Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H] (EC 1.5.1.1) (characterized)
to candidate 5210527 Shew_2955 ornithine cyclodeaminase (RefSeq)
Query= BRENDA::Q485R8 (316 letters) >FitnessBrowser__PV4:5210527 Length = 314 Score = 332 bits (851), Expect = 7e-96 Identities = 169/316 (53%), Positives = 221/316 (69%), Gaps = 3/316 (0%) Query: 1 MKIISAEQVHQNLNFEELIPLLKQSFSRPFSMPQRQVYSLAPEQSENHDAFALLPSWNEE 60 M++I AE VHQ L+F L L+ +F++P MPQRQV+ L + S + DAFA+LP+WN++ Sbjct: 1 MQVIDAEAVHQALDFPSLTAALRDTFAQPAGMPQRQVFPL--DDSSHSDAFAVLPAWNQK 58 Query: 61 VIGNKAFTYFPDNAKKH-DLPGLFSKIMLFKRQTGEPLALVDGTSVTYWRTAAISALASQ 119 I KAFTYFP N KK +L L+SKI++F R+TGEP ALVDGTSVTYWRTAAISALASQ Sbjct: 59 TIAVKAFTYFPGNPKKSPELESLYSKILIFNRETGEPQALVDGTSVTYWRTAAISALASQ 118 Query: 120 LLSRKNSQHLMLFGTGNLASYLVKAHLTVRDIKQVTLWGRNAKKVSKLIADFSILYPAVT 179 LSR +++HL+LFGTG LA+++ AH +VR +K +T+WGR+ KV K I+ P + Sbjct: 119 YLSRSDAKHLLLFGTGRLATFMALAHASVRQLKTITVWGRSPDKVDKTISAIQAAAPQIE 178 Query: 180 FKTSVDVNAEVASADIICCATGAKTPLFDGNSVSAGCHIDCLGNHMTDARECDTTTILRA 239 K D+ VA+ADII CATGA PLFD V+ G H+D +GNH D RECD+ +++A Sbjct: 179 VKACEDLPKAVAAADIISCATGAPAPLFDSAWVAPGTHVDLVGNHNHDRRECDSELVVKA 238 Query: 240 RVFVDSLTNTLNEAGELLIPMAEDAFNKDEIVGELADMCKTPSMLRQSSDEITLFKSVGT 299 V+VD+ N EAGELLIP++E F ++ GELAD+C+ RQ ITLFKSVGT Sbjct: 239 EVYVDAKVNVFAEAGELLIPVSEGVFELSQVKGELADLCRGDIPGRQGEQGITLFKSVGT 298 Query: 300 AISDLVAAHSVVEKLA 315 A++DLV A V EK A Sbjct: 299 ALADLVGAQLVYEKQA 314 Lambda K H 0.318 0.131 0.379 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: 284 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: 316 Length of database: 314 Length adjustment: 27 Effective length of query: 289 Effective length of database: 287 Effective search space: 82943 Effective search space used: 82943 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