Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate 3608400 Dshi_1800 Indole-3-glycerol-phosphate synthase (RefSeq)
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__Dino:3608400 Length = 271 Score = 155 bits (391), Expect = 2e-42 Identities = 102/261 (39%), Positives = 150/261 (57%), Gaps = 7/261 (2%) Query: 1 MMQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPST--RHFYDALQGART---AFILEC 55 M T+L +I A K V ARK +PLA + + ++ R F AL+ A A I E Sbjct: 1 MTDTILDRIKAYKLEEVAARKAARPLAEVEAAARQASPVRPFAGALRAAAQNGYALIAEV 60 Query: 56 KKASPSKGVIRDDFDPARIAAIYKHYASA-ISVLTDEKYFQGSFNFLPIVSQIAPQPILC 114 KKASPSKG+IR DFDP IA Y +A +SVLTD FQG ++L P+L Sbjct: 61 KKASPSKGLIRADFDPPAIARAYAAGGAACLSVLTDAPSFQGHEDYLVAARAACALPVLR 120 Query: 115 KDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERA 174 KDF+ DPYQ+ AR AD L++++ + D Q +L A S M L EV + +E +RA Sbjct: 121 KDFMYDPYQVPEARAMGADCILIIMASVSDAQAVELEDAATSWGMDALIEVHDGDELDRA 180 Query: 175 IALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHF-ANG 233 + L + ++GINNR+L+ L+ TR LAP++ + +++ESG++ ++ +L+ + A Sbjct: 181 LRLNSPLMGINNRNLKTFETTLDTTRTLAPRIPGDRMIVAESGLSGPTELADLAGYGART 240 Query: 234 FLIGSALMAHDDLHAAVRRVL 254 FLIG +LM D+ A R +L Sbjct: 241 FLIGESLMRQADVAEATRALL 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: 241 Number of extensions: 11 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: 271 Length adjustment: 29 Effective length of query: 424 Effective length of database: 242 Effective search space: 102608 Effective search space used: 102608 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