Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate WP_072906575.1 BUB13_RS05615 indole-3-glycerol phosphate synthase TrpC
Query= BRENDA::P00909 (453 letters) >NCBI__GCF_900142125.1:WP_072906575.1 Length = 262 Score = 179 bits (454), Expect = 9e-50 Identities = 109/259 (42%), Positives = 155/259 (59%), Gaps = 9/259 (3%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQ---NEVQPSTRHFYDALQGAR----TAFILECKK 57 +L KI+ K V A K ++PL + +++ R F AL+ R TA I E KK Sbjct: 2 ILDKILKTKTEEVAAAKLREPLVELELRVGDLEDQPRGFARALRTMRDSGGTALITEVKK 61 Query: 58 ASPSKGVIRDDFDPARIAAIYKHY-ASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKD 116 SPSKG+IR+DFDP IA Y++ A+ +SVLTDE+YF G FL + + P+L KD Sbjct: 62 GSPSKGIIREDFDPVEIAITYENGGATCLSVLTDEQYFYGHLRFLWDIREQVSLPLLRKD 121 Query: 117 FIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIA 176 FIIDPYQ+ AR ADA LL+ S L+D+Q ++LA A SL++ L EV +E E ERA+ Sbjct: 122 FIIDPYQVVEARVAGADAILLIASALNDEQLQELAEKARSLKLDTLLEVHDEAELERALQ 181 Query: 177 LGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHF-ANGFL 235 L ++GINNR+L DL + +LA ++ ++ESGIN+ A + L+ A FL Sbjct: 182 LPVDLIGINNRNLSTFVTDLAVSEQLAGRIPKQQLAVAESGINSRADIERLTAAGAGAFL 241 Query: 236 IGSALMAHDDLHAAVRRVL 254 IG +LM DD+ A + ++ Sbjct: 242 IGESLMREDDIEAKLAELI 260 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: 261 Number of extensions: 13 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: 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 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