Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate 3607477 Dshi_0890 Ornithine cyclodeaminase (RefSeq)
Query= BRENDA::O54983 (313 letters) >FitnessBrowser__Dino:3607477 Length = 330 Score = 114 bits (284), Expect = 4e-30 Identities = 79/253 (31%), Positives = 129/253 (50%), Gaps = 11/253 (4%) Query: 60 GVMPAYSAAEDALTTKLVTFYEGHSNTAVPSHQASVLLFDPSNGSLLAVMDGNVITAKRT 119 G + A L K ++ + + +HQ++V LFDP G L A++ GN +TA RT Sbjct: 61 GFKSGFDKAGMVLGVKAGGYWPNNMAKGIINHQSTVFLFDPDTGKLKALVGGNYLTAIRT 120 Query: 120 AAVSAIATKLLKPPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMWNRTRE---NAEKF 176 AA SA++ L + VL ++GAG Q+ EQ F++V WN + N K Sbjct: 121 AASSAVSIDQLARKDAKVLGMVGAGHQSTFQLRAAVEQRDFEKVVCWNPHPDMIPNLGKV 180 Query: 177 ASTVQGDVRVCSSVQEAVTGADVIITVTMATEPILFGEWVKPGAHINAVGASRPDWRELD 236 A+ + G S +E +DVIIT+T A EP++ ++KPG H+ +G +E+ Sbjct: 181 AAEI-GIPFEAVSREELGAQSDVIITITSAFEPLIEAGYIKPGTHLACMGTDTKGKQEVA 239 Query: 237 DELMRQAVLYVD--SREAALKESGDVLLSGA---DIFAELGEVISGAKPAHC--EKTTVF 289 EL+ +A L+ D ++ + E+ + SGA D +G+VI+G P ++ T+F Sbjct: 240 AELVAKATLFTDEVAQSTTIGETQHAIASGAITQDDVTPIGKVINGDHPGRTSDDEITLF 299 Query: 290 KSLGMAVEDLVAA 302 G+ ++DL A Sbjct: 300 DGTGVGLQDLAVA 312 Lambda K H 0.316 0.131 0.376 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: 240 Number of extensions: 8 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: 313 Length of database: 330 Length adjustment: 28 Effective length of query: 285 Effective length of database: 302 Effective search space: 86070 Effective search space used: 86070 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