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 AO353_23830 AO353_23830 lactate dehydrogenase
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__pseudo3_N2E3:AO353_23830 Length = 346 Score = 522 bits (1345), Expect = e-153 Identities = 255/334 (76%), Positives = 290/334 (86%) Query: 10 TQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASG 69 +Q +SY +L+ LL IF+ HGTSPEVA VLA+NCA A+RDG+HSHG+FR+PGY+S+L SG Sbjct: 13 SQHLSYEELVGLLESIFLRHGTSPEVARVLAQNCAGAERDGAHSHGVFRMPGYVSTLNSG 72 Query: 70 WVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAA 129 WV+GKAVPVVEDV + FVRVDA NGFAQPALAA R LL+ KARSAG+A++AIR SHHFAA Sbjct: 73 WVNGKAVPVVEDVASGFVRVDAGNGFAQPALAAGRELLVAKARSAGIAVMAIRNSHHFAA 132 Query: 130 LWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSA 189 LWPDVEPFA +GLVALS+VNSMTCVVPHGA +PLFGTNPIAF APRAG +PIVFDLATSA Sbjct: 133 LWPDVEPFAYEGLVALSVVNSMTCVVPHGADRPLFGTNPIAFAAPRAGADPIVFDLATSA 192 Query: 190 IAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLA 249 IAHGDVQIAAR+G LP GMGVD G PTQ+P+AIL+GGALLPFGGHKGSALSMMVELLA Sbjct: 193 IAHGDVQIAARKGERLPPGMGVDSLGQPTQDPKAILEGGALLPFGGHKGSALSMMVELLA 252 Query: 250 AGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEELVRQLHGVGQER 309 A LTGGNFSFEFDWS HPGA+TPWTGQLLIVIDP K AGQ+FA+RSEELVRQ+H VG R Sbjct: 253 AALTGGNFSFEFDWSNHPGAKTPWTGQLLIVIDPSKAAGQNFAERSEELVRQMHAVGLRR 312 Query: 310 LPGDRRYLERARSMAHGIVIAQADLERLQELAGH 343 LPGDRR+ ERA+S GI + L +L ELAG+ Sbjct: 313 LPGDRRHRERAKSQTEGIALDAQTLAQLHELAGN 346 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: 509 Number of extensions: 15 Number of successful extensions: 1 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: 346 Length adjustment: 29 Effective length of query: 314 Effective length of database: 317 Effective search space: 99538 Effective search space used: 99538 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