Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate YP_426984.1 Rru_A1897 indole-3-glycerol phosphate synthase
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_000013085.1:YP_426984.1 Length = 263 Score = 150 bits (380), Expect = 4e-41 Identities = 104/263 (39%), Positives = 142/263 (53%), Gaps = 11/263 (4%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPST--RHFYDAL----QGARTAFILEC 55 M +L +I V RK PLA + + R F +AL R A I E Sbjct: 1 MSDILREICDTTRAEVARRKAALPLADVTARAEDANAPRGFANALTRTADSGRPALIAEI 60 Query: 56 KKASPSKGVIRDDFDPARIAAIYKHYASA--ISVLTDEKYFQGSFNFLPIVSQIAPQPIL 113 KKASPS G+IR DF+PA +A Y H A A +SVLTD YFQG +FL P P+L Sbjct: 61 KKASPSAGLIRPDFNPAVLARAY-HAAGATCLSVLTDGPYFQGHADFLIAARAAVPLPVL 119 Query: 114 CKDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQER 173 KDF++DP+Q+ AR AD L++L+ LDD ++ A AH M VL EV NEEE R Sbjct: 120 RKDFMVDPWQVVEARAMGADCILVILAALDDGAAAEIEACAHDWGMDVLAEVHNEEECAR 179 Query: 174 AI-ALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHF-A 231 A+ L ++G+NNR+L+ L DL T LA + + +++ESG+ T + ++ A Sbjct: 180 ALTCLTTPLLGVNNRNLKTLVTDLAVTERLAKMVPADRVLVAESGLRTRKDLDRMTAVGA 239 Query: 232 NGFLIGSALMAHDDLHAAVRRVL 254 FLIG M D+ AVR ++ Sbjct: 240 RRFLIGEHFMRQPDVGDAVRALI 262 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: 250 Number of extensions: 15 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: 263 Length adjustment: 29 Effective length of query: 424 Effective length of database: 234 Effective search space: 99216 Effective search space used: 99216 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 10 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