Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__PV4:5208455 Length = 498 Score = 299 bits (766), Expect = 1e-85 Identities = 174/477 (36%), Positives = 265/477 (55%), Gaps = 16/477 (3%) Query: 13 FIDGKFLPCSSY--IDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFP--SWSSRSPQE 68 FI+G++ S D P G V +V + + AV ARE F WS P + Sbjct: 24 FINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGDWSQLPPVK 83 Query: 69 RSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFF--ASSSLHHTS 126 R +V+ + ADLLE + +E A E+ D GK + + +D+ + + R+ A ++ Sbjct: 84 RKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEAVDKIYDEI 143 Query: 127 ECTQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVT 186 T + +G + R PVGV I PWN PL + WK+ PA+A GN+V+ KPSE + +T Sbjct: 144 APTAHNEIGMI---TREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLT 200 Query: 187 AWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP- 245 A + +L +AG+P GV+N++ G G VG+AL H +V + FTGS A+++ + Sbjct: 201 AIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGES 260 Query: 246 HCKKLSLELGGKNPAIIFEDA-NLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFL 304 + K++ LE GGK+P I+F DA NL E A + NQGE+C SR+ V+ + E + Sbjct: 261 NMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESGVKEELI 320 Query: 305 KRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLP 364 + W+ G P DP + GA++ + LE V Y++ +AEGAQ+ G G L+ Sbjct: 321 NLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQG-GQQVLA-- 377 Query: 365 ARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVW 424 G ++ PT+ ++K+E EEIFGPV V+ FD EE I N+ YGLAA VW Sbjct: 378 --ETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAGVW 435 Query: 425 SSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIK 481 +S++ + H+ AK L+SG+VW N + ++ PFGG K SG GR+ + ++D +TEIK Sbjct: 436 TSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFDKYTEIK 492 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: 596 Number of extensions: 28 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: 487 Length of database: 498 Length adjustment: 34 Effective length of query: 453 Effective length of database: 464 Effective search space: 210192 Effective search space used: 210192 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