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 8501262 DvMF_1995 Malate/L-lactate dehydrogenase (RefSeq)
Query= SwissProt::Q5FB93 (341 letters) >FitnessBrowser__Miya:8501262 Length = 356 Score = 225 bits (573), Expect = 2e-63 Identities = 138/332 (41%), Positives = 185/332 (55%), Gaps = 25/332 (7%) Query: 16 ELQSLLQAIFQRHGCSEAVARVLAHNCASAQRDGAHSHGVFRMPGYVSTLASGWVDGQAT 75 +L +L + + +R G A A +A +A+ G SHGV R+P Y +A+G V G A Sbjct: 9 DLAALCRTVLERAGVLPAAASSVAGALVAAECMGIPSHGVARLPQYADQVAAGKVRGDAV 68 Query: 76 PQVSDVAAGYVRVDAAGGFAQPALAAARELLVAKARSAGIAVLAIHNSHHFAALWPDVEP 135 P+V VRVDA GFA PAL A ++ V A G A L + NSHH VE Sbjct: 69 PRVETPLPATVRVDAGCGFAYPALEAGLDVAVPLALRMGCAALGVTNSHHCGVAGLHVER 128 Query: 136 FAEEGLVALSVVNSMTCVVPHGARKPLFGTNPIAFAAPC---------------AEHDPI 180 A +GLVAL N+ + P G + GTNP+AFA P EHDP+ Sbjct: 129 AARQGLVALLFANTPAAMAPWGGNRASLGTNPLAFACPAPPEDAPEPTAAAGAGPEHDPL 188 Query: 181 VFDMATSAMAHGDVQIAARAGQQLPEGMGVDADGQPTTDPKAILEGGALLPFGGHKGSAL 240 V D++ S +A G + AAR GQ +P G VDA G PTTD +A L GG LLPFGG KG+AL Sbjct: 189 VMDLSLSTVARGKIVAAAREGQPIPAGWAVDAHGSPTTDARAAL-GGMLLPFGGAKGAAL 247 Query: 241 SMMVELLAAALTGGHFSWE----FDWSGHPGAKTPWTGQLIIVINPGKAEGERFAQRSRE 296 ++MVELLAA+LTG + ++E D +G P P TGQ +++I P +A G F+ R+ Sbjct: 248 ALMVELLAASLTGSNHAYEASSFLDAAGGP----PRTGQCMLLIAP-QAFGADFSGRAAA 302 Query: 297 LVEHMQAVGLTRMPGERRYREREVAEEEGVAV 328 L+ H+ TR+PG RR+ + A EGVA+ Sbjct: 303 LLGHVLDQPCTRLPGARRFERQRRAHREGVAI 334 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: 341 Number of extensions: 20 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: 356 Length adjustment: 29 Effective length of query: 312 Effective length of database: 327 Effective search space: 102024 Effective search space used: 102024 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