS +P+T + + ++P++ + ++E AV+AA+ AF S W Sbjct: 3 LVRFQMCIDGQWRDAQSGKTFDSLNPATAQAWAQLPDADEADVELAVQAAQRAFDSKAWR 62 Query: 63 SRSPQERSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSL 122 S + R ++L ++ DL+ ++ E AQ ES+D GK + R + + F + A + Sbjct: 63 SITATARGKLLRRLGDLIAENKEHLAQLESRDNGKLIRETRGQ-VGYLPEFFHYTAGLAD 121 Query: 123 HHTSECTQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSEL 182 +D YTV P+GV I PWN PLYL K+APA+AAGNT++ KPSE Sbjct: 122 KLEGGTLPLDKPDLFAYTVHEPIGVVAGIIPWNSPLYLTAIKLAPALAAGNTIVLKPSEH 181 Query: 183 TSVTAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQL 242 S T L +L +AG P GVVN+V G GP G AL HP V I+FTG TA + + Sbjct: 182 ASATILELARLALEAGFPAGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHVVRS 241 Query: 243 SAPHCKKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSE 302 SA + KLSLELGGK+P IIF DA+LD I V +A G+ C+ SR+ VQ I+ E Sbjct: 242 SAENFAKLSLELGGKSPNIIFADADLDSAINGAVAGIYAASGQSCVAGSRLLVQDEIFDE 301 Query: 303 FLKRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLS 362 F++R + ++ ++G P D +G + + L V V A AEGA++ G + Sbjct: 302 FVERLIARAKRIRIGNPQDDASEMGPMATAQQLAVVEGLVAAAKAEGAKLHMGGKRADV- 360 Query: 363 LPARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAAT 422 G+F PT+ + M EE+FGPV V+ F +EEE + AN+ ++GLAA Sbjct: 361 ----EGDGWFYEPTLFECDSNAMTIMQEEVFGPVAAVIRFKTEEEALAMANDSQFGLAAG 416 Query: 423 VWSSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKT 482 +W+ ++GR HR+A+ ++SG++W N + P GG K+SG GRE DS +TE+KT Sbjct: 417 IWTRDLGRAHRLARDVRSGIIWVNTYRAVSAMAPIGGFKNSGYGRESGIDSVLAYTELKT 476 Query: 483 ITV 485 + + Sbjct: 477 VWI 479 Lambda K H 0.319 0.133 0.404 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: 559 Number of extensions: 18 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: 487 Length of database: 493 Length adjustment: 34 Effective length of query: 453 Effective length of database: 459 Effective search space: 207927 Effective search space used: 207927 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 (21.8 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