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 GFF2454 PS417_12515 lactate dehydrogenase
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__WCS417:GFF2454 Length = 345 Score = 518 bits (1334), Expect = e-152 Identities = 259/343 (75%), Positives = 292/343 (85%), Gaps = 2/343 (0%) Query: 1 MSASHADQPTQT--VSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFR 58 MSAS D T +SY L LL+RIF+ GTS VA VLAENCASA+RDG+HSHG+FR Sbjct: 1 MSASPLDHAPSTTHLSYEALTLLLQRIFIRQGTSESVAQVLAENCASAERDGAHSHGVFR 60 Query: 59 IPGYLSSLASGWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAI 118 +PGY+S+L SGWVDGKAVP+VEDV + FVRVDA NGFAQPALAAARSLL+DKARSAG+A+ Sbjct: 61 VPGYVSTLNSGWVDGKAVPIVEDVASGFVRVDAVNGFAQPALAAARSLLVDKARSAGIAL 120 Query: 119 LAIRGSHHFAALWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGG 178 LAI SHHFAALWPDVEPFAE+GLVALS+VNSMTCVVPHGA +PLFGTNPIAF APRA G Sbjct: 121 LAIHNSHHFAALWPDVEPFAEEGLVALSVVNSMTCVVPHGADRPLFGTNPIAFAAPRADG 180 Query: 179 EPIVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKG 238 PIVFDLATSAIAHGDVQIAAR+G LP GMGVD G PTQ+P+AIL+GGALLPFGGHKG Sbjct: 181 PPIVFDLATSAIAHGDVQIAARKGERLPPGMGVDSLGQPTQDPKAILEGGALLPFGGHKG 240 Query: 239 SALSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEEL 298 SALSMMVELLAA LTGGNFSFEF+WS HPGA+TPWTGQL+I+IDP K GQ+FA+RS+EL Sbjct: 241 SALSMMVELLAAALTGGNFSFEFNWSDHPGARTPWTGQLVILIDPSKTTGQNFAERSQEL 300 Query: 299 VRQLHGVGQERLPGDRRYLERARSMAHGIVIAQADLERLQELA 341 VRQ+H G RLPGDRR+ RA+S GI I DL++LQELA Sbjct: 301 VRQMHAAGLRRLPGDRRHRSRAKSQEIGIEINAQDLKQLQELA 343 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: 507 Number of extensions: 14 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: 345 Length adjustment: 29 Effective length of query: 314 Effective length of database: 316 Effective search space: 99224 Effective search space used: 99224 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