Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; NMAADH; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate 14926 b0801 predicted dehydrogenase (NCBI)
Query= SwissProt::Q5FB93 (341 letters) >FitnessBrowser__Keio:14926 Length = 361 Score = 145 bits (365), Expect = 2e-39 Identities = 103/331 (31%), Positives = 156/331 (47%), Gaps = 15/331 (4%) Query: 17 LQSLLQAIFQRHGCSEAVARVLAHNCASAQRDGAHSHGVFRMPGYVSTLASGWVDGQATP 76 L S +QA+F++ G E A+++A + +A G SHG+ +P YV + + G + Sbjct: 12 LHSFIQAVFRQMGSEEQEAKLVADHLIAANLAGHDSHGIGMIPSYVRSWSQGHLQINHHA 71 Query: 77 QVSDVAAGYVRVDAAGGFAQPALAAARELLVAKARSAGIAVLAIHNSHHFAALWPDVEPF 136 + A V +D F Q A A L + KA GIA +A+HNSHH + E Sbjct: 72 KTVKEAGAAVTLDGDRAFGQVAAHEAMALGIEKAHQHGIAAVALHNSHHIGRIGYWAEQC 131 Query: 137 AEEGLVALSVVN--SMTCVVPHGARKPLFGTNPIAFAAPCAEHDPIVFDMATSAMAHGDV 194 A G V++ V+ + V P R FGTNP P ++ P++ D ATSA+A G Sbjct: 132 AAAGFVSIHFVSVVGIPMVAPFHGRDSRFGTNPFCVVFPRKDNFPLLLDYATSAIAFGKT 191 Query: 195 QIAARAGQQLPEGMGVDADGQPTTDPKAILEG--GALLPFGGHKGSALSMMVELLAAALT 252 ++A G +P G +D +G PTT+P + E G+LL F HKG AL+ M E+L AL+ Sbjct: 192 RVAWHKGVPVPPGCLIDVNGVPTTNPAVMQESPLGSLLTFAEHKGYALAAMCEILGGALS 251 Query: 253 GGHFSWEFDWSGHPGAKTPWTGQLIIVINPG-------KAEGERFAQRSRELVEHMQAVG 305 GG + + P A I+INP A+ E FA+ + Sbjct: 252 GGKTTHQETLQTSPDAIL--NCMTTIIINPELFGAPDCNAQTEAFAEWVKASPHDDDKPI 309 Query: 306 LTRMPGERRYREREVAEEEGVAVTEQELQGL 336 L +PGE R +++G+ + Q + Sbjct: 310 L--LPGEWEVNTRRERQKQGIPLDAGSWQAI 338 Lambda K H 0.318 0.132 0.398 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: 348 Number of extensions: 22 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: 341 Length of database: 361 Length adjustment: 29 Effective length of query: 312 Effective length of database: 332 Effective search space: 103584 Effective search space used: 103584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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