Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 278 bits (710), Expect = 4e-79 Identities = 177/465 (38%), Positives = 254/465 (54%), Gaps = 20/465 (4%) Query: 10 YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69 Y NFI G++V G+ V +P D + V A D+E A+ AA++A AW + + Sbjct: 22 YDNFIGGKFVPPVDGEYFDVISPVD-GQVFTKVARGKAADIELALDAAHKAFPAWSRTSA 80 Query: 70 AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEA-KGETARGIAILRYYAGEGMRKTG 128 ER L K AD +E +LE +AA T + GK + E + A + RY+AG + G Sbjct: 81 TERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEG 140 Query: 129 DVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT 188 I D+ + + P+G+VG I PWNFP+ + WKMAPAL G ++KPA +T Sbjct: 141 S-IAELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTP-- 197 Query: 189 CAKIIACFEEAG--LPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAAL 246 A I+ E G LPAGV+N+V G G G+ LA+ ++ V FTG G++I Q A Sbjct: 198 -ASIMILMEVIGDLLPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYAS 256 Query: 247 ARGAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSG 300 +E+GGK+P V+ ADD L+ E + A G+ CT SR++V Sbjct: 257 ENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQ-GEVCTCPSRILVHEK 315 Query: 301 IYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGE- 359 IY+ F EK++ R + I +G L + MG ASK+Q + LSYI+ GKQEGA +L GGE Sbjct: 316 IYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEV 375 Query: 360 -KLENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418 KL +G +NGYYV+P + ++M + QEEIFGPV ++ +EEA++I+ND +GL Sbjct: 376 AKLNSG-LENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGL 433 Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQS 463 A ++T + I AG V +N A APFGG K+S Sbjct: 434 GAGVWTRDAHEAYQVPRAIKAGRVWVNCYHA-YPAHAPFGGYKKS 477 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: 576 Number of extensions: 32 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: 509 Length adjustment: 34 Effective length of query: 454 Effective length of database: 475 Effective search space: 215650 Effective search space used: 215650 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