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 14654 b0517 ureidoglycolate dehydrogenase (NCBI)
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__Keio:14654 Length = 349 Score = 131 bits (330), Expect = 2e-35 Identities = 104/328 (31%), Positives = 150/328 (45%), Gaps = 18/328 (5%) Query: 13 VSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASGWVD 72 +S L L+ G E A +AE A G HSHG R+ Y ++ G + Sbjct: 3 ISRETLHQLIENKLCQAGLKREHAATVAEVLVYADARGIHSHGAVRVEYYAERISKGGTN 62 Query: 73 GKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAALWP 132 + +E+ G + A N Q A I A+ GVA++ I H A+ Sbjct: 63 REPEFRLEETGPCSAILHADNAAGQVAAKMGMEHAIKTAQQNGVAVVGISRMGHSGAISY 122 Query: 133 DVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSAIAH 192 V+ A G + +SM S VVP G + +GTNP+AF AP G E + FD+AT+ A Sbjct: 123 FVQQAARAGFIGISMCQSDPMVVPFGGAEIYYGTNPLAFAAPGEGDEILTFDMATTVQAW 182 Query: 193 GDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLAAGL 252 G V A +P VD++G+PT +P A+ ALLP G KG L MM+++L+ L Sbjct: 183 GKVLDARSRNMSIPDTWAVDKNGVPTTDPFAV---HALLPAAGPKGYGLMMMIDVLSGVL 239 Query: 253 TGGNF----SFEFDWSKHPGAQTPWTGQLLIVIDPDKGAG-----QHFAQRSEEL--VRQ 301 G F S +D H G GQL IVI+P+ + QH +Q EL + Sbjct: 240 LGLPFGRQVSSMYD-DLHAGRN---LGQLHIVINPNFFSSSELFRQHLSQTMRELNAITP 295 Query: 302 LHGVGQERLPGDRRYLERARSMAHGIVI 329 G Q PG + +++ ++ GI I Sbjct: 296 APGFNQVYYPGQDQDIKQRKAAVEGIEI 323 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: 304 Number of extensions: 12 Number of successful extensions: 2 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: 349 Length adjustment: 29 Effective length of query: 314 Effective length of database: 320 Effective search space: 100480 Effective search space used: 100480 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