Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate WP_057687530.1 ABB28_RS16890 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-12387 (496 letters) >NCBI__GCF_001431535.1:WP_057687530.1 Length = 490 Score = 172 bits (437), Expect = 2e-47 Identities = 125/401 (31%), Positives = 189/401 (47%), Gaps = 10/401 (2%) Query: 25 VDLTAVKATPHGPHPLTGADLFGLRAHTPEDVDRAVEAAHTAFLTWRTTPAPVRGALVKR 84 VD T+ K T +P TG + ++ DV+RAV +A W A R +++R Sbjct: 16 VDATSGK-TFQSINPATGKVIAEVQIANQADVERAVASAAEGQKVWAAMTAMERSRILRR 74 Query: 85 FGELLTEHKQDLADLVTIEAGKIRSEALG-EVQEMIDICDFAVGLSRQLYGRTMPSERPG 143 +LL E LA L T++ GK SE ++ D+ ++ GL+ + G +P R Sbjct: 75 AVDLLRERNDALAQLETLDTGKALSETTTVDIVTGADVLEYYAGLATAIEGNQVPL-RES 133 Query: 144 HRLMETWHPLGVVGVISAFNFPVAVWAWNAAVALVCGDTVVWKPSELTPLNRAACAALLD 203 PLGVV I A+N+PV + W +A AL G+ +V+KPSE+TPL A + Sbjct: 134 SFFYTRREPLGVVAGIGAWNYPVQIALWKSAPALAAGNAMVFKPSEVTPLTVIELAKIY- 192 Query: 204 LAIADAGAPKGLNQVVVGAA-DVGERLVDSPRVPLVSATGSTRMGRAVGPRVAARFGRTI 262 +AG P G+ VV G +VG+ L + P + +S TG G+ V A+ + + Sbjct: 193 ---TEAGVPDGVFNVVQGPGREVGQWLTEHPVIEKISFTGGVETGKKVMASAASSSLKEV 249 Query: 263 -LELGGNNAAVVTPSADLDLTVNAAVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAA 321 +ELGG + V+ A L+ + AV A ++GQ CT R+ V + + Sbjct: 250 TMELGGKSPLVICDDAQLERAADIAVMANFFSSGQVCTNGTRVFVPRPMLAAFEAAVVER 309 Query: 322 FERLPIGDPFQDTTLVGPLVNEAAFGRMREAVERATAEGGTLCAGGERQFPDA-APGAYY 380 +R+ IGDP T GP+ + A + +E EG L GG R A A GAY Sbjct: 310 VKRIRIGDPQDAQTNFGPMTSFAHMDNVLRLIETGKREGARLLTGGGRATDGALAKGAYV 369 Query: 381 VRPALVRMPAQTAVVREETFAPILYVLTYRDLDEAIRLNNE 421 + +VREE F P++ +L Y D +E I N+ Sbjct: 370 LPTVFSDCRDDMTIVREEIFGPVMSILAYDDEEEVIARAND 410 Lambda K H 0.320 0.135 0.406 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: 474 Number of extensions: 30 Number of successful extensions: 5 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: 496 Length of database: 490 Length adjustment: 34 Effective length of query: 462 Effective length of database: 456 Effective search space: 210672 Effective search space used: 210672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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