Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_011940134.1 GURA_RS16875 aldehyde dehydrogenase family protein
Query= SwissProt::P42236 (488 letters) >NCBI__GCF_000016745.1:WP_011940134.1 Length = 496 Score = 384 bits (985), Expect = e-111 Identities = 199/476 (41%), Positives = 280/476 (58%), Gaps = 2/476 (0%) Query: 12 NFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTGAE 71 NFI G W+ G NPAD + + V S DV+RAV AA EA WR + Sbjct: 7 NFIGGAWIPPAGGKRFASVNPADNRETIAEVSLSERGDVDRAVAAAREAFRTWRLMPPPR 66 Query: 72 RGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEGMRKTGDVI 131 RG+ L++ A+++ R E+ TREMGK L E G+ I + Y AGEG R G+ + Sbjct: 67 RGEILFRAAELLAGRKAELGELVTREMGKVLAEGLGDVQEAIDMAYYMAGEGRRWQGETV 126 Query: 132 PSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCAK 191 PS D + R PLGVV +++PWNFP AIP WK+ PAL+ GNTV+ KP++ T A Sbjct: 127 PSELPDKDCKSVRQPLGVVALVTPWNFPTAIPAWKLFPALICGNTVIFKPSSATPACAAA 186 Query: 192 IIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARGAK 251 I+ EAG+P GV+NLV GPG +G+ L H GV+A +FTGS G+ + Sbjct: 187 IVETLSEAGIPPGVVNLVHGPGEEIGEYLLTHPGVDAASFTGSCAAGERLEGLLGKMHRP 246 Query: 252 YQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKLLQ 311 LEMGGKN VIV DADL A E V+ G F ++GQ+CT+ SRVIV +Y+RF E L++ Sbjct: 247 LALEMGGKNAVIVMADADLSLALEGVLWGGFGTSGQRCTSASRVIVNEQVYDRFVEMLVE 306 Query: 312 RTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNGYY 371 K + +G+ L ++ +GP+ ++ Q L YI G EG LL GG ++ G NG++ Sbjct: 307 GAKRLRLGNGLHKETDVGPLINEQQCRKVLDYIRIGIGEGGELLTGGRQVTEGGCGNGWF 366 Query: 372 VQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGRML 431 ++P +F V EM IA+EEIFGPV+++IK EA+ IANDV GLS++I++ ++ Sbjct: 367 IEPTVFGGVRPEMRIAREEIFGPVVSVIKCGGFAEAVEIANDVPMGLSSAIYSRDVNLTA 426 Query: 432 SFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQG--EAAKDFFTAIKTVF 485 ++ +G+V INA + G E+ PFGG K S S E G A DF++ +K ++ Sbjct: 427 RAERDLQSGIVYINASTIGAEIHLPFGGWKHSGSGHPEAGGRGGALDFYSRVKVIY 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: 588 Number of extensions: 20 Number of successful extensions: 2 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 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