Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate Echvi_2509 Echvi_2509 Phosphoribosylanthranilate isomerase
Query= reanno::Btheta:350056 (207 letters) >FitnessBrowser__Cola:Echvi_2509 Length = 206 Score = 166 bits (420), Expect = 3e-46 Identities = 92/205 (44%), Positives = 124/205 (60%), Gaps = 3/205 (1%) Query: 6 IIKVCGMREAQNIRDVESLQRVDMMGFIFYPKSPRYIYELPAYLPVHARRVGVFVNEDKD 65 I+KVCGMR+A NIR+++ + D+MG IFYPKSPRY+ + A +A +VGVFVN Sbjct: 2 IVKVCGMRDADNIRELDEKVQPDLMGMIFYPKSPRYVADHSAIPATNAAKVGVFVNAPVA 61 Query: 66 VITMYADRFGLEYIQLHGKESPEYCQSLR-TSGLKIIKAFSVARPKDLNHVSEYEKTCNL 124 I FGL+YIQLHG E + L+ + +IK F V D + +E Sbjct: 62 EIVETVQGFGLDYIQLHGNEDVAFVAELKQKTTANVIKVFRVTAEVDWEFLKGFEPHVAY 121 Query: 125 FLFDTKCEQYGGSGNQFDWNILHTYNGQVPFLLSGGINSHS-ANALK-AFDHPRLAGYDL 182 FLFDT+ + YGGSG QFDW +L Y PFLLSGGI+ S A+ L+ P+LAG D+ Sbjct: 122 FLFDTETKGYGGSGKQFDWQLLGAYPLDKPFLLSGGIDQESVADILRLKQQQPQLAGVDI 181 Query: 183 NSRFELKPGEKDPERIRIFLNELKS 207 NS+FE +P KD +I F+ +LK+ Sbjct: 182 NSKFEREPAVKDIVKISRFVKQLKN 206 Lambda K H 0.322 0.140 0.424 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: 157 Number of extensions: 6 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: 207 Length of database: 206 Length adjustment: 21 Effective length of query: 186 Effective length of database: 185 Effective search space: 34410 Effective search space used: 34410 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: 45 (21.9 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