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) >FitnessBrowser__Dyella79:N515DRAFT_0954 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:
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