Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate HSERO_RS22840 HSERO_RS22840 ornithine cyclodeaminase
Query= SwissProt::Q59701 (356 letters) >FitnessBrowser__HerbieS:HSERO_RS22840 Length = 306 Score = 67.0 bits (162), Expect = 6e-16 Identities = 66/221 (29%), Positives = 100/221 (45%), Gaps = 14/221 (6%) Query: 105 GYPLLLSEMTILTALRTAATSALAAKYLARPNSKTMAIIGNGAQSEFQARAFRAILGIQK 164 G PL E +T LRTAA +A+A LARP++ +A+IG G Q+ A + ++ Sbjct: 85 GAPLCTMEGDAMTGLRTAAATAVACDALARPDAGVLAVIGTGVQARSHIPALLQVRPFKE 144 Query: 165 LRLFDIDTSATRKCARNLTGPGFDIVECGSVAEAVEGADVITTVTADKQFATILSDNH-V 223 + + S + A +T S+ EA ADV+ TVT + AT L D + Sbjct: 145 VLI--AGRSGQQALAEEVTRTLGVPARMVSIDEAAAQADVLVTVT---RSATPLFDGELL 199 Query: 224 GPGVHINAVGGDCPGKTEISMEVLLR-SDIFVEYPPQTWIE-GDIQQLP----RTHPVTE 277 PG + AVG E+ + R + +FVE+ PQ E GD+ Q V E Sbjct: 200 RPGAFVAAVGASKANVRELDDTAIGRAAALFVEWKPQAQQEAGDLVQCAPGVFDWAQVME 259 Query: 278 LWQVMTGEKTGRVGDRQITMFDSVGFAIED--FSALRYVRA 316 L Q + G + I ++ +G +ED + L Y +A Sbjct: 260 LAQAVDGSMPYQRRPDDIVIYKGIGIGLEDVALAGLAYRKA 300 Lambda K H 0.320 0.137 0.405 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: 178 Number of extensions: 18 Number of successful extensions: 2 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: 356 Length of database: 306 Length adjustment: 28 Effective length of query: 328 Effective length of database: 278 Effective search space: 91184 Effective search space used: 91184 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