Align Glutamine amidotransferase of anthranilate synthase (characterized, see rationale)
to candidate 8501597 DvMF_2316 glutamine amidotransferase class-I (RefSeq)
Query= uniprot:B8DM46_DESVM (192 letters) >FitnessBrowser__Miya:8501597 Length = 280 Score = 82.8 bits (203), Expect = 5e-21 Identities = 58/147 (39%), Positives = 70/147 (47%), Gaps = 20/147 (13%) Query: 34 PAVPAMAEDPALEMVCISPGPSH-PRNAGFCLDFLSRLPHRVPVLGVCLGHQVLGLFAGA 92 PAVPA P + +SP P P A C P VPVLG+CLG Q++ G Sbjct: 140 PAVPAATSSP--DQSAVSPSPRRLPHCAPPC-------PVPVPVLGICLGLQIINAHFGG 190 Query: 93 TVDVGPRIMHGKTSDITHDGQGLFHGVPSPMQVGRYHSLIVHAEERPDLLAVTARAPEGE 152 P +HGK + + GQ V RYHSL H + V AR +G Sbjct: 191 VTAPLPGCVHGKPDTLHYAGQA--------RTVARYHSL--HLSAMGAGMRVLARNGQGV 240 Query: 153 VMALRYTDRPWVGVQFHPESVLTPDGV 179 VMA R+ P +G QFHPES LTPDGV Sbjct: 241 VMAARHRCLPLLGYQFHPESFLTPDGV 267 Score = 32.0 bits (71), Expect = 1e-05 Identities = 40/123 (32%), Positives = 46/123 (37%), Gaps = 27/123 (21%) Query: 3 LLIDNYDSFTFNLVQAFY-GLGLHPVVVRND-----------DPAVPAMAEDPA-LEMVC 49 LL DN+DSFT NL G PVVV D P PA A A +++ Sbjct: 4 LLADNHDSFTRNLEHLLVAATGCAPVVVPVDRLGEATTGWPHAPGGPAPAALAARWDLLV 63 Query: 50 ISPGPSHPRNAGFCLDFLSRLPHRVPVL-GVCLGHQVLGLFAGATVDVGPRIMHGKTSDI 108 ISPGP P P P+L G + AG T G G T D Sbjct: 64 ISPGPGTP----------EEYPQYAPLLGGAATRVERASHMAGTTDTTGTM---GATGDD 110 Query: 109 THD 111 T D Sbjct: 111 TDD 113 Lambda K H 0.325 0.142 0.453 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: 238 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 192 Length of database: 280 Length adjustment: 23 Effective length of query: 169 Effective length of database: 257 Effective search space: 43433 Effective search space used: 43433 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 46 (22.3 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