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 AO356_26080 AO356_26080 lactate dehydrogenase
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26080 Length = 343 Score = 518 bits (1334), Expect = e-152 Identities = 256/342 (74%), Positives = 293/342 (85%) Query: 1 MSASHADQPTQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIP 60 MSA + T+S+ L+ LL +IF+ HGTS EVA LAENCA A+RDG+HSHG+FR+P Sbjct: 1 MSAPSDHAASCTLSFDALVSLLEKIFLRHGTSTEVARCLAENCAGAERDGAHSHGVFRLP 60 Query: 61 GYLSSLASGWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILA 120 GY+S+L SGWV+GKAVPVVEDV + FV VDA NGFAQPALAAAR LL++KARSAG+A+LA Sbjct: 61 GYVSTLNSGWVNGKAVPVVEDVASGFVAVDAGNGFAQPALAAARPLLVEKARSAGIAVLA 120 Query: 121 IRGSHHFAALWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEP 180 IR SHHFAALWPDVEPFA +GLVALS+VNSMTCVVPHGA +PLFGTNPIAF APRA GEP Sbjct: 121 IRNSHHFAALWPDVEPFAYEGLVALSVVNSMTCVVPHGADRPLFGTNPIAFAAPRADGEP 180 Query: 181 IVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSA 240 IVFDLATSAIAHGDVQIAAR+G LLP GMGVD G PT++P+AIL+GGALLPFGGHKGSA Sbjct: 181 IVFDLATSAIAHGDVQIAARKGELLPPGMGVDSLGQPTRDPKAILEGGALLPFGGHKGSA 240 Query: 241 LSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEELVR 300 LSMMVELLAA LTGGNFSFEFDWS HPGA+TPWTGQLLIVIDP K AGQ FA+RS ELVR Sbjct: 241 LSMMVELLAAALTGGNFSFEFDWSNHPGAKTPWTGQLLIVIDPSKTAGQDFAERSRELVR 300 Query: 301 QLHGVGQERLPGDRRYLERARSMAHGIVIAQADLERLQELAG 342 Q+HGVG RLPGDRR+ ER+++ GI + + L +L+ELAG Sbjct: 301 QMHGVGLRRLPGDRRHRERSKANEQGISLDEQTLAQLRELAG 342 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: 503 Number of extensions: 17 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: 343 Length adjustment: 29 Effective length of query: 314 Effective length of database: 314 Effective search space: 98596 Effective search space used: 98596 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