Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__Dyella79:N515DRAFT_0465 Length = 511 Score = 236 bits (602), Expect = 1e-66 Identities = 147/474 (31%), Positives = 235/474 (49%), Gaps = 16/474 (3%) Query: 9 TYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLT 68 TYL GEW ++ ++ NPA +++G V S+A D E V A EA WR Sbjct: 18 TYLG--QGEWSRTSDAGALQPVNPA-TGEVIGTVHASSAADYETIVKRAQEAFKTWRTTP 74 Query: 69 GAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTG 128 RG+ + + + + + + + EMGK PE GE I I + G+ G Sbjct: 75 APRRGEAVRLCGEALRKHKDALGSLVALEMGKIKPEGDGEVQEMIDIADFAVGQSRMLYG 134 Query: 129 DVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT 188 + S M+ PLG+VG+IS +NFPVA+ W A + G+ + KP+ +T ++ Sbjct: 135 YTMHSERPGHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDICIWKPSPKTPLS 194 Query: 189 CAKIIACFEEAGLPAG----VINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQA 244 + EA L AG + L G+ + QG + + ++FTGS +VG+++G+ Sbjct: 195 AIATMKICNEA-LKAGGFPDIFFLFNDAGTDLSQGFVDDKRIPLISFTGSTKVGRMVGER 253 Query: 245 ALARGAKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYER 304 R + LE+GG N +I+ ADL+ A A++ GA + GQ+CT T R+ V I Sbjct: 254 VARRMGRSLLELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTRRLFVHESIVGE 313 Query: 305 FKEKLLQRTKDI--TIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLE 362 +KL+ K + IGD MGP+ S++ + L +EK K G +L GG L Sbjct: 314 VTDKLVAAYKQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASGGKVLTGGAALS 373 Query: 363 NGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASI 422 + K G +V P I V + + Q E F P++ ++ S++EA+ + NDV GLS++I Sbjct: 374 DRK---GNFVLPTIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQNDVPQGLSSAI 430 Query: 423 FTENIGRMLSFIDEI--DAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAA 474 FT ++ ++ D G+ +N ++G E+ FGG K++ RE G A Sbjct: 431 FTRDLKAAEQYLSSAGSDCGIANVNIGTSGAEIGGAFGGEKETGG-GRESGSDA 483 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: 565 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 488 Length of database: 511 Length adjustment: 34 Effective length of query: 454 Effective length of database: 477 Effective search space: 216558 Effective search space used: 216558 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