Align Δ1-piperideine-6-carboxylate dehydrogenase (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-12387 (496 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 163 bits (412), Expect = 2e-44 Identities = 116/377 (30%), Positives = 187/377 (49%), Gaps = 18/377 (4%) Query: 55 DVDRAVEAAHTAFLTWRTTPAPVRGALVKRFGELLTEHKQDLADLVTIEAGK-IRSEALG 113 D++ A++AAH AF W T A R ++ + + + + LA + TI+ GK +R Sbjct: 60 DIELALDAAHKAFPAWSRTSATERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINA 119 Query: 114 EVQEMIDICDFAVGLSRQLYGRTMPSERPGHRL-METWHPLGVVGVISAFNFPVAVWAWN 172 ++ ++D + G+ R G +E H + + P+G+VG I +NFP+ + W Sbjct: 120 DLALVVDHFRYFAGVIRAEEGSI--AELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWK 177 Query: 173 AAVALVCGDTVVWKPSELTPLNRAACAALLDLAIADAGAPKGLNQVVVG-AADVGERLVD 231 A AL G + KP+E TP A +L I D P G+ VV G + G+ L Sbjct: 178 MAPALAAGCCTIVKPAEQTP----ASIMILMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQ 232 Query: 232 SPRVPLVSATGSTRMGRAVGPRVAARFGRTILELGGNNAAVVTPS---AD---LDLTVNA 285 SPR+ V+ TG T GR + + +ELGG + V PS AD LD + Sbjct: 233 SPRLDKVAFTGETTTGRLIMQYASENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEG 292 Query: 286 AVFAAAGTAGQRCTTLRRLIVHEDIADTVVERLTAAFERLPIGDPFQDTTLVGPLVNEAA 345 AV A G+ CT R++VHE I D +E++ A E + +G P TT++G ++ Sbjct: 293 AVMFALNQ-GEVCTCPSRILVHEKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQ 351 Query: 346 FGRMREAVERATAEGGTLCAGGE-RQFPDAAPGAYYVRPALVRMPAQTAVVREETFAPIL 404 F ++ ++ EG + GGE + YYV+P L++ + V +EE F P+ Sbjct: 352 FEKILSYIDIGKQEGAEVLTGGEVAKLNSGLENGYYVKPTLLKGHNKMRVFQEEIFGPVC 411 Query: 405 YVLTYRDLDEAIRLNNE 421 V T++D++EAI ++N+ Sbjct: 412 SVATFKDVEEAISISND 428 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: 432 Number of extensions: 20 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: 509 Length adjustment: 34 Effective length of query: 462 Effective length of database: 475 Effective search space: 219450 Effective search space used: 219450 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 17 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