Align Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized, see rationale)
to candidate GFF4507 PS417_23070 GMP synthase
Query= uniprot:Q72EV2_DESVH (209 letters) >FitnessBrowser__WCS417:GFF4507 Length = 525 Score = 48.5 bits (114), Expect = 2e-10 Identities = 46/153 (30%), Positives = 61/153 (39%), Gaps = 24/153 (15%) Query: 48 VCISPGPSHPRNAGGCLAFLDVLPRTVPVLGVCLGHQVLGLYAGATVE------------ 95 V ++ GP A V VPV G+C G Q + G VE Sbjct: 54 VILAGGPESVHEANSPRCPQAVFDLGVPVFGICYGMQTMAEQLGGKVEGSELREFGYARV 113 Query: 96 --VGP-RIMHGKTSDITHDGAGLFAGLPQPMTVGRYHSLIVRAEEKPDLLEVTARTPEGE 152 VG R++ G I D GLF GL M+ G + + P+ + A TP Sbjct: 114 DVVGKSRLLDGIEDHI--DADGLF-GLDVWMSHGD------KVTKMPEDFHILASTPSCP 164 Query: 153 VMAMRYRDRPWVGVQFHPESVLTPDGVRLLGNF 185 + M +R + GVQFHPE T G R+L F Sbjct: 165 IAGMFSDERRYYGVQFHPEVTHTKQGGRILSRF 197 Lambda K H 0.323 0.141 0.444 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: 309 Number of extensions: 19 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: 209 Length of database: 525 Length adjustment: 28 Effective length of query: 181 Effective length of database: 497 Effective search space: 89957 Effective search space used: 89957 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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