Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate RR42_RS16980 RR42_RS16980 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:Q1MDE9 (367 letters) >FitnessBrowser__Cup4G11:RR42_RS16980 Length = 401 Score = 214 bits (544), Expect = 4e-60 Identities = 132/363 (36%), Positives = 194/363 (53%), Gaps = 10/363 (2%) Query: 8 ATLVASLAFAPLAHAD---ITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKG-GILGE 63 A + A AP A + + IG APLTG +A G +NGA+ AV+E+NK G I G+ Sbjct: 32 AASAPAAATAPAAGSGDVVVKIGHAAPLTGGIAHLGKDNENGARLAVEEVNKTGLEINGK 91 Query: 64 KVVLELA--DDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPT 121 K+ LEL DDAG+PK G + A K+V + VVG + SGV+IP S + ++ G++ ++P+ Sbjct: 92 KIKLELVGEDDAGDPKTGTAVAQKLVDAKVVAVVGHLNSGVSIPASKIYSDAGIVQISPS 151 Query: 122 ATAPDLTKRGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKA 181 +T PD TK+G R D QQ A Y K+ K VAIV+D AYGKGLAD F+ Sbjct: 152 STNPDYTKQGFKTTFRVVATDAQQGPALANYATKSLHAKSVAIVDDATAYGKGLADEFEK 211 Query: 182 TLNAGGITEVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANA 241 T A G+ V +A DF A+ T+IK +K DV+ +GG GG A+Q +L ++ Sbjct: 212 TAKASGVNVVAREATNDKATDFKAILTKIKGKKPDVIMYGGMDATGGPFAKQAKELGISS 271 Query: 242 TIIGGDGLSNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADA--LAAKNIPAEAFTLN 299 I+GGDG+ + + DA I + A A + A D A N P + + Sbjct: 272 KIVGGDGVCTDKVAELAGDAVSNIICSEAGLALSKMEQGADFDKRYQARFNAPVQIYAPF 331 Query: 300 AYAAVEVLKAGIEKAGSAEDAEAVATALKDGKEIPTAIGKVTYGETGDLTSQSFSLYKWE 359 Y AV V+ +++A S E A +A K + IG + + E GD+ + +LY+++ Sbjct: 332 TYDAVMVIVDAMKRANSTEPAAILAEMPKTNYK--GLIGNIAFDEKGDMKEGTITLYEYK 389 Query: 360 AGK 362 K Sbjct: 390 DKK 392 Lambda K H 0.312 0.131 0.362 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: 434 Number of extensions: 27 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: 367 Length of database: 401 Length adjustment: 30 Effective length of query: 337 Effective length of database: 371 Effective search space: 125027 Effective search space used: 125027 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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