Align phosphoribosylanthranilate isomerase; EC 5.3.1.24 (characterized)
to candidate N515DRAFT_0113 N515DRAFT_0113 phosphoribosylanthranilate isomerase
Query= CharProtDB::CH_021917 (235 letters) >FitnessBrowser__Dyella79:N515DRAFT_0113 Length = 204 Score = 178 bits (451), Expect = 8e-50 Identities = 102/212 (48%), Positives = 136/212 (64%), Gaps = 10/212 (4%) Query: 22 TRIKLCGLSRPDDVLHAAALGADAIGLVFYAKSPRAVTIAQAAELARLAPPFVSVVGLFV 81 TRIK CG++R +D L AA GADAIG++F A+S R V IA A + PPFVS V LF+ Sbjct: 2 TRIKCCGMTRMEDALLAAQYGADAIGVIFTARSRRRVDIADARAICAELPPFVSTVALFM 61 Query: 82 NATAAEIEAVVRDVPLTLLQFHGDETPEQCDALGRAARLPWVRAVRVGPSTQSADLVESS 141 + A + V+R+V LLQFHGDE+ E C G +++A+ +G + + + Sbjct: 62 DDEPAYVREVLREVQPDLLQFHGDESDEWCAQFGHR----YLKAIAMGEGAAALPRLRA- 116 Query: 142 LHYSKARGLLFDTL-VPDYGGSGKVFDWSLIPAELARRAVLSGGLNAQNVGDAIRQLRPF 200 Y +A GLL D + + GGSGK FDWSL+PA+LA+ +L+GGL A NV A+R RP+ Sbjct: 117 --YPRAAGLLLDGHGLGEAGGSGKAFDWSLMPADLAQPLILAGGLTADNVAHAVRVARPW 174 Query: 201 AVDVSSGIEVEGAKGVKDHARMAAFVRAVRDA 232 AVDVSSGI E A G+KD A+M AF+ AVR A Sbjct: 175 AVDVSSGI--ESAPGIKDAAKMHAFIEAVRQA 204 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: 145 Number of extensions: 6 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: 235 Length of database: 204 Length adjustment: 22 Effective length of query: 213 Effective length of database: 182 Effective search space: 38766 Effective search space used: 38766 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: 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