Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate N515DRAFT_0954 N515DRAFT_0954 NADP-dependent aldehyde dehydrogenase
Query= metacyc::G1G01-1343-MONOMER (525 letters) >lcl|FitnessBrowser__Dyella79:N515DRAFT_0954 N515DRAFT_0954 NADP-dependent aldehyde dehydrogenase Length = 533 Score = 331 bits (848), Expect = 5e-95 Identities = 220/506 (43%), Positives = 277/506 (54%), Gaps = 18/506 (3%) Query: 22 RAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRETSLEQRAEFLEAIATQIEALG 81 RA +PTTG+ + PA+ V A A A AA T E+ A FLEA A IEA Sbjct: 28 RAENPTTGEAIGPAFPICGAADVEAALAAATAAAAELAATPPERIAAFLEAYADAIEADA 87 Query: 82 DALIDRAVIETGLPKA-RIQG-ERGRTCTQLRTFARTVRAGEWLDVRIDSALPERQPLPR 139 +AL+D A ET LPK R+ E RT QLR A+ VR+ W ID+A Sbjct: 88 EALVDIAHAETALPKQPRLAAVELPRTTNQLRLAAKAVRSYAWTQPVIDTA--------- 138 Query: 140 ADLRQRQVALG-PVAVFGASNFPLAFS-VAGGDTASALAAGCPVVVKAHSAHPGTSELVG 197 A+LR LG PV VFG +NFP AF+ +AG D ASA+AA PV+ KAH +HPGTSE + Sbjct: 139 ANLRSHLAPLGKPVLVFGPNNFPFAFNAIAGSDFASAIAARNPVIAKAHPSHPGTSERLA 198 Query: 198 QAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFTGSRSGGMALCQAAQARP 257 +A A++Q GLP +LY +G L D R+ A+GFTGSR+GG+AL AA A Sbjct: 199 RAAFAALRQAGLPAASVQMLYHFDHAIGGKLAGDARLGAIGFTGSRAGGLALKAAADA-- 256 Query: 258 EPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQFCTNPGLVIARQGPALQ 317 IP Y E+SS+NPVFL AL R ALAQ F S T G+GQFCTNPG+VI +G A Sbjct: 257 AGIPAYVELSSVNPVFLLPGALAERGIALAQEFFTSCTMGSGQFCTNPGVVIVPRGEAGD 316 Query: 318 RFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAITSGQAGQGPNQCQAQLF 377 F+ AA + A + + G+ Q GIA L AQ + G G + L Sbjct: 317 AFVEAAKAHFAAAAPSVLFSGGVLEHLQKGIATLR-AAGAQLLAGGDTGSPGYRHAPTLL 375 Query: 378 VTQAEAFLADP-ALQAEVFGAASLVVACTDDEQVRQVAEHLEGQLTATLQLDEADIDSAR 436 A FL +P ALQ E FG ASL+V Q+ QVA EG LT TL + AD + Sbjct: 376 EVDATQFLREPQALQTEAFGPASLLVRVDGVAQMVQVATAFEGNLTGTLYANSADDAAWN 435 Query: 437 ALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTSVG-TAAILRFLRPVCY 495 + L + GR++ N PTGV V AM HGGP+P+T T+VG AAI RF Y Sbjct: 436 DVAQALRPRVGRLIANRMPTGVAVSAAMNHGGPYPSTGHPGFTAVGMPAAIRRFAALHSY 495 Query: 496 QDVPDALLPQALKHGNPLQLRRLLDG 521 +VP+ LLP L+ NP + R +DG Sbjct: 496 DNVPEHLLPPELRDHNPGGVARQIDG 521 Lambda K H 0.319 0.134 0.391 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: 781 Number of extensions: 44 Number of successful extensions: 7 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: 525 Length of database: 533 Length adjustment: 35 Effective length of query: 490 Effective length of database: 498 Effective search space: 244020 Effective search space used: 244020 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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