Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_085972619.1 BBTA_RS18005 betaine-aldehyde dehydrogenase
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_000015165.1:WP_085972619.1 Length = 496 Score = 338 bits (867), Expect = 3e-97 Identities = 197/475 (41%), Positives = 282/475 (59%), Gaps = 10/475 (2%) Query: 14 INGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEA-KTAWRKLTGAER 72 I G V S SG NPA + + + AEDV+ AV AA A + WR + AER Sbjct: 26 IGGRHVPSVSGRTFTTLNPATEQPLATIAEGN-AEDVDLAVAAARRAFEGPWRTMRAAER 84 Query: 73 GQYLYKTADIMEQRLEEIAACATREMGKTLPEA-KGETARGIAILRYYAGEGMRKTGDVI 131 G L K A ++ R EI + + GK + + + I L YYAG + +G+V+ Sbjct: 85 GAILLKWAQLVRDRSAEIVELESLDAGKPVSAILRQDLPAAIDTLTYYAGWADKISGEVV 144 Query: 132 PSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCAK 191 ST DAL +T R P+GVV I PWNFP+ I +WK+APAL G TVV+KPA T+++ + Sbjct: 145 -STRDDALTYTVREPVGVVAAIVPWNFPLMIGMWKLAPALACGCTVVMKPAELTSLSALR 203 Query: 192 IIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARGAK 251 I EAGLP GV+N+VTGPG +VG+ L H V+ VTFTGS VG+ I +AA + Sbjct: 204 IAELALEAGLPPGVLNIVTGPGRIVGEALVNHPDVDKVTFTGSPGVGRGIMKAAAGNFKR 263 Query: 252 YQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKLLQ 311 LE+GGK+ I+ DDA++EAAA+A +G F + GQ C+A SRV+VQ Y+ E+L Sbjct: 264 VSLELGGKSANIIFDDANIEAAAKAAASGIFFNAGQVCSAGSRVLVQERAYDEVVERLTA 323 Query: 312 RTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNGYY 371 R + + IGD L +GP+ S+ Q+ L Y++ G++EGA+L+ GGE+ GY+ Sbjct: 324 RARALRIGDPLDRATSLGPVISERQMKTILDYVDIGRREGATLVTGGERAA----ARGYF 379 Query: 372 VQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGRML 431 + PA+F VT EM I+QEEIFGPV+++IK +AL +AN + L+A +++ ++GR+ Sbjct: 380 ISPAVFAGVTHEMRISQEEIFGPVVSVIKFKDEADALRMANGTAYSLAAGVWSRDLGRVQ 439 Query: 432 SFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVFV 486 F + AG V IN +++ P+GG + S RE G AA D FT K V++ Sbjct: 440 RFAKRLRAGTVWINTYGY-TDVRLPWGG-DRDSGLGREHGTAALDNFTEPKAVWM 492 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: 522 Number of extensions: 21 Number of successful extensions: 4 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: 496 Length adjustment: 34 Effective length of query: 454 Effective length of database: 462 Effective search space: 209748 Effective search space used: 209748 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