Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_000021485.1:WP_012607209.1 Length = 506 Score = 285 bits (728), Expect = 3e-81 Identities = 186/488 (38%), Positives = 256/488 (52%), Gaps = 15/488 (3%) Query: 7 QNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRK 66 ++ Y NFI G+WV G V P + STAED+E A+ AA+ W K Sbjct: 16 KSKYDNFIGGKWVAPVKGQYFDVITPINGKSYT-QAARSTAEDIELALDAAHAIADKWGK 74 Query: 67 LTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEA-KGETARGIAILRYYAGEGMR 125 + AER L K AD +E LE +A T + GK + E + + RY+AG Sbjct: 75 TSPAERANILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRA 134 Query: 126 KTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATET 185 + G I D++ + + PLGVVG I PWNFP+ + WK+APAL GN VV+KPA T Sbjct: 135 QEGG-ISDIDENTVAYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAEST 193 Query: 186 AVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAA 245 ++ + + LP GV+N+V G G G LA + + FTGS G++I QAA Sbjct: 194 PISILILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAA 252 Query: 246 LARGAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQS 299 LE+GGK+P V+ DD+ L+ A E ++ AF G+ CT SR ++Q Sbjct: 253 ANSLIPATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAFNQ-GEVCTCPSRALIQE 311 Query: 300 GIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGG- 358 IY++F E+ L R K I G+ L + +G ASK QL LSY++ GKQEGA +LIGG Sbjct: 312 SIYDKFMERCLDRIKAIKQGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEGAQVLIGGS 371 Query: 359 EKLENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418 + + +G GYYVQP +F ++M I QEEIFGPV+A+ EAL+IAND +GL Sbjct: 372 QAIVDGDLDGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGL 430 Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFF 478 A +++ N I AG V IN A A FGG K+S RE + D + Sbjct: 431 GAGVWSRNGNVAYRMGRAIKAGRVWINCYHA-YPAHAAFGGYKESGI-GRETHKVMLDHY 488 Query: 479 TAIKTVFV 486 K + V Sbjct: 489 QQTKNLLV 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: 580 Number of extensions: 28 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: 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 Apr 09 2024. 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