Align Anthranilate 1,2-dioxygenase electron transfer component; EC 1.18.1.3 (characterized)
to candidate WP_086509265.1 BZY95_RS07140 CDP-6-deoxy-delta-3,4-glucoseen reductase
Query= SwissProt::O85675 (343 letters) >NCBI__GCF_002151265.1:WP_086509265.1 Length = 338 Score = 154 bits (390), Expect = 2e-42 Identities = 103/321 (32%), Positives = 162/321 (50%), Gaps = 15/321 (4%) Query: 20 QEDELLLDAAVRQGINLPLDCREGVCGTCQGTCETGIYEQEYVDEDALSERDLAKRKMLA 79 Q E LL+AA R G L DCR G CG C+ G E L+E + LA Sbjct: 17 QPGEPLLEAAERAGFPLAHDCRFGGCGACRVKLMEGSVEYNEFPF-GLTEEEAEAGYALA 75 Query: 80 CQTRVKSNAAFYFDHHSSICNAGET---LKIATVVTGVELVSETT-AILHLDASQHVKQL 135 CQ +S+ + + AG +AT+ +L + T +L + ++ V Sbjct: 76 CQACAQSDLTI----SAKLLPAGHIPADFHVATIERLEKLSHDVTHLVLRIPSASEVV-- 129 Query: 136 DFLPGQYARLQIPDTDDWRSYSFANRPNASNQLQFLIRLLPNGVMSNYLRERCQVGQTLI 195 F PGQY + + D RS+S A+ P+ F IR +P G + L + G TL Sbjct: 130 -FHPGQYLNVMLDDGSP-RSFSMAS-PHRGELFDFHIRRVPGGHFTGRLETHYRPGDTLD 186 Query: 196 MEAPLGSF-YLREVERPLVFIAGGTGLSAFLGMLDNIAEQPNQPSVHLYYGVNTEADLCE 254 +E PLG+F + E R L+ + GGTGL+ +++++ ++P +P + LY+GV DL Sbjct: 187 VELPLGNFRHDAESPRDLLMVGGGTGLAPLKSIIESLLDEPGRPGITLYWGVRRAEDLYL 246 Query: 255 QKRLTTYAERIKNFSYHPIISKASEQWQGKSGFIHEHLDKNQLSEQSFDMYLCGPPPMIE 314 ++L +A + +F Y P++S+ +W G+ GF+HE + ++ FD YLCGPPPMI Sbjct: 247 DEQLNHWARTLPDFRYVPVLSEPDPEWGGRRGFVHEAVCQDFDDLSPFDAYLCGPPPMIA 306 Query: 315 AVKTWLDEQAIADCHIYSEKF 335 A KT ++ + IY++ F Sbjct: 307 AAKTSFAQRGLDVERIYADSF 327 Lambda K H 0.319 0.134 0.401 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: 311 Number of extensions: 16 Number of successful extensions: 3 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: 343 Length of database: 338 Length adjustment: 28 Effective length of query: 315 Effective length of database: 310 Effective search space: 97650 Effective search space used: 97650 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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