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 BPHYT_RS27110 BPHYT_RS27110 dehydrogenase
Query= SwissProt::Q4U331 (343 letters) >FitnessBrowser__BFirm:BPHYT_RS27110 Length = 367 Score = 146 bits (368), Expect = 9e-40 Identities = 107/340 (31%), Positives = 161/340 (47%), Gaps = 15/340 (4%) Query: 4 SHADQPTQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYL 63 S A T + QL +R I+ G++P A+++A++ +A G SHG+ IP Y+ Sbjct: 5 STAQPVTPRIPADQLHAYVRAIWEQAGSTPREAELVADHLVAANLTGHDSHGVGMIPRYV 64 Query: 64 SSLASGWVD-GKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIR 122 +SLA G + VV+D GA V+ GF Q A I++A+ G+ + +R Sbjct: 65 ASLADGELQLNLHADVVKDAGAVLT-VEGGRGFGQVVAFEAMEQGIERAKRLGICAVGLR 123 Query: 123 GSHHFAALWPDVEPFAEQGLVALSMVNSM--TCVVPHGARQPLFGTNPIAFGAPRAGGEP 180 G+HH + E A GLV+ VN V P G GTNP PR G P Sbjct: 124 GAHHIGRIGHWAEQCARAGLVSFHFVNVAGDPLVAPFGGADRRIGTNPFCAAYPRPGKPP 183 Query: 181 IVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDG--GALLPFGGHKG 238 +V D ATS +A+G ++A +G+ + G +D +G T EP+ + + G+L PFGGHKG Sbjct: 184 LVLDFATSTVAYGKTRVAYNQGKQVQPGALIDHEGRATLEPKVMHEAPFGSLTPFGGHKG 243 Query: 239 SALSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDP---DKGAGQHFAQRS 295 L+ M E+ L+GG F + L ++IDP D Q A Sbjct: 244 FGLAAMCEIFGGALSGG---FTTHSTTLGTTNAIINCMLSVIIDPAAFDAPDAQAEADAF 300 Query: 296 EELVRQLH-GVGQERL--PGDRRYLERARSMAHGIVIAQA 332 + V+ G +R+ PG+ + RA+ A GI + A Sbjct: 301 IDWVKASPLAAGADRIYEPGEPERVTRAQREAEGIPVDAA 340 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: 414 Number of extensions: 28 Number of successful extensions: 4 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: 367 Length adjustment: 29 Effective length of query: 314 Effective length of database: 338 Effective search space: 106132 Effective search space used: 106132 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