Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate 3609158 Dshi_2546 Malate/L-lactate dehydrogenase (RefSeq)
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__Dino:3609158 Length = 351 Score = 162 bits (411), Expect = 9e-45 Identities = 119/346 (34%), Positives = 168/346 (48%), Gaps = 14/346 (4%) Query: 9 PTQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLAS 68 P T+S L D + R G + A+ +A A G +HG+FR+ YL+ L Sbjct: 2 PDDTISAEALQDFVARALSARGVPTQDANKVAGLMVEADIYGYGTHGVFRLRQYLARLEG 61 Query: 69 GWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFA 128 G + V A +D NGF A+AAAR L ++KAR AG+ + +R +H Sbjct: 62 GGCNPAPNISVLQQTVATALIDGDNGFGHLAMAAARDLAMEKARQAGIGWVGVRRGNHAG 121 Query: 129 ALWPDVEPFAEQGLVALSM-VNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLAT 187 L V P AE GL+ ++ V S V P+G L GTNPIAF AP G +P VFD+AT Sbjct: 122 PLALYVRPQAEAGLLGMAAAVGSANHVPPYGGTDLLLGTNPIAFSAPAEGPDPFVFDMAT 181 Query: 188 SAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVEL 247 + A G ++ ++G +P G V RDG P +P A G LLP GG KG LS+ + L Sbjct: 182 TVAAMGKIKTLLQQGADMPEGWMVGRDGKPLTDP-ARKSEGFLLPIGGPKGFGLSVAIGL 240 Query: 248 LAAGLTGGNFSFE-FDWSKHPGAQTPWTGQLLIVIDPDK-GAGQHFAQRSEELVRQ---- 301 +A L G F + D++ + T TGQ ++ +DP G G FA+ + + + Sbjct: 241 MAGVLNGAAFGSDVVDFTSDTTSPTN-TGQFVMALDPAAFGLGDGFAETARRVFGEMRAS 299 Query: 302 --LHGVGQERLPGDRRYLERARSMAHGIVIAQA---DLERLQELAG 342 L G RLPGD + G+ + A DL+ L E G Sbjct: 300 PPLPGHHPVRLPGDGKTQAAETRRRQGLTLNPALRKDLDALAEKYG 345 Lambda K H 0.320 0.137 0.412 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: 372 Number of extensions: 29 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: 343 Length of database: 351 Length adjustment: 29 Effective length of query: 314 Effective length of database: 322 Effective search space: 101108 Effective search space used: 101108 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: 49 (23.5 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