Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate GFF521 PS417_02655 amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__WCS417:GFF521 Length = 378 Score = 205 bits (521), Expect = 2e-57 Identities = 129/362 (35%), Positives = 195/362 (53%), Gaps = 7/362 (1%) Query: 12 AIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKF 71 A+AAA GV++ + VKIG P++GA A +G+ GA+ A + +N G I G+KI Sbjct: 14 AVAAALGVSTFVQADVKIGVAGPMTGANAAFGEQYMKGAQAAADVINKAG-GINGEKIV- 71 Query: 72 ELVAEDDAADPKQGTAAAQKLCDA-KVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATN 130 LVA DDA +PKQ A A +L D KV GVVGH S TIPAS+VY++ GI +T +TN Sbjct: 72 -LVAGDDACEPKQAVAVANRLADQDKVIGVVGHFCSSNTIPASEVYDEAGIIAITPGSTN 130 Query: 131 PNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTAT 190 P +T+ G FR+ D+ G Y VD LK K VA+I+D+ YG+G+AD T Sbjct: 131 PQVTERGLGAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVINDKDTYGKGLADATAAQLT 190 Query: 191 AKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKY 250 +G+K V E+ T DF A++T I++ D +++GG+ P+ GP++RQ+ + G+ +VK+ Sbjct: 191 KRGVKPVLEEGLTRGEKDFSALVTKIRSTGADVVYFGGLHPEAGPLVRQIREAGLKDVKF 250 Query: 251 FGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPY 310 DG+ T E+ A GA+ + V G +P A ++ K + + Y+ Y Sbjct: 251 MSDDGVVTDELVATAGGAQYVDGVYMTFGADP-RLLPDSKAVVEEF-RKNGTEPEGYTLY 308 Query: 311 TYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVY-KD 369 Y + + A S + L K V A++ G++K +Y + KD Sbjct: 309 AYASVQALAAGFNGAKSNKGEDAAKWLKAHPVKTVMGEKAWDSKGDLKISDYVVYQWDKD 368 Query: 370 GK 371 GK Sbjct: 369 GK 370 Lambda K H 0.315 0.131 0.375 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: 387 Number of extensions: 19 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: 375 Length of database: 378 Length adjustment: 30 Effective length of query: 345 Effective length of database: 348 Effective search space: 120060 Effective search space used: 120060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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