Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate PP_0422 PP_0422 Indole-3-glycerol phosphate synthase
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__Putida:PP_0422 Length = 277 Score = 149 bits (377), Expect = 8e-41 Identities = 102/263 (38%), Positives = 145/263 (55%), Gaps = 9/263 (3%) Query: 4 TVLAKIVADKAIWVEARKQQQPLASFQN--EVQPSTRHFYDAL----QGARTAFILECKK 57 TVL +I+A K V R LA + + + R F +AL + + A I E KK Sbjct: 5 TVLERIIARKFQEVAERSAHVSLAELEGLAKAADAPRGFANALIEQAKRKQPAVIAEIKK 64 Query: 58 ASPSKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKD 116 ASPSKGVIR+ F PA IA Y K A+ +SVLTD YFQG+ +L P++ KD Sbjct: 65 ASPSKGVIREHFVPAEIAVSYEKGGATCLSVLTDVDYFQGADEYLQQARAAVSLPVIRKD 124 Query: 117 FIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAI- 175 F++DPYQI AR AD LL++S LDD + +LAA A + + VL EV + +E ERA+ Sbjct: 125 FMVDPYQIVEARALGADCVLLIVSALDDVKMAELAATAKDVGLDVLVEVHDGDELERALK 184 Query: 176 ALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELS-HFANGF 234 L +VG+NNR+L + L T +L P++ + I+ESGI A V ++ + F Sbjct: 185 TLDTPLVGVNNRNLHTFEVSLETTLDLLPRIPRDRLAITESGILNRADVELMAINEVYSF 244 Query: 235 LIGSALMAHDDLHAAVRRVLLGE 257 L+G A M + ++R+ E Sbjct: 245 LVGEAFMRAEQPGLELQRLFFPE 267 Lambda K H 0.320 0.135 0.389 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: 253 Number of extensions: 16 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: 453 Length of database: 277 Length adjustment: 29 Effective length of query: 424 Effective length of database: 248 Effective search space: 105152 Effective search space used: 105152 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: 49 (23.5 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