Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate SMa1871 SMa1871 cyclodeaminase
Query= BRENDA::Q9QYU4 (313 letters) >FitnessBrowser__Smeli:SMa1871 Length = 330 Score = 137 bits (345), Expect = 3e-37 Identities = 97/316 (30%), Positives = 158/316 (50%), Gaps = 20/316 (6%) Query: 8 LSADEVQDHLRSSSLLIPPLEAALANFSKGPDGGVMQPVRTVVPVAKHRGFLGVMPAYSA 67 L DEV+ L + +I +E A FS V QP + RG + Y Sbjct: 6 LKKDEVR-RLIGMAEVIGAVEEAYKAFSSDQ---VEQPDYIGIHHPSLRGEIDFKLGYYK 61 Query: 68 AEDALTTKLVT--FYEGHSNNAVPSHQASVLLFDPSNGSLLAVMDGNVITAKRTAAVSAI 125 A + ++ K + F + + VP+ ++LLFD + +L+ +MDG++IT RT A A+ Sbjct: 62 ANEIISMKAHSGGFTNNPAEHGVPNSIGTILLFDARSCALICIMDGSLITGLRTGASGAV 121 Query: 126 ATKFLKPPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMWNRTRENAEKFASSVQGD-- 183 + K L + + +G G QA E +++ W+RT E+ ++ + +Q + Sbjct: 122 SVKALARKNARTVASIGTGNQARMQIRAVNEIMKIEKIHAWSRTPESLSRYKTDIQREFG 181 Query: 184 --VRVCSSVQEAVTGADVIITVTMATEPILFGEWVKPGAHINAVGASRPDWRELDDELMK 241 V V SS +EAV AD++IT T ++ +WVKPG HI A+G + +ELD E+ + Sbjct: 182 IPVIVASSKKEAVEQADILITTTRGKGSLVEADWVKPGTHIVAIGTDQRGKQELDPEIFR 241 Query: 242 QAVLYVDSREAALKESGDV-------LLSGADIFAELGEVVSGAKPA--YCEKTTVFKSL 292 A + VDS A E G+ +++ DI E+GEV+ G KP ++ T+F S Sbjct: 242 NAKVVVDS-VAQCTEKGETWHPLNKNIITKDDIHGEIGEVLLGRKPGRESDDEITIFDST 300 Query: 293 GMAVEDLVAAKLVYDS 308 GMA++D A +Y + Sbjct: 301 GMAIQDNTTASKIYQN 316 Lambda K H 0.317 0.131 0.377 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: 227 Number of extensions: 12 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: 313 Length of database: 330 Length adjustment: 28 Effective length of query: 285 Effective length of database: 302 Effective search space: 86070 Effective search space used: 86070 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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