Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H] (EC 1.5.1.1) (characterized)
to candidate 6938507 Sama_2610 ornithine cyclodeaminase (RefSeq)
Query= BRENDA::Q485R8 (316 letters) >FitnessBrowser__SB2B:6938507 Length = 317 Score = 299 bits (766), Expect = 5e-86 Identities = 154/319 (48%), Positives = 215/319 (67%), Gaps = 6/319 (1%) Query: 1 MKIISAEQVHQNLNFEELIPLLKQSFSRPFSMPQRQVYSLAPEQSENHDAFALLPSWNEE 60 MKII QV Q L F L+ L+Q RPF+MPQRQVY+L+ + ++N AFALLP+W+EE Sbjct: 1 MKIIDGNQVQQKLTFPPLVEALRQQLCRPFTMPQRQVYALS-DTADNQHAFALLPAWDEE 59 Query: 61 VIGNKAFTYFPDNAKKHDLPG---LFSKIMLFKRQTGEPLALVDGTSVTYWRTAAISALA 117 I KAFTY PDN K+ PG L+S+I+LF R+TG P AL+DGTSVTYWRTAA SALA Sbjct: 60 SIAVKAFTYLPDNPVKN--PGCESLYSQILLFDRKTGVPQALIDGTSVTYWRTAATSALA 117 Query: 118 SQLLSRKNSQHLMLFGTGNLASYLVKAHLTVRDIKQVTLWGRNAKKVSKLIADFSILYPA 177 + L+RK+S L++ TGNLA Y+ AH +VR I+++ +WGRN +K+ IA Sbjct: 118 ASFLARKDSSRLLMCATGNLAVYMALAHASVRPIREIRIWGRNTQKIDSTIATIRAQRTD 177 Query: 178 VTFKTSVDVNAEVASADIICCATGAKTPLFDGNSVSAGCHIDCLGNHMTDARECDTTTIL 237 + + + +V ADII CATG+ TPLF G V+ G H D +GNH D RECD+ I Sbjct: 178 IEVTAANALQLDVPWADIISCATGSPTPLFPGEWVTPGTHTDFVGNHHKDCRECDSHLIT 237 Query: 238 RARVFVDSLTNTLNEAGELLIPMAEDAFNKDEIVGELADMCKTPSMLRQSSDEITLFKSV 297 ++V+VD+ N +EAGELLIP++E F+ DE+ EL+++C+ ++ R + +IT+FKSV Sbjct: 238 NSQVYVDARLNVFSEAGELLIPVSEGRFSLDEVRAELSELCQGTALGRVNDKDITMFKSV 297 Query: 298 GTAISDLVAAHSVVEKLAD 316 G+A++DL A + + L + Sbjct: 298 GSALADLAGARLLFKMLQE 316 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: 291 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: 316 Length of database: 317 Length adjustment: 27 Effective length of query: 289 Effective length of database: 290 Effective search space: 83810 Effective search space used: 83810 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