Align N-(5'-phosphoribosyl)anthranilate isomerase; Short=PRAI; EC 5.3.1.24 (characterized, see rationale)
to candidate AZOBR_RS03140 AZOBR_RS03140 N-(5'-phosphoribosyl)anthranilate isomerase
Query= uniprot:A0A1L6JC25_9SPHN (212 letters) >FitnessBrowser__azobra:AZOBR_RS03140 Length = 214 Score = 191 bits (484), Expect = 1e-53 Identities = 108/214 (50%), Positives = 128/214 (59%), Gaps = 2/214 (0%) Query: 1 MPVTAKICGLSTAATLDTALAGGASHVGFVFFPPSPRHVTFDQAGSLSTRVPAQTGKVGV 60 MPV+ KICGL+ +L A+AGGA +VGFVF+PPSPR + A L+ VP VG+ Sbjct: 1 MPVSVKICGLTEPLSLHAAVAGGARYVGFVFYPPSPRSIAPSMAAELARLVPTGVRTVGL 60 Query: 61 FVDPEDALLESAIRAARLDAIQLH-RVTPERAAAIGARTRLPVWAAVAVKTRADLDAANG 119 FVDPE+ LE + D IQLH + TP R A + A +PV A+ V DL AA Sbjct: 61 FVDPENDFLEHVVSQVPFDLIQLHGKETPRRIAEVKAAFNIPVMKAIKVGGPEDLAAALE 120 Query: 120 FRGAVQRILYDAKVPEDAK-LPGGMGIRFDWTLLQGFAHPLPWALSGGLDPANVAEAVGI 178 R+L+DAK P LPGG GI FDWTLL G + P PW LSGGL P N AEAV Sbjct: 121 AAEVADRLLFDAKPPAKVSALPGGNGIAFDWTLLAGRSWPNPWMLSGGLKPENAAEAVRT 180 Query: 179 TGARLVDVSSGVESAPGVKDEAKIAAFLKTVATL 212 TGA +DVSSGVE PG KD I FL +VA L Sbjct: 181 TGATALDVSSGVEDRPGHKDPELIRRFLDSVAGL 214 Lambda K H 0.320 0.134 0.398 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: 155 Number of extensions: 6 Number of successful extensions: 3 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: 212 Length of database: 214 Length adjustment: 22 Effective length of query: 190 Effective length of database: 192 Effective search space: 36480 Effective search space used: 36480 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