Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate BPHYT_RS17405 BPHYT_RS17405 indole-3-glycerol phosphate synthase
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__BFirm:BPHYT_RS17405 Length = 261 Score = 156 bits (395), Expect = 6e-43 Identities = 101/247 (40%), Positives = 138/247 (55%), Gaps = 7/247 (2%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQP-STRHFYDALQGARTA----FILECK 56 M +L +I+A K V A +Q PL + E R F AL+ TA I E K Sbjct: 1 MSDILDRIIAVKREEVRAAEQSAPLEELRLEASSRDIRDFVGALRAKHTAGLAAVISEVK 60 Query: 57 KASPSKGVIRDDFDPARIAAIY-KHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCK 115 KASPSKGV+R+ F PA IA Y KH A+ +SVLTD ++FQGS +L P+L K Sbjct: 61 KASPSKGVLREHFVPAEIARSYEKHGAACLSVLTDVQFFQGSVAYLEEARAACNLPVLRK 120 Query: 116 DFIIDPYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAI 175 DFI+DPYQI AR ADA LL+ + L+ Q + L A+AHSL + VL EV + +E ++ Sbjct: 121 DFIVDPYQIVEARAMGADAILLIAAALETSQMQDLEALAHSLGLAVLVEVHDHDELMESL 180 Query: 176 ALGAKVVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHF-ANGF 234 L ++GINNR+LR + T + + + V++ESGI + A V L + F Sbjct: 181 TLKTPLIGINNRNLRTFETSIETTIGMLEAIPDDRIVVTESGILSRADVERLRAMDVHTF 240 Query: 235 LIGSALM 241 L+G A M Sbjct: 241 LVGEAFM 247 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: 227 Number of extensions: 12 Number of successful extensions: 2 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: 261 Length adjustment: 29 Effective length of query: 424 Effective length of database: 232 Effective search space: 98368 Effective search space used: 98368 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