Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate HSERO_RS11020 HSERO_RS11020 GMP synthase
Query= curated2:O28670 (178 letters) >FitnessBrowser__HerbieS:HSERO_RS11020 Length = 530 Score = 73.9 bits (180), Expect = 4e-18 Identities = 54/157 (34%), Positives = 77/157 (49%), Gaps = 17/157 (10%) Query: 36 LRKMSFDGVVISPGP-----GKPDRSLEFVFKMGVPVLGVCLGHQMIAEVFGGKV----- 85 +R GV++S GP G R+ + VF++GVPVLG+C G Q +AE GGKV Sbjct: 45 VRNYGAAGVILSGGPNSVTEGDTPRAPQAVFELGVPVLGICYGMQTMAEQLGGKVDNGHL 104 Query: 86 ---GRVE-PVHGKTSLVEHDGRGIFKGVRNPLRAGRYHSLAVLEPPEGFEVCAKSEDGVV 141 G E HG T L+++ L+ H V E P GF++ A + + + Sbjct: 105 REFGYAEVRAHGHTKLLDNISDFTNAQGHGMLKVWMSHGDKVNEMPAGFKLMASTGNCPI 164 Query: 142 MGL--RRGKIHGVQFHPESVLTEDGVRMIRNFV-EMC 175 G+ + +GVQFHPE T G M+ FV E+C Sbjct: 165 AGMADEERRFYGVQFHPEVTHTVQGKAMLGRFVHEIC 201 Lambda K H 0.323 0.144 0.434 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: 275 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: 178 Length of database: 530 Length adjustment: 27 Effective length of query: 151 Effective length of database: 503 Effective search space: 75953 Effective search space used: 75953 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: 48 (23.1 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