Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate HSERO_RS01185 HSERO_RS01185 amino acid ABC transporter
Query= BRENDA::Q01269 (268 letters) >FitnessBrowser__HerbieS:HSERO_RS01185 Length = 269 Score = 77.8 bits (190), Expect = 2e-19 Identities = 64/208 (30%), Positives = 98/208 (47%), Gaps = 8/208 (3%) Query: 2 PKSFRHLVQALACLALLASASLQAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAG 61 P S VQ +A L LL + AQ +LD IL + LRVA P+S + ++ G Sbjct: 4 PSSPARRVQ-MALLGLLLLGAGAAQADQLDTILAAKKLRVAIDLAVPPYSMKDDKLRLIG 62 Query: 62 FDVDMAQRLAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYL 121 DV+ AQR+A+ G +L VVPT+ N + ++ DI +S SI ER + FS+PY Sbjct: 63 SDVETAQRMAKDFGLELEVVPTTLTNRVPYLQTNKADIVISAFSITPERAKVIDFSVPY- 121 Query: 122 RDGKTPITLCSEEAR-FQTLEQIDQPGVTAIVNPGGTN-EKFARANLKKARILVHPDNVT 179 PI + R + D G I G TN ++ + A I D+ T Sbjct: 122 ----APILVVVGAPRSMKITSPADLAGKKIIATRGTTNDQELTKIAPSSATITRFDDDAT 177 Query: 180 IFQQIVDGKADLMMTDAIEARLQSRLHP 207 +V G+AD+ T + ++ ++ +P Sbjct: 178 SMTAMVSGQADIWATSPMLLKVVNQKNP 205 Lambda K H 0.322 0.135 0.406 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: 126 Number of extensions: 7 Number of successful extensions: 1 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: 268 Length of database: 269 Length adjustment: 25 Effective length of query: 243 Effective length of database: 244 Effective search space: 59292 Effective search space used: 59292 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 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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