Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; NMAADH; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate WP_086509097.1 BZY95_RS06175 oxidoreductase
Query= SwissProt::Q5FB93 (341 letters) >NCBI__GCF_002151265.1:WP_086509097.1 Length = 357 Score = 137 bits (345), Expect = 4e-37 Identities = 111/348 (31%), Positives = 156/348 (44%), Gaps = 22/348 (6%) Query: 7 STVVRVPFTELQSLLQAIFQRHGCSEAVARVLAHNCASAQRDGAHSHGVFRMPGYVSTLA 66 +T RV EL+ + A R G EA A +A R G SHG+ +P YV L Sbjct: 4 ATDYRVAREELERFMLAALARAGADEASAGAATRALVTASRMGTDSHGLRLLPHYVQALQ 63 Query: 67 SGWVDGQATPQVSD--VAAGYVRVDAAGGF--AQPALAAARELLVAKARSAGIAVLAIHN 122 G + G + A GY+ D G A A+A A E+ A G+ +A+ N Sbjct: 64 GGRLKGAPEMRFERRLPATGYLDADHGLGHLAAYTAMAHAAEM----AEQVGMGAVAVGN 119 Query: 123 SHHFAALWPDVEPFAEEGLVALSVVNSMTCVVPHGARKPLFGTNPIAFAAPCAEHDPIVF 182 + HF A AE GL+ L NS V+ H +P GTNPIAFAAP A P + Sbjct: 120 ASHFGAAGCYALAAAERGLIGLVTCNSDPFVLLHQGSRPFHGTNPIAFAAPVAGESPYLL 179 Query: 183 DMATSAMAHGDVQIAARAGQQLPEGMGVDADGQPTTDPKAILEGGALLPFG----GHKGS 238 DMATSA+ VQ G++LP+ + DA+G+ T P E ALLP G G KG+ Sbjct: 180 DMATSAIPWNRVQQYGAIGRELPDQVAADAEGRVTRTPG---EVAALLPLGGSDFGFKGA 236 Query: 239 ALSMMVELLAAALTGGHFSWEFDWSGHPGAKTP-WTGQLIIVINPGK-AEGERFAQRSRE 296 L MVE+L++ L G + G P TP ++ + P A G+ F R Sbjct: 237 GLGGMVEVLSSMLAGMQHGYRLLPMGGPDMATPRGVAHFVMALKPDAFAPGDPFPACLRR 296 Query: 297 LVEHMQAVG-----LTRMPGERRYREREVAEEEGVAVTEQELQGLKEL 339 ++ ++A +PGER + + + G+ + EL Sbjct: 297 YLDDLRAQPGRNGCEVLVPGEREWGCQAQRDARGIPLDSANQAAYAEL 344 Lambda K H 0.318 0.132 0.398 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: 339 Number of extensions: 21 Number of successful extensions: 3 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: 341 Length of database: 357 Length adjustment: 29 Effective length of query: 312 Effective length of database: 328 Effective search space: 102336 Effective search space used: 102336 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 (21.7 bits) S2: 49 (23.5 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