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 SMa1459 SMa1459 Dehydrogenase, malate/L-lactate family
Query= SwissProt::Q5FB93 (341 letters) >FitnessBrowser__Smeli:SMa1459 Length = 334 Score = 194 bits (493), Expect = 3e-54 Identities = 118/305 (38%), Positives = 168/305 (55%), Gaps = 4/305 (1%) Query: 8 TVVRVPFTELQSLLQAIFQRHGCSEAVARVLAHNCASAQRDGAHSHGVFRMPGYVSTLAS 67 T V + E++++ HG + AR +A A+ DG G++ +P + LA Sbjct: 2 TPVETSWEEIEAVCLEALTLHGAAAETARAVAGAITRAEADGNRVCGLYYLPIFCRHLAI 61 Query: 68 GWVDGQATPQVSDVAAGYVRVDAAGGFAQPALAAARELLVAKARSAGIAVLAIHNSHHFA 127 G VDG+A P+V+ V VDA GFA PA+AA L+ AR AG+A +A+ NS++ Sbjct: 62 GKVDGEAVPEVTTRGVT-VTVDARSGFAHPAIAAGTPALIDLARQAGLAAMAVRNSYNCL 120 Query: 128 ALWPDVEPFAEEGLVALSVVNSMTCVVPHGARKPLFGTNPIAFAAPCAEHDP-IVFDMAT 186 AL V P A+ GL+ + V N+ V P GA + LFGTNP+AFA P E P IV D + Sbjct: 121 ALGHHVRPLADAGLIGICVSNAPASVAPPGATRALFGTNPLAFAVPSKEGAPTIVVDQSM 180 Query: 187 SAMAHGDVQIAARAGQQLPEGMGVDADGQPTTDPKAILEGGALLPFGGHKGSALSMMVEL 246 SA+ ++ + G+ +P G D +GQPTTD LE G+LLP GG KG+ ++++VE+ Sbjct: 181 SAVTKTEMILRRDRGEAIPIGWAQDGNGQPTTDAATGLE-GSLLPAGGRKGANIALLVEV 239 Query: 247 LAAALTGGHFSWEFDWSGHPGAKTPWTGQLIIVINPGKAEGERFAQRSRELVEHMQAVGL 306 LAAALTG S E G+ P GQ +I I+P F++ LV A G+ Sbjct: 240 LAAALTGSALSTEASAFGNEEGGPPHVGQFLIAIDPDHFAAGHFSEAMDNLVASHDAAGV 299 Query: 307 TRMPG 311 R+PG Sbjct: 300 -RLPG 303 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: 332 Number of extensions: 17 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: 341 Length of database: 334 Length adjustment: 28 Effective length of query: 313 Effective length of database: 306 Effective search space: 95778 Effective search space used: 95778 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 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