Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate BWI76_RS07260 BWI76_RS07260 branched chain amino acid ABC transporter substrate-binding protein
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Koxy:BWI76_RS07260 Length = 385 Score = 208 bits (530), Expect = 2e-58 Identities = 126/367 (34%), Positives = 201/367 (54%), Gaps = 11/367 (2%) Query: 5 TQRLSRLFAAMAIAGFAS---YSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQIN 61 T ++S L AA+ ++GFAS +S A++T+ I LAGP+TGP A+ G GA +AI+ IN Sbjct: 3 TVKISALSAAILLSGFASSAAWSAASETVIIGLAGPLTGPSARIGKDLENGAQLAIDDIN 62 Query: 62 KAGGVNGAQLEGVIY-----DDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIY 116 K G + V + DD DP+ AVAVA ++V+ GV VVGH + ++ PA +Y Sbjct: 63 KQHPTIGGK--AVTFKLQSEDDQSDPRTAVAVAQRLVDSGVAGVVGHWNTGTSIPAARVY 120 Query: 117 EDEGVLMITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQ 176 D G+ + P AT T +G+ FR +G D+ G AG++ + K K IAV+ D+ Sbjct: 121 HDAGIAQVAPVATGHAYTKQGFDTSFRVMGHDDDGGQFAGQYAVQTLKAKRIAVIDDRTA 180 Query: 177 YGEGIATEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLL 236 +G+G+A E K++E GI + + ++ DF+A+++ ++ ++FGG + L Sbjct: 181 FGQGLADEFIKSLEVQGINIVDRQYVDDKTVDFSAVLTAIRSKNADLIFFGGVDSQAAPL 240 Query: 237 LRQAKQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLP-RAFEQDPKNKALIDAFKAK 295 R+ KQ G++A MG G + +A +G++A P E+ P KA A++++ Sbjct: 241 ARRIKQLGMNATLMGAGGFVSQTFLQLAQKEGDGVVALEPGLPVERMPGGKAFEQAYQSR 300 Query: 296 NQDPSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKN 355 + AY A V+ +EKA DP ALRA + TG + FD++G+LK+ Sbjct: 301 YHTHIELHAPFAYDATRVLVAAMEKADSVDPADYLPALRAINYAGVTGQIAFDKEGNLKS 360 Query: 356 FDFTVYE 362 FTVY+ Sbjct: 361 PTFTVYK 367 Lambda K H 0.316 0.133 0.377 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: 369 Number of extensions: 18 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: 373 Length of database: 385 Length adjustment: 30 Effective length of query: 343 Effective length of database: 355 Effective search space: 121765 Effective search space used: 121765 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: 41 (21.6 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