Align Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized, see rationale)
to candidate 206477 DVU1043 GMP synthase
Query= uniprot:Q72EV2_DESVH (209 letters) >MicrobesOnline__882:206477 Length = 515 Score = 52.4 bits (124), Expect = 2e-11 Identities = 41/138 (29%), Positives = 57/138 (41%) Query: 48 VCISPGPSHPRNAGGCLAFLDVLPRTVPVLGVCLGHQVLGLYAGATVEVGPRIMHGKTSD 107 + +S GP+ +L VPVLG+C G Q+LG G + +G Sbjct: 51 IILSGGPASVGEKDAPALEKGLLDLGVPVLGICYGMQLLGQDLGGELATSETREYGPADL 110 Query: 108 ITHDGAGLFAGLPQPMTVGRYHSLIVRAEEKPDLLEVTARTPEGEVMAMRYRDRPWVGVQ 167 L+ GL T + S + + P +V RT EV AM R VQ Sbjct: 111 TLTAPCPLWDGLDLGTTSRVWMSHGDKVKTPPPGFKVVGRTATLEVAAMADEARRIYAVQ 170 Query: 168 FHPESVLTPDGVRLLGNF 185 FHPE + DG R++ NF Sbjct: 171 FHPEVHHSEDGARIINNF 188 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: 286 Number of extensions: 26 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: 515 Length adjustment: 28 Effective length of query: 181 Effective length of database: 487 Effective search space: 88147 Effective search space used: 88147 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