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_092484923.1 BM299_RS12810 Ldh family oxidoreductase
Query= SwissProt::Q5FB93 (341 letters) >NCBI__GCF_900115975.1:WP_092484923.1 Length = 343 Score = 132 bits (333), Expect = 1e-35 Identities = 83/247 (33%), Positives = 123/247 (49%), Gaps = 5/247 (2%) Query: 13 PFTELQSLLQAIFQRHGCSEAVARVLAHNCASAQRDGAHSHGVFRMPGYVSTLASGWVDG 72 P +L+ + + + +G E A + A SA G SHG+ +P YV + G VD Sbjct: 5 PAADLKKICVDVLKGYGVPEENADITASVMISASLRGIDSHGIAYLPVYVERIKRGVVDP 64 Query: 73 QATPQVSDVAAGYVRVDAAGGFAQPALAAARELLVAKARSAGIAVLAIHNSHHFAALWPD 132 +A P++ A VD G Q A L V KA ++ + + NS HF + Sbjct: 65 KAQPEIVTETANTAVVDCKNGLGQVGGVFAMNLAVKKALASNTGFVGLRNSGHFGMVSYY 124 Query: 133 VEPFAEEGLVALSVVNSMTCVVPHGARKPLFGTNPIAFAAPCAEHDPIVFDMATSAMAHG 192 A+ + L++ N+ + V P G +PLFGTNPI+FA P + IV D ATSA+A Sbjct: 125 TMQAAKNNCIGLAMTNAPSSVAPFGGMEPLFGTNPISFAFPVKDRPDIVIDFATSAIART 184 Query: 193 DVQIAARAGQQLPEGMGVDADGQPTTDPKAILEG--GALLPFGGHKGSALSMMVELLAAA 250 ++ A Q++PEG + +G K EG G LLP G KG L+++ E+L+A Sbjct: 185 KLRNMAAEKQEIPEGWALSKEGYMA---KTADEGYEGVLLPAAGVKGYGLAIIAEVLSAV 241 Query: 251 LTGGHFS 257 LTG F+ Sbjct: 242 LTGAAFT 248 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: 213 Number of extensions: 10 Number of successful extensions: 2 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: 343 Length adjustment: 29 Effective length of query: 312 Effective length of database: 314 Effective search space: 97968 Effective search space used: 97968 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 Apr 09 2024. 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