Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_027179997.1 G496_RS0115120 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000429985.1:WP_027179997.1 Length = 455 Score = 219 bits (559), Expect = 1e-61 Identities = 134/453 (29%), Positives = 216/453 (47%), Gaps = 3/453 (0%) Query: 40 TVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHAD 99 +++P+TEE + +EA+S++ ++ TAA + W R +L K A+++ E + Sbjct: 5 SLNPATEE-VVATFEAYSDEKVQSILDLTAAAWADWKEKSYSERKVLLKKAAEILRERSV 63 Query: 100 TLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGV 159 LA I A++ GK + K + A A + + + Y R +P+G Sbjct: 64 ELARIAAVEMGKPVKLGKAEAEKCALVCDYYAEEGEAMLAPEPVSDAAKKVYVRFDPLGT 123 Query: 160 CGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVV 219 ++PWNFP P L G VLK A + P AL + + K+AG P V + Sbjct: 124 VLTVMPWNFPFWQVFRIAAPSLMAGNCVVLKHASNVPQCALTIEKIFKDAGFPDNVFRTL 183 Query: 220 SGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPNIVFDDA 279 G + H + V+ TGS G+ + AA + LKK +ELGG P IV DA Sbjct: 184 L-IGSDQVEAVLDHDSVFAVSLTGSEGAGKSVASAAG-ARLKKSVMELGGSDPLIVLADA 241 Query: 280 DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFM 339 DVK + N G+ C A R V +YD+ + + K + + K GDP T M Sbjct: 242 DVKKAAETAAVSRCGNAGQACIAAKRFIVMAEVYDEFIEQLKLSMSAYKPGDPLDPATEM 301 Query: 340 GAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQIVRDEIF 399 G +S+ + + + + G V++ G KG++ PTI +V D + ++E F Sbjct: 302 GPMSSKGLRETLEDQVKRCVEAGGKVLSLGSMPEGKGFYYLPTIIENVPVDSDVCQEEFF 361 Query: 400 GPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHP 459 GP + K +++E I LAND+ +GL + + N+ A ++ KI +G +++N Sbjct: 362 GPAALVFKVSSIDEAIRLANDTPFGLGGSIWSANIPLAEKLAAKIRTGNVYINALVRSDV 421 Query: 460 MVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492 VPFGG SG GRE+G + + VK+V +G Sbjct: 422 HVPFGGVGISGFGRELGSYGIREFVNVKSVCVG 454 Lambda K H 0.316 0.133 0.389 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: 509 Number of extensions: 27 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: 495 Length of database: 455 Length adjustment: 33 Effective length of query: 462 Effective length of database: 422 Effective search space: 194964 Effective search space used: 194964 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 (21.6 bits) S2: 51 (24.3 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