Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate RR42_RS11115 RR42_RS11115 ornithine cyclodeaminase
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__Cup4G11:RR42_RS11115 Length = 323 Score = 110 bits (276), Expect = 4e-29 Identities = 87/270 (32%), Positives = 123/270 (45%), Gaps = 13/270 (4%) Query: 60 VADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLM 119 V + FK PAN A +L D +G PV + + T +RT A + Sbjct: 63 VQSQGLLGFKAAGFWPANREVGGEPHQATIMLIDPATGRPVCMIDGNAVTTMRTGAAGGL 122 Query: 120 AAQALARPNARKMALIGNGAQSEFQ---ALAFHKHLG-IEEIVAYDTDPLATAKLIANLK 175 Q LAR ++ ++ L G G Q+ Q ALA L ++ + A + A Sbjct: 123 GLQWLARQDSERLCLFGTGVQARIQLTFALALLPSLKQVQYVTVTGQHDAAFERAFAERC 182 Query: 176 EYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTEL 235 E S R A AV G D++ +TA + ++PG HLN VG D GK EL Sbjct: 183 EISHAPDRNA-----AVAGSDVV--ITATPGGGALFDLQAVQPGTHLNCVGADTRGKREL 235 Query: 236 HADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVG 295 +L AR+FV+ Q R GE Q P D P ++ VL G+ + + D+ +TVFD G Sbjct: 236 PDGLLARARLFVDDRAQARQIGETQWAP-DTPCTEIGDVLGGKVQVERHDTDITVFDMTG 294 Query: 296 FALEDYTVLRYVLQQAEKRGMGTKIDLVPW 325 AL+D TV R + ++A GT I PW Sbjct: 295 LALQDLTVARLLQRRAATAQAGTSIHW-PW 323 Lambda K H 0.320 0.134 0.387 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: 225 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: 350 Length of database: 323 Length adjustment: 28 Effective length of query: 322 Effective length of database: 295 Effective search space: 94990 Effective search space used: 94990 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: 49 (23.5 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