Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; EC 1.5.1.1 (characterized)
to candidate Ac3H11_1121 Ornithine cyclodeaminase (EC 4.3.1.12)
Query= SwissProt::V5YW53 (311 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1121 Length = 337 Score = 162 bits (410), Expect = 1e-44 Identities = 113/299 (37%), Positives = 150/299 (50%), Gaps = 12/299 (4%) Query: 11 DAADTAALLAYPALLATLGQAVADYAAGEIVSPERLVVPLQAGGVMLSMPSSARDLATHK 70 DAA TA L + AL + Q + D + P R V+PL GG + MP++ R +A K Sbjct: 31 DAAATAQRLPWSALADEIAQLLHD---STVSVPARSVLPLAQGGSLFLMPATDRSVAMTK 87 Query: 71 LVNVCPGNGARGLPTILGQVTAYDASTGEMRFALDGPTVTGRRTAAVTALGIQALHGAAP 130 L+ P N G P+I G V +D +TG + LDGPTVT RRTAAV+ L + L A Sbjct: 88 LITFTPANAGTGRPSIQGDVVVFDIATGARQLVLDGPTVTARRTAAVSLLAARHLAPAPQ 147 Query: 131 RDILLIGTGKQAANHAEALAAIFPEARLHVRGTSADSAAAFCAAHRAQAPRL-VPLDGDA 189 +L++G G Q HAEA + + SA SA A RA ++ V D DA Sbjct: 148 GPLLIVGAGVQGLAHAEAFVLGLGVQEVWISSRSAASAEALATQVRALGAQVRVVADADA 207 Query: 190 IPDAIDVVVTLTTSRTPVYREAAREGRLVVGVGAFTADAAEID----ANTVRASRLVVDD 245 +V TT+ + V R + VGAFT AE+ + R+VV D Sbjct: 208 ALAHCPLVAACTTASSLVLHATPRADAFITAVGAFTPAMAELAPALCQHVAEHGRIVV-D 266 Query: 246 PAGARHEAGDLIVAQVDWQHVASLADVLGGTFD---RSGPLLFKSVGCAAWDLAACRTA 301 A A HEAGDL+ A +D + L DV+ G + +GP+LFKS G A WDLAA R A Sbjct: 267 TADASHEAGDLLQAGLDVAALPVLRDVVCGPWTPRAPAGPVLFKSCGWAGWDLAAARLA 325 Lambda K H 0.320 0.133 0.386 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: 249 Number of extensions: 15 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: 311 Length of database: 337 Length adjustment: 28 Effective length of query: 283 Effective length of database: 309 Effective search space: 87447 Effective search space used: 87447 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: 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