Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; EC 1.5.1.1 (characterized)
to candidate BPHYT_RS24365 BPHYT_RS24365 ornithine cyclodeaminase
Query= SwissProt::V5YW53 (311 letters) >FitnessBrowser__BFirm:BPHYT_RS24365 Length = 311 Score = 339 bits (869), Expect = 6e-98 Identities = 179/301 (59%), Positives = 212/301 (70%), Gaps = 4/301 (1%) Query: 10 FDAADTAALLAYPALLATLGQAVADYAAGEIVSPERLVVPLQAGGVMLSMPSSARDLATH 69 FDAA T L+ Y AL+ L +A DYA I SPERLVVPL G+MLSMP++A DLA H Sbjct: 9 FDAAATTRLIPYAALVDALKRATIDYAQRRIASPERLVVPLNEDGIMLSMPATAPDLAIH 68 Query: 70 KLVNVCPGNGARGLPTILGQVTAYDASTGEMRFALDGPTVTGRRTAAVTALGIQALHGAA 129 KLVNVCP N ARGLPTI G+V A+DA TGE F LDGPTVTGRRTAA++ LG+ A Sbjct: 69 KLVNVCPANRARGLPTIHGKVMAFDADTGETLFILDGPTVTGRRTAAISMLGVDTFAAAT 128 Query: 130 PRDILLIGTGKQAANHAEALAAIFPEARLHVRGTSADSAAAFCAAHRAQAPRLVPLD--G 187 PR+ LLIGTG QA NH EA+ +FP AR+ V+G++ A AFCAAH+ +A L PL G Sbjct: 129 PREFLLIGTGTQALNHLEAIGELFPSARVWVKGSAPARAEAFCAAHQGKAHDLRPLTQAG 188 Query: 188 DAIPDAIDVVVTLTTSRTPVYREAAREGRLVVGVGAFTADAAEIDANTVRASRLVVDDPA 247 IPD++DVV+ LTTSR PVY EAAR RLV+GVGAFT EI A T+ S L VDD A Sbjct: 189 ATIPDSVDVVIALTTSRQPVYDEAARAERLVIGVGAFTPAMVEIGARTLGESALFVDDEA 248 Query: 248 GARHEAGDLIVAQVDWQHVASLADVLG--GTFDRSGPLLFKSVGCAAWDLAACRTARDAL 305 GARHEAGD I A VDW V +A VL + P++FK+VGCAAWDLAACR AR++L Sbjct: 249 GARHEAGDFIQAGVDWAQVGGIASVLDNPALLPQKKPIVFKTVGCAAWDLAACRVARESL 308 Query: 306 A 306 + Sbjct: 309 S 309 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: 252 Number of extensions: 8 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: 311 Length of database: 311 Length adjustment: 27 Effective length of query: 284 Effective length of database: 284 Effective search space: 80656 Effective search space used: 80656 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