Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 281 bits (719), Expect = 4e-80 Identities = 184/485 (37%), Positives = 264/485 (54%), Gaps = 15/485 (3%) Query: 10 YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69 Y NFI G+WV + G + +P D ++ V S+AEDVE A+ AA+ A+ AW + + Sbjct: 19 YDNFIGGKWVPAVKGQTFENISPID-GRVICTVARSSAEDVELALDAAHAARGAWGRTSP 77 Query: 70 AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYYAGEGMRKTG 128 AER L + AD +EQ+L+ +A T + GK + E K + + RY+AG +R Sbjct: 78 AERSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAG-CLRAQE 136 Query: 129 DVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVT 188 I D D + + PLGVV I PWNFP+ + +WK+APAL GN V++KPA +T ++ Sbjct: 137 GGISEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMS 196 Query: 189 CAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALAR 248 ++ + LP GV+N++ G G G+ LA++ + V FTG G++I Q A Sbjct: 197 VMVLVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYASEN 255 Query: 249 GAKYQLEMGGKNPVI----VADDAD--LEAAAEAVITGAFRSTGQKCTATSRVIVQSGIY 302 LE+GGK+P I VAD+ D + A E A G+ CT SR +VQ IY Sbjct: 256 IIPVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQ-GEVCTCPSRALVQEKIY 314 Query: 303 ERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLE 362 +RF E+ + R K I G+ L +G AS +QL+ LSY++ G+QEGA +L GG + + Sbjct: 315 DRFMERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGGGRAD 374 Query: 363 NG-KYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSAS 421 G + G+YVQP I + ++M I QEEIFGPV+++ EEAL IAND +GL A Sbjct: 375 VGPELAGGFYVQPTILEG-HNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAG 433 Query: 422 IFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAI 481 ++T N R F I+AG V N A FGG KQS RE + D + Sbjct: 434 VWTRNGTRAYRFGRAIEAGRVWTNCYHL-YPAHAAFGGYKQSGI-GRENHKMMLDHYQKT 491 Query: 482 KTVFV 486 K + V Sbjct: 492 KNMLV 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: 541 Number of extensions: 21 Number of successful extensions: 6 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 Sep 24 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