Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate GFF1668 PGA1_c16910 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__Phaeo:GFF1668 Length = 270 Score = 163 bits (413), Expect = 5e-45 Identities = 107/261 (40%), Positives = 155/261 (59%), Gaps = 7/261 (2%) Query: 1 MMQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPST--RHFYDAL-QGARTAF--ILEC 55 M +TVL KI A K + A K +PL + + E + ++ R F AL Q +R + I E Sbjct: 1 MTETVLDKIKAYKLEEIAADKAAKPLEAVEAEARDASPVRGFAKALMQASRDGYGLIAEI 60 Query: 56 KKASPSKGVIRDDFDPARIAAIYKHY-ASAISVLTDEKYFQGSFNFLPIVSQIAPQPILC 114 KKASPSKG+IR+DF PA +A Y+ A+ +SVLTD FQG+ +FL + P L Sbjct: 61 KKASPSKGLIREDFHPADLARAYEAGGATCLSVLTDTPSFQGAKSFLTEAREACALPALR 120 Query: 115 KDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERA 174 KDF+ DPYQ+ AR AD L++L+ + D Q +L A A M VL EV +EEE RA Sbjct: 121 KDFMYDPYQVAEARALGADCILIILASVSDTQAAELEAAAADWNMDVLLEVHDEEELHRA 180 Query: 175 IALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHF-ANG 233 L + ++GINNR+L+ L+ TR L+ + + T++ ES ++T A + +++ + A Sbjct: 181 CKLTSPLLGINNRNLKTFETTLDTTRTLSRLVPADRTIVCESALSTPADLSDMARYGARS 240 Query: 234 FLIGSALMAHDDLHAAVRRVL 254 FLIG +LM DD+ AA R +L Sbjct: 241 FLIGESLMRQDDVAAATRDIL 261 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: 274 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: 453 Length of database: 270 Length adjustment: 29 Effective length of query: 424 Effective length of database: 241 Effective search space: 102184 Effective search space used: 102184 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