Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 288 bits (738), Expect = 2e-82 Identities = 182/462 (39%), Positives = 254/462 (54%), Gaps = 14/462 (3%) Query: 10 YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69 Y N+I G++V G +P D + +ST ED+E AV AA+EA W K + Sbjct: 14 YDNYIGGKFVAPVKGAYFDNISPID-GKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSS 72 Query: 70 AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEA-KGETARGIAILRYYAGEGMRKTG 128 ER L K A ME LE +AA T + GK + E + G+ RY+AG + G Sbjct: 73 TERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEG 132 Query: 129 DVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT 188 + D++ + P+GVV I PWNFP+ + IWK+APAL GN VV+KPA T V+ Sbjct: 133 S-LSELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVS 191 Query: 189 CAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALAR 248 ++ + LP GV+N+V G GS +G+ L + V+ FTGS G+++ Q A Sbjct: 192 IMVLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATEN 250 Query: 249 GAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIY 302 LE+GGK+P V+ DDA L+ A E + A G+ CT SR+++Q IY Sbjct: 251 IIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFALNQ-GEICTCPSRLLIQEDIY 309 Query: 303 ERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLE 362 E+F K+++RTK I IG L V MG ASK Q + +YI+ GK+EGA +L GGE E Sbjct: 310 EKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINE 369 Query: 363 -NGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSAS 421 G+ GYY++P IF ++M I QEEIFGPV+A+ ++EEA+ IAND +GL A Sbjct: 370 LPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAG 428 Query: 422 IFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQS 463 ++T + + I AG V +N A APFGG KQS Sbjct: 429 VWTRDAHELYQVPRAIQAGRVWVNQYHA-YPAGAPFGGYKQS 469 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: 573 Number of extensions: 25 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: 501 Length adjustment: 34 Effective length of query: 454 Effective length of database: 467 Effective search space: 212018 Effective search space used: 212018 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