Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_085772038.1 B1812_RS13395 aldehyde dehydrogenase family protein
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_002117405.1:WP_085772038.1 Length = 506 Score = 274 bits (701), Expect = 5e-78 Identities = 180/485 (37%), Positives = 253/485 (52%), Gaps = 15/485 (3%) Query: 10 YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69 Y NFI G+WV G+ +P + I V A DVE A+ AA++AK AW K Sbjct: 19 YDNFIGGQWVAPLGGEYFDNISPITGHPIC-QVARGRAADVELALDAAHKAKDAWGKTPA 77 Query: 70 AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYYAGEGMRKTG 128 AER L K A ++ L +A T + GK + E + I RY+AG +R Sbjct: 78 AERANMLNKIAQRLDDNLSALALVETIDNGKPIRETTAADIPLAIDHFRYFAG-CLRAQE 136 Query: 129 DVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT 188 + D D + + PLGVVG I PWNFP+ + WK++PAL GN VV+KPA +T ++ Sbjct: 137 GSLSEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLSPALAAGNCVVLKPAEQTPMS 196 Query: 189 CAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALAR 248 + + LP GV+N+V G G G+ LA + + + FTG G++I Q A Sbjct: 197 ILAVAELIADL-LPPGVLNIVNGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAAEN 255 Query: 249 GAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIY 302 LE+GGK+P V+ DDA L+ A E + A G+ CT SR +VQ IY Sbjct: 256 LIPVTLELGGKSPNIFFADVMAEDDAFLDKALEGFASFALNQ-GEVCTCPSRALVQRSIY 314 Query: 303 ERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEK-L 361 ++F EK L R I G L +G AS +QL+ LSY++ G++EGA +LIGGE+ + Sbjct: 315 DKFMEKALARVAKIRQGHPLDPATMIGAQASNDQLEKILSYVDIGRKEGAKVLIGGERSV 374 Query: 362 ENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSAS 421 G+ + GYY+QP + + M + QEEIFGPV+++ ++ EEAL IAND +GL A Sbjct: 375 LEGELKEGYYMQPTALEG-HNRMRVFQEEIFGPVVSVTTFETEEEALQIANDTLYGLGAG 433 Query: 422 IFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAI 481 ++T + R I AG V N A A FGG KQS RE + D + Sbjct: 434 LWTRDGSRAYRCGRAIRAGRVWTNCYHA-YPAHAAFGGYKQSGI-GRENHKMMLDHYQQT 491 Query: 482 KTVFV 486 K + V Sbjct: 492 KNLLV 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: 529 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: 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