Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate 202144 SO3022 indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase (NCBI ptt file)
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__MR1:202144 Length = 469 Score = 384 bits (985), Expect = e-111 Identities = 227/463 (49%), Positives = 297/463 (64%), Gaps = 20/463 (4%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNEVQPSTRHFYDALQGARTAFILECKKASPSKGV 64 VL +IV KA + A K + P AS +V S R + AL+ + +ILECKKASPSKG+ Sbjct: 10 VLTRIVDTKAAHIAALKLRFPEASLVPKV--SDRSLFAALKAPKAGYILECKKASPSKGL 67 Query: 65 IRDDFDPARIAAIYKHYASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFIIDPYQI 124 IR DFD IA+IY YA+ ISVLTDE++FQG +++P V QPILCKDF +D YQ+ Sbjct: 68 IRKDFDVEAIASIYTKYAAGISVLTDEQFFQGDMDYIPKVRAKVSQPILCKDFFVDEYQV 127 Query: 125 YLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIALGAKVVGI 184 LA + ADA LLMLSVLDD++Y+QLA+ A ++ VLTE+SNEEE +RAIAL A ++GI Sbjct: 128 KLAAHQGADAILLMLSVLDDERYQQLASEAAKYQLDVLTEISNEEELKRAIALNAPIIGI 187 Query: 185 NNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHFANGFLIGSALMAHD 244 NNR+LRDLS DL T LAP +G + VISESGI T QVR LS +GFL+GS++MA + Sbjct: 188 NNRNLRDLSTDLATTEALAPHIGSDRVVISESGIYTNDQVRRLSPLVDGFLVGSSIMAEE 247 Query: 245 DLHAAVRRVLLGENKVCGLTRGQDAKAAYDAGAIYGGLIFVATSPRCVNVEQAQEVM--- 301 D+ A R+++ G NKVCGLTR +D +AA +AGA+Y GLIF SPR + + A++++ Sbjct: 248 DIDLACRKLIFGHNKVCGLTRLEDIEAAANAGAVYAGLIFAEKSPRALTKDAAKQLVEQY 307 Query: 302 --AAAP-LQYVGVFRNHDIADVVDKAKVLSLAAVQLHGNEEQLYIDTLREALP---AHVA 355 A P +++VGVF N+ + AK LAAVQLHG+E +L I L + L Sbjct: 308 RAAKLPAIEFVGVFVNNTPKLIASIAKACDLAAVQLHGSETELEITELSQLLQQAGLKTH 367 Query: 356 IWKALSVGET---LPAREFQHVDKYVLDN----GQGGSGQRFDWSLLNGQSLGNVLLAGG 408 IWKA+SV T L A + V +Y+ D+ G GG+GQ F+W L LLAGG Sbjct: 368 IWKAVSVDATSGELGAMP-KGVQRYLFDSKNNAGFGGTGQPFNWHLPLAHK-AKALLAGG 425 Query: 409 LGADNCVEAAQTGCAGLDFNSAVESQPGIKDARLLASVFQTLR 451 L A N A G GLDFNS +E+ PGIK A + + F LR Sbjct: 426 LNAANAANANAQGFYGLDFNSGLETAPGIKSAEQIQTAFAQLR 468 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: 476 Number of extensions: 24 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: 469 Length adjustment: 33 Effective length of query: 420 Effective length of database: 436 Effective search space: 183120 Effective search space used: 183120 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