Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate GFF3114 PGA1_c31650 putative ornithine cyclodeaminase/mu-crystallin family protein
Query= BRENDA::Q9QYU4 (313 letters) >FitnessBrowser__Phaeo:GFF3114 Length = 306 Score = 135 bits (339), Expect = 2e-36 Identities = 80/249 (32%), Positives = 134/249 (53%), Gaps = 11/249 (4%) Query: 72 LTTKLVTFYEGHSNNAVPSHQASVLLFDPSNGSLLAVMDGNVITAKRTAAVSAIATKFLK 131 L K T + G+ + P +V L+ +G L A++D +++T +TA S + L Sbjct: 60 LAVKSATIFPGNPDQGHPMVNGAVCLYADQSGMLEALVDFHLVTKWKTAGDSLLGALRLA 119 Query: 132 PPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMWNRTRENAEKFASSVQGDVRVCSSVQ 191 P S + I+GAG S E F + ++R+WNRT E AE A + +V + ++ Sbjct: 120 NPDSREVLIVGAGTVGASLIEAFGTAYPKAQIRIWNRTAEKAEALAEQYP-NAKVAADLE 178 Query: 192 EAVTGADVIITVTMATEPILFGEWVKPGAHINAVGASRPDWRELDDELMKQAVLYVDSRE 251 AV AD+I+T TM++ P++ G W++PG H+N +GA RPD RE D+E +++A +Y DS E Sbjct: 179 AAVQAADIILTCTMSSTPVIKGAWLRPGQHLNLIGAYRPDMRETDNEALQRADIYCDSFE 238 Query: 252 AALKESGDV-------LLSGADIFAELGEVVSGAKPAY-CEKTTVFKSLGMAVEDLVAAK 303 + G+ ++S D+ A+ + A P + + T+FK+ G A DL+ ++ Sbjct: 239 TTVDHIGEFKIPLSEGVISRDDVRADFYNLT--AFPRFDPTRITLFKNGGGAHMDLMTSR 296 Query: 304 LVYDSWSSG 312 + D W G Sbjct: 297 HILDCWQGG 305 Lambda K H 0.317 0.131 0.377 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: 213 Number of extensions: 9 Number of successful extensions: 3 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: 313 Length of database: 306 Length adjustment: 27 Effective length of query: 286 Effective length of database: 279 Effective search space: 79794 Effective search space used: 79794 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: 48 (23.1 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