Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate 5208561 Shew_1072 chorismate mutase (RefSeq)
Query= BRENDA::Q9SSE7 (381 letters) >FitnessBrowser__PV4:5208561 Length = 654 Score = 172 bits (435), Expect = 3e-47 Identities = 104/328 (31%), Positives = 174/328 (53%), Gaps = 19/328 (5%) Query: 60 GRDNSVRAMEV----KKIFEDSPLLPKPLSSNQLTESVSNGSRVRVAYQGVRGAYSESAA 115 GR+ + A V + I EDS L + + + + +AY G RG+YS AA Sbjct: 63 GREQGLDAHYVLSLYQSIIEDSVLNQQAYLQGRANPDLQK-QQYNIAYLGARGSYSYLAA 121 Query: 116 ----EKAYPNCEAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHNLHI 171 E+ + + C+ FD +AVE D LPIEN+ GSI+ YD+L +L I Sbjct: 122 TRYCERRQVGMQDLGCKSFDEIVQAVESGHADYGFLPIENTSSGSINEVYDVLQHTSLAI 181 Query: 172 VGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTKLGLVR-EAVDDTAGAAKQ 230 VGE + V HCLLA G N++ ++ + +HPQ ++QC L++ G + E +A A ++ Sbjct: 182 VGETTIEVGHCLLAKPGTNVKQIKTIYAHPQPISQCSRYLSQHGEFKLEYCSSSAEAMER 241 Query: 231 IAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAREPIIPGTNRLFKTSI 290 + + N AA+ S + +Y L V ++ + N +RF+++AR+ I KT++ Sbjct: 242 VLEADDNSVAAIGSVEGGALYQLEAVEHELANQKINQSRFIVVARKAIAVPEQLPAKTTL 301 Query: 291 VFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLKYFDYLFYVDFEASMA 350 + + + PG L +AL + +N++K+ESRP+ P ++ +FY+D +A++A Sbjct: 302 IMATGQKPGALVEALLILKAHDLNMSKLESRPIPGTP---------WEEMFYLDLDANLA 352 Query: 351 DEVAQNALRHLEEFATFLRVLGSYPVDT 378 + Q AL+ LE F++VLG YP +T Sbjct: 353 SDEMQQALKELERITRFIKVLGCYPCET 380 Lambda K H 0.319 0.134 0.384 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: 430 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: 381 Length of database: 654 Length adjustment: 34 Effective length of query: 347 Effective length of database: 620 Effective search space: 215140 Effective search space used: 215140 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: 52 (24.6 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