Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H] (EC 1.5.1.1) (characterized)
to candidate WP_110804622.1 C8J30_RS05020 ornithine cyclodeaminase
Query= BRENDA::Q485R8 (316 letters) >NCBI__GCF_003217355.1:WP_110804622.1 Length = 304 Score = 125 bits (315), Expect = 1e-33 Identities = 79/249 (31%), Positives = 130/249 (52%), Gaps = 9/249 (3%) Query: 65 KAFTYFPDNAKKHDLPGLFSKIMLFKRQTGEPLALVDGTSVTYWRTAAISALASQLLSRK 124 KA T P NA DLP + +ML + +TG A++D VT W+TA S LA++LL+R Sbjct: 61 KAATIVPGNAGV-DLPTVNGGVMLMEDRTGLLSAVLDFALVTKWKTAGDSLLAARLLARP 119 Query: 125 NSQHLMLFGTGNLASYLVKAHLTVRDIKQVTLWGRNAKKVSKLIADFSILYPAVTFKTSV 184 + +++ G G +A+ +++A+ + T+W R+ A L A + + Sbjct: 120 EATEILICGAGKVAAAMIEAYRAAFPAARFTIWNRSQ-------AGAEALAEATGARVEM 172 Query: 185 DVNAEVASADIICCATGAKTPLFDGNSVSAGCHIDCLGNHMTDARECDTTTILRARVFVD 244 ++ + A+I+ T AK P G+ + G HID +G D RE D T+ RAR+F D Sbjct: 173 NLETALGQAEIVAGTTMAKDPWLRGDWLQPGTHIDLIGAFRPDMREADDATLRRARLFCD 232 Query: 245 SLTNTLNEAGELLIPMAEDAFNKDEIVGELADMCKTPSMLRQSSDEITLFKSVGTAISDL 304 + TL+ GE P++ + ++V + D+ T R+S+DEITL K+ G A DL Sbjct: 233 ARATTLHHIGEFRDPLSRGVIAETDVVADFYDIA-TGRFARESADEITLSKNGGGAHLDL 291 Query: 305 VAAHSVVEK 313 + A + ++ Sbjct: 292 MTASFIRDR 300 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: 183 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: 304 Length adjustment: 27 Effective length of query: 289 Effective length of database: 277 Effective search space: 80053 Effective search space used: 80053 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 24 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