Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_200825325.1 BZY95_RS07130 aldehyde dehydrogenase family protein
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_002151265.1:WP_200825325.1 Length = 484 Score = 412 bits (1060), Expect = e-119 Identities = 208/478 (43%), Positives = 308/478 (64%), Gaps = 3/478 (0%) Query: 10 YLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTG 69 +LN+I+G+WV S SG + NPAD +D++G Q S +D RA+ AA+ A TAWR+ Sbjct: 7 FLNYIDGQWVASGSGATFENRNPADQDDLLGLFQASGVDDARRAIAAADRAFTAWRETPI 66 Query: 70 AERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTGD 129 ++R + L + AD + + +E+ A TRE GK L ++ E R LR+YA EG TG+ Sbjct: 67 SQRAKILNRAADYLMENVEQFARELTREEGKLLANSRDEVTRSAQTLRFYAVEGQTITGE 126 Query: 130 VIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTC 189 P D ++T R PLGV +I+PWNFP++IP K+APAL+ GNTVV KP+++ + Sbjct: 127 TFPQDDAKMTVYTQREPLGVATIITPWNFPISIPARKIAPALITGNTVVFKPSSDAPLIG 186 Query: 190 AKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARG 249 ++ AG+PAGV N +TG S +G+ + + V A++FTGS G+ I +AA A Sbjct: 187 YRLAEALHHAGVPAGVFNFITGAASAIGEEITANPVVKAISFTGSTAAGERIHRAA-AMA 245 Query: 250 AKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKL 309 + Q+E+GGKNP+IV +DAD++ A + + G F TGQ CT TSRV++ + + +L Sbjct: 246 TRTQMELGGKNPLIVLEDADIDTAVDLTVKGGFSLTGQACTGTSRVLIARSRKQEYLTRL 305 Query: 310 LQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNG 369 +++ K + IG+ + E + +GP+A++ QLD L Y+E G++E A+ + GGE L G Y G Sbjct: 306 VEQVKTLKIGNGMSEGIQIGPLATRQQLDTVLGYVETGRKE-ATHVYGGEHLTEGDYAKG 364 Query: 370 YYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGR 429 +YV PAIF +VT EM IA+EEIFGPV+A+I+VD E+A+ AND +GL+A + T+N Sbjct: 365 FYVTPAIFSDVTQEMRIAREEIFGPVVAVIEVDGYEDAIAKANDTPYGLAAGLVTKNFDY 424 Query: 430 MLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHS-REQGEAAKDFFTAIKTVFV 486 + F +I AG V+IN + G + APFGG+KQSS+ + RE G A DFFT KTV++ Sbjct: 425 IQRFPLDIQAGTVKINRTTTGNLVNAPFGGLKQSSTSTFRESGRAGLDFFTQTKTVYL 482 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: 589 Number of extensions: 26 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: 484 Length adjustment: 34 Effective length of query: 454 Effective length of database: 450 Effective search space: 204300 Effective search space used: 204300 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