Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H] (EC 1.5.1.1) (characterized)
to candidate RR42_RS27960 RR42_RS27960 ornithine cyclodeaminase
Query= BRENDA::Q485R8 (316 letters) >FitnessBrowser__Cup4G11:RR42_RS27960 Length = 330 Score = 158 bits (399), Expect = 2e-43 Identities = 105/312 (33%), Positives = 160/312 (51%), Gaps = 14/312 (4%) Query: 1 MKIISAEQVHQNLNFEELIPLLKQSFSRPFSMPQRQVYSLAPEQSENHDA----FALLPS 56 M I+ ++ L F +L+P L+ +F R +PQR + + + H A L+P+ Sbjct: 1 MLILDSDTTRALLPFAKLVPALRDAFIRGCEVPQRHSHVI-----DTHGAAPGTMLLMPA 55 Query: 57 WNEEV-IGNKAFTYFPDNAKKHDLPGLFSKIMLFKRQTGEPLALVDGTSVTYWRTAAISA 115 W + +G K T +P N LPGL+S +L TG+PL+++DG +T RTAA SA Sbjct: 56 WQADAYLGVKTVTIYPGNTLS-GLPGLYSTYLLHDACTGKPLSMIDGNEITSRRTAAASA 114 Query: 116 LASQLLSRKNSQHLMLFGTGNLASYLVKAHLTVRDIKQVTLWGRNAKKVSKLIADFSILY 175 LA+ LS + +++ G G +AS L +A+ VR I++V +W NA + L A Sbjct: 115 LAASYLSPNYASSMLVLGAGRVASLLPQAYRAVRPIQRVAVWDINASQGEALAARLRADG 174 Query: 176 PAVTFKTSVDVNAEVASADIICCATGAKTPLFDGNSVSAGCHIDCLGNHMTDARECDTTT 235 F ++ E ADI+ AT + +PL + G H+D +G RE D Sbjct: 175 FEARFVATIAAACE--DADIVTSATLSTSPLVQRAWLRPGTHLDLIGGFTPAMREADDGC 232 Query: 236 ILRARVFVDSLTNTLNEAGELLIPMAEDAFNKDEIVGELADMCKTPSMLRQSSDEITLFK 295 VFVD+ + + +AG+LL P+ +I G LAD+C+ R EIT+FK Sbjct: 233 FESTAVFVDT-SEAVLKAGDLLHPIEAGVLKATDIRGTLADLCQQRHRGRTDDTEITVFK 291 Query: 296 SVGTAISDLVAA 307 +VGTA+ DL AA Sbjct: 292 AVGTALEDLAAA 303 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: 207 Number of extensions: 13 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: 316 Length of database: 330 Length adjustment: 28 Effective length of query: 288 Effective length of database: 302 Effective search space: 86976 Effective search space used: 86976 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