Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__Dino:3607686 Length = 506 Score = 276 bits (705), Expect = 2e-78 Identities = 175/488 (35%), Positives = 256/488 (52%), Gaps = 15/488 (3%) Query: 7 QNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRK 66 ++ Y NFI G++V G P ++VG + S+A DVE A+ AA+ AK AW K Sbjct: 16 KDRYDNFIGGKFVPPVEGRYFDNVTPI-TGEVVGQIARSSAADVELALDAAHAAKDAWGK 74 Query: 67 LTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAK-GETARGIAILRYYAGEGMR 125 + ER + K AD +E+ L+ IA T + GK + E + + RY+AG Sbjct: 75 TSVTERANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRG 134 Query: 126 KTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATET 185 + G + D D + + PLGVVG I PWNF + + WK+APA+ GN +V+KPA +T Sbjct: 135 QEGSM-SEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQT 193 Query: 186 AVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAA 245 ++ + LPAGV+N+V G G VG LA D + + FTGS G+ I +AA Sbjct: 194 PAAIMVLVELISDL-LPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAA 252 Query: 246 LARGAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQS 299 LE+GGK+P V+ DDA L+ A E + AF G+ CT SR ++ Sbjct: 253 TVNLIPVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAFNQ-GEVCTCPSRALIHE 311 Query: 300 GIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGE 359 IYE F + + R K I GD K + +G ASK Q D LSY + G +EGA +L GG+ Sbjct: 312 DIYEEFIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGK 371 Query: 360 KLE-NGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418 + + ++G+Y++P I ++M + QEEIFGPV+++ + EEAL +AND +GL Sbjct: 372 VADVSDDLKDGFYIEPTILKG-HNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGL 430 Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFF 478 A +++ + F + AG V +N A A FGG KQS RE + D + Sbjct: 431 GAGVWSRDQNTCYRFGRGVQAGRVWVNNYHA-YPAHAAFGGYKQSGI-GRENHKMMLDHY 488 Query: 479 TAIKTVFV 486 K + V Sbjct: 489 QQTKNMLV 496 Lambda K H 0.315 0.132 0.374 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: 582 Number of extensions: 32 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: 488 Length of database: 506 Length adjustment: 34 Effective length of query: 454 Effective length of database: 472 Effective search space: 214288 Effective search space used: 214288 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 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