Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate BWI76_RS07260 BWI76_RS07260 branched chain amino acid ABC transporter substrate-binding protein
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__Koxy:BWI76_RS07260 Length = 385 Score = 318 bits (816), Expect = 1e-91 Identities = 162/366 (44%), Positives = 239/366 (65%), Gaps = 4/366 (1%) Query: 9 VVAAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKK 68 +++ A++A ++A E V+ IG P++G A GKD ENGA++AI+++N Q TIGGK Sbjct: 14 LLSGFASSAAWSAASETVI-IGLAGPLTGPSARIGKDLENGAQLAIDDINKQHPTIGGKA 72 Query: 69 IKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAA 128 + F+L +EDD +DP+ A AQ+L D+ VAGVVGH N+GT+IPA++VY+D GI V A Sbjct: 73 VTFKLQSEDDQSDPRTAVAVAQRLVDSGVAGVVGHWNTGTSIPAARVYHDAGIAQVAPVA 132 Query: 129 TNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKT 188 T TK G+ T+FR++ +D+ G YAV TLK K +A+IDDRTA+GQG+AD F K+ Sbjct: 133 TGHAYTKQGFDTSFRVMGHDDDGGQFAGQYAVQTLKAKRIAVIDDRTAFGQGLADEFIKS 192 Query: 189 ATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNV 248 +G+ +VD Q+ DK DF A+LTAI++KN D IF+GG+D Q P+ R+++QLGM N Sbjct: 193 LEVQGINIVDRQYVDDKTVDFSAVLTAIRSKNADLIFFGGVDSQAAPLARRIKQLGM-NA 251 Query: 249 KYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYS 308 G G + +LA K V+ E G + +MPGG A++ Y ++Y ++++ Sbjct: 252 TLMGAGGFVSQTFLQLA--QKEGDGVVALEPGLPVERMPGGKAFEQAYQSRYHTHIELHA 309 Query: 309 PYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYK 368 P+ YDAT ++V AM++A+SVDP Y P L ++ GVT IAF+ G +K+P T+Y Sbjct: 310 PFAYDATRVLVAAMEKADSVDPADYLPALRAINYAGVTGQIAFDKEGNLKSPTFTVYKVV 369 Query: 369 DGKKTP 374 +GK P Sbjct: 370 EGKWQP 375 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: 372 Number of extensions: 13 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: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 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