Align phosphoribosylanthranilate isomerase (EC 5.3.1.24) (characterized)
to candidate CA265_RS22900 CA265_RS22900 indole-3-glycerol phosphate synthase
Query= BRENDA::P00909 (453 letters) >FitnessBrowser__Pedo557:CA265_RS22900 Length = 260 Score = 130 bits (328), Expect = 4e-35 Identities = 93/252 (36%), Positives = 129/252 (51%), Gaps = 5/252 (1%) Query: 5 VLAKIVADKAIWVEARKQQQPLASFQNEV--QPSTRHFYDALQGA-RTAFILECKKASPS 61 +L KIV K V A K + +N V + + F + L A RT I E K+ SPS Sbjct: 3 ILDKIVLRKKEEVAAAKALVSVQDLENSVHFKRAPYSFKEFLLAADRTGIIAEFKRRSPS 62 Query: 62 KGVIRDDFDPARIAAIYKHY-ASAISVLTDEKYFQGSFNFLPIVSQIAPQPILCKDFIID 120 KG+I D A + Y ASA+SVLTD +F G + + PIL KDF+ID Sbjct: 63 KGLINGVADVAEVTQAYNAAGASALSVLTDVDFFGGKTDDILAARAANHIPILRKDFMID 122 Query: 121 PYQIYLARYYQADACLLMLSVLDDDQYRQLAAVAHSLEMGVLTEVSNEEEQERAIALGAK 180 YQI A+ + AD LL+ S+L Q A L + VL EV N EE ER+I Sbjct: 123 TYQILEAKAWGADIILLIASILTPQQINDFGKFAKDLGLNVLLEVHNLEELERSICPNLD 182 Query: 181 VVGINNRDLRDLSIDLNRTRELAPKLGHNVTVISESGINTYAQVRELSHFA-NGFLIGSA 239 +G+NNR+L D ++D+ + +L K+ + ISES I+ +++L NGFLIG Sbjct: 183 AIGVNNRNLGDFTVDIQTSFDLVNKIPNEFLKISESAISNTQTIKDLKAAGFNGFLIGEN 242 Query: 240 LMAHDDLHAAVR 251 M DD A++ Sbjct: 243 FMKTDDPGVAIK 254 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: 251 Number of extensions: 12 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: 260 Length adjustment: 29 Effective length of query: 424 Effective length of database: 231 Effective search space: 97944 Effective search space used: 97944 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