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 PfGW456L13_2974 Delta 1-piperideine-2-carboxylate reductase (EC 1.5.1.21) / Delta 1-pyrroline-2-carboxylate reductase (EC 1.5.1.1)
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2974 Length = 346 Score = 518 bits (1333), Expect = e-151 Identities = 260/345 (75%), Positives = 293/345 (84%), Gaps = 3/345 (0%) Query: 1 MSASHADQPTQTVSY---PQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIF 57 MSA H T S+ L LL +IF+ HGTS EVA VLA+NCA A+RDG+HSHG+F Sbjct: 1 MSAPHDHASTAVPSHLSLEALSALLEKIFLRHGTSVEVARVLAQNCACAERDGAHSHGVF 60 Query: 58 RIPGYLSSLASGWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVA 117 RIPGY+S+L SGWV+G+AVP+VEDV + FVRVDA NGFAQPALAAAR LL+ KARSAG+A Sbjct: 61 RIPGYVSTLQSGWVNGQAVPLVEDVASGFVRVDANNGFAQPALAAARELLVQKARSAGIA 120 Query: 118 ILAIRGSHHFAALWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAG 177 +LAIR SHHFAALWPDVEPFAE+GLVALS+VNSMTCVVPHGA +PLFGTNPIAF APRA Sbjct: 121 VLAIRNSHHFAALWPDVEPFAEEGLVALSVVNSMTCVVPHGADRPLFGTNPIAFAAPRAE 180 Query: 178 GEPIVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHK 237 G PIVFDLATSAIAHGDVQIAAREG LP GMGVD G PT +P+AIL+GGALLPFGGHK Sbjct: 181 GGPIVFDLATSAIAHGDVQIAAREGERLPEGMGVDSLGQPTTDPKAILEGGALLPFGGHK 240 Query: 238 GSALSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEE 297 GSALSMMVELLAA LTGGNFSFEFDW HPGA+TPWTGQLLIVIDPDK AGQ FA+RS+E Sbjct: 241 GSALSMMVELLAAALTGGNFSFEFDWKNHPGAKTPWTGQLLIVIDPDKAAGQSFAERSQE 300 Query: 298 LVRQLHGVGQERLPGDRRYLERARSMAHGIVIAQADLERLQELAG 342 LVRQ+HGVG +RLPGDRR+ +RARS+A+GI + L L+ELAG Sbjct: 301 LVRQMHGVGLKRLPGDRRHHQRARSLANGIELDARTLANLRELAG 345 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: 526 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: 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