Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_085770964.1 B1812_RS07050 aldehyde dehydrogenase
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_002117405.1:WP_085770964.1 Length = 505 Score = 272 bits (696), Expect = 2e-77 Identities = 186/488 (38%), Positives = 254/488 (52%), Gaps = 21/488 (4%) Query: 10 YLNFINGEWVKSQSGDMVKVENPADVND-IVGYVQNSTAEDVERAVTAANEAKTAWRKLT 68 Y NFI GEW+ ++G EN VN ++ V S D+E A+ AA+ AK AW + + Sbjct: 18 YENFIGGEWLAPRAGRYF--ENVTPVNGRMLCEVPRSDEIDIELALDAAHAAKEAWGRTS 75 Query: 69 GAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYYAGEGMRKT 127 A R + L AD MEQ L +A + + GK + E + I RY+A + Sbjct: 76 VAARSRLLNAVADRMEQNLAALAEAESWDNGKPIRETTAADIPLAIDHFRYFASVIRAQE 135 Query: 128 GDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAV 187 G V D D + + PLGVVG I PWNFP+ + WK+APAL GN VV+KPA T Sbjct: 136 GGV-SELDHDTVAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCVVLKPAEPTP- 193 Query: 188 TCAKIIACFEEAG--LPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAA 245 A I+ E G LP GV+N+V G G G+ LA + + FTG G++IG+ A Sbjct: 194 --ASILVWAELVGDLLPPGVVNIVNGFGLEAGKPLASSSRIAKIAFTGDTGTGRLIGEYA 251 Query: 246 LARGAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQS 299 LE+GGK+P V+ DDA L+ A E A G+ CT SR +V Sbjct: 252 ARNLIPATLELGGKSPNIFFADVMADDDAFLDKALEGFAMFALNQ-GEVCTCPSRALVHR 310 Query: 300 GIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGE 359 IY+RF E+ L+R I GD L + +G AS+ Q++ L+YI+ G++EGA +LIGG Sbjct: 311 SIYDRFMERALKRVGAIVQGDPLDKRTMVGAQASREQMEKILAYIDIGRKEGAEILIGGG 370 Query: 360 KLENG-KYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418 + + G GYYV+P + ++M + QEEIFGPV+++ D+ EEA IAND FGL Sbjct: 371 RADLGADLSGGYYVRPTVLLG-NNKMRVFQEEIFGPVLSVTVFDTDEEAAAIANDTVFGL 429 Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFF 478 A ++T +I R I AG V N A A FGG KQS RE D + Sbjct: 430 GAGVWTRDINRAYRMGRAIQAGRVWTNCYHA-YPAHAAFGGYKQSGV-GRENHRMMLDHY 487 Query: 479 TAIKTVFV 486 K + V Sbjct: 488 QQTKNLLV 495 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: 551 Number of extensions: 24 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: 505 Length adjustment: 34 Effective length of query: 454 Effective length of database: 471 Effective search space: 213834 Effective search space used: 213834 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