Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate 5209801 Shew_2254 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase (RefSeq)
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__PV4:5209801 Length = 483 Score = 407 bits (1045), Expect = e-118 Identities = 238/476 (50%), Positives = 299/476 (62%), Gaps = 37/476 (7%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQGARTAFILECKKASPSKGV 64 VL +IV K + A KQ+ P AS +V S R Y AL+ FI ECKKASPSKG+ Sbjct: 18 VLTRIVDTKPAHIAALKQRFPEASLAPKV--SDRSLYQALKAPNAGFIFECKKASPSKGL 75 Query: 65 IRDDFDPARIAAIYKHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFIIDPYQI 124 IR FD IA +Y HYA+AISVLTDE++FQG ++LP V QPILCKDF +DPYQ+ Sbjct: 76 IRQAFDVEAIADVYNHYAAAISVLTDEQFFQGDMDYLPKVRARVSQPILCKDFFVDPYQV 135 Query: 125 YLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIALGAKVVGI 184 LA + ADA LLMLSVLDDD YRQLA++A ++ VLTEVSNEEE +RAIAL A ++GI Sbjct: 136 KLAAHQGADAILLMLSVLDDDHYRQLASLAAQYQLDVLTEVSNEEELKRAIALDAAIIGI 195 Query: 185 NNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHFANGFLIGSALMAHD 244 NNR+LRDL+ DL T LAP + + V+SESGI T QVR LS +GFL+GS+LMA Sbjct: 196 NNRNLRDLTTDLATTEALAPHIPADRVVVSESGIYTQQQVRRLSPLVDGFLVGSSLMAEA 255 Query: 245 DLHAAVRRVLLGENKVCGLTRGQDAKAAYDAGAIYGGLIFVATSPRCVNVEQA-----QE 299 DL A R + LG NKVCGLTR +D +A DAGA+YGGLIF SPR V+ EQA Q+ Sbjct: 256 DLDLACRALTLGHNKVCGLTRSEDVRAVIDAGALYGGLIFAKKSPRYVSPEQALDLVEQQ 315 Query: 300 VMAAAPLQYVGVFRNHDIADVVDKAKVLSLAAVQLHGNEEQLYIDTLR---EALPAHVAI 356 + L +VGVF N +++ + + AK L+L AVQLHG+E + ID LR L I Sbjct: 316 RSSGKGLNFVGVFVNEELSTIAELAKRLNLFAVQLHGSESEYDIDQLRFKLNELDCQTQI 375 Query: 357 WKALSV--------GETLPAREFQHVDKYVLDNGQ--------GGSGQRFDWSLLNGQSL 400 WKA++V + PA + D+ + D+ GG+G F+W Q L Sbjct: 376 WKAVAVSVDSDDCQAPSTPA----NADRLLYDSKTKATDGVQFGGTGHAFNWQ----QQL 427 Query: 401 GN---VLLAGGLGADNCVEAAQTGCAGLDFNSAVESQPGIKDARLLASVFQTLRAY 453 N +LAGGL A N +AA+ G GLDFNS +ES PG+KDA L+ F LR Y Sbjct: 428 PNKADAMLAGGLNAGNAFDAARQGFFGLDFNSGLESAPGVKDAELIKQAFTALREY 483 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: 523 Number of extensions: 31 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: 483 Length adjustment: 33 Effective length of query: 420 Effective length of database: 450 Effective search space: 189000 Effective search space used: 189000 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: 51 (24.3 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