Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate 6937999 Sama_2132 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase (RefSeq)
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__SB2B:6937999 Length = 462 Score = 419 bits (1077), Expect = e-121 Identities = 241/466 (51%), Positives = 298/466 (63%), Gaps = 18/466 (3%) Query: 2 MQTVLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQGARTAFILECKKASPS 61 M VL KI+ K ++A KQ+ P AS ++ S R Y AL FILECKKASPS Sbjct: 1 MSNVLTKIIDTKYAHIDALKQRFPEASLTPKI--SDRSLYQALAAPNAGFILECKKASPS 58 Query: 62 KGVIRDDFDPARIAAIYKHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFIIDP 121 KG+IR DFDP I +IY YA+ ISVLTDE++FQG +++P V QP+LCKDF I P Sbjct: 59 KGLIRADFDPVAIVSIYSRYAAGISVLTDEQFFQGDMDYIPQVRAAVSQPVLCKDFFISP 118 Query: 122 YQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIALGAKV 181 YQ+ LA + ADA LLMLSVLDDD YR+LA A ++ +LTEVSNE+E RAIAL A + Sbjct: 119 YQVRLAAHQGADAILLMLSVLDDDDYRRLADEAAKYQLDILTEVSNEDELRRAIALRAPI 178 Query: 182 VGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHFANGFLIGSALM 241 +GINNR+LRDLS DL T LAP + + VISESGI T+ QV+ L+ GFL+GS+LM Sbjct: 179 IGINNRNLRDLSTDLATTEALAPHIPADTLVISESGIYTHEQVKRLAPLVQGFLVGSSLM 238 Query: 242 AHDDLHAAVRRVLLGENKVCGLTRGQDAKAAYDAGAIYGGLIFVATSPRCVNVEQAQEV- 300 A +L A RR++ GENKVCGLTR D AA +AGA+YGGLIF SPRCV+ ++A+ + Sbjct: 239 AEANLDLACRRLIYGENKVCGLTREADITAAANAGAVYGGLIFAEKSPRCVSEDRARALS 298 Query: 301 ----MAAAPLQYVGVFRNHDIADVVDKAKVLSLAAVQLHGNEEQLYIDTLR----EALPA 352 A+ PL VGVF + A VV AK L LAAVQLHG E++ YID LR + LP Sbjct: 299 AFNRAASQPLALVGVFVDEAAAKVVSLAKTLGLAAVQLHGKEDEAYIDDLRSQLSQELPE 358 Query: 353 HVAIWKALSVGETLPAREFQH-VDKYVLDN----GQGGSGQRFDWSLLNGQSLGNVLLAG 407 IWKA++V E A H D+ V D+ G GG+G FDW LN +LAG Sbjct: 359 GCEIWKAVAV-EAGKASAIPHGADRIVYDSKNSAGFGGTGVCFDWQ-LNLADKHRAMLAG 416 Query: 408 GLGADNCVEAAQTGCAGLDFNSAVESQPGIKDARLLASVFQTLRAY 453 GL A+N AA G GLDFNS +E PGIK A L+ F +LR Y Sbjct: 417 GLNANNAATAANQGFLGLDFNSGLEEAPGIKSAALIEQAFASLRNY 462 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: 496 Number of extensions: 22 Number of successful extensions: 5 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: 462 Length adjustment: 33 Effective length of query: 420 Effective length of database: 429 Effective search space: 180180 Effective search space used: 180180 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