Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate H281DRAFT_03016 H281DRAFT_03016 aldehyde dehydrogenase (acceptor)
Query= SwissProt::Q9H2A2 (487 letters) >FitnessBrowser__Burk376:H281DRAFT_03016 Length = 483 Score = 339 bits (869), Expect = 1e-97 Identities = 187/472 (39%), Positives = 269/472 (56%), Gaps = 10/472 (2%) Query: 14 IDGKFLP--CSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSR 71 IDGK LP Y + +P+T E V +++ AV+AAR A W+ ER R Sbjct: 14 IDGKRLPPGTGEYSVNINPATEEPIAHVAQGSAADVDTAVRAARAALKVWNGIKAAERGR 73 Query: 72 VLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQM 131 +L+++A L+ +L+E A ES D GK +A D+P ++ ++A + + Sbjct: 74 ILSRLAGLMRANLDELAALESLDAGKPIAAVMRQDVPAAIDTLEYYAGWCDKINGQVVPV 133 Query: 132 DHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWMLC 191 + YT+R PVGV I PWN PL + WKIAPA+A G T+I KP+E+T ++A + Sbjct: 134 -RPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLSALRIG 192 Query: 192 KLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLS 251 +L +AGVPPGV+NIV G G VG+ALV+HP V ++FTGS I Q +A + K+++ Sbjct: 193 ELALEAGVPPGVLNIVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAAGNFKRVT 252 Query: 252 LELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVEAT 311 LELGGK+ +IF DANLD + A F N G++C SRI + +Y E ++R Sbjct: 253 LELGGKSANLIFPDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLAARA 312 Query: 312 RKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQAGY 371 + KVG PS S+G LIS A ++ V YV +EGA + G G + G+ Sbjct: 313 KSIKVGDPSSRETSMGPLISAAQMKTVLGYVDAGRSEGASLVTGGG-------RIGERGF 365 Query: 372 FMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVGRV 431 F+ PTV +++ E EEIFGPV V+ F+ E + I AN Y LAA VWS+++GRV Sbjct: 366 FVEPTVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRV 425 Query: 432 HRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTI 483 HRVA+ L++G VW N + ++ LP+GG SG GRE + + FTE K + Sbjct: 426 HRVARDLRAGTVWINTYGYTDVRLPWGGSGDSGFGREHGDVAIENFTEPKAV 477 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: 538 Number of extensions: 21 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: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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