Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate CCNA_01976 CCNA_01976 Indole-3-glycerol phosphate synthase
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__Caulo:CCNA_01976 Length = 262 Score = 157 bits (396), Expect = 5e-43 Identities = 102/261 (39%), Positives = 151/261 (57%), Gaps = 8/261 (3%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPST--RHFYDALQG----ARTAFILEC 55 M +LAKI A K V ARK ++ A + ++ R F AL+ R + I E Sbjct: 1 MTDILAKIAAYKREDVAARKAERSQAEIDAAAKAASAPRGFKAALEAHHAPGRLSLIAEI 60 Query: 56 KKASPSKGVIRDDFDPARIAAIYKHYASA-ISVLTDEKYFQGSFNFLPIVSQIAPQPILC 114 KKASPSKG+IR+DFDP +A Y+ +A +SVLTD FQG+ ++L P + Sbjct: 61 KKASPSKGLIREDFDPPVLAKAYEAGGAACLSVLTDGPSFQGADDYLVTARAAVALPCIR 120 Query: 115 KDFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERA 174 KDF++DP+Q+ +R ADA L++L+++DD +L + A L M L EV +E E RA Sbjct: 121 KDFLVDPWQVAESRALGADAILVILAMIDDVLAAELMSEARRLGMDALVEVHDEAEMARA 180 Query: 175 IALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQ-VRELSHFANG 233 ALG+ +VGINNRDL+ +DL T L+ + + +++ESGI T+ VR + A Sbjct: 181 GALGSDLVGINNRDLKSFVVDLAVTERLSAQAPRDALLVTESGIFTHDDVVRMEATGAKA 240 Query: 234 FLIGSALMAHDDLHAAVRRVL 254 L+G +LM H D+ +A R ++ Sbjct: 241 MLVGESLMRHADVTSATRALI 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: 256 Number of extensions: 17 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: 262 Length adjustment: 29 Effective length of query: 424 Effective length of database: 233 Effective search space: 98792 Effective search space used: 98792 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