Align ABC transporter substrate-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate BWI76_RS05995 BWI76_RS05995 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q8DQI1 (386 letters) >FitnessBrowser__Koxy:BWI76_RS05995 Length = 378 Score = 184 bits (467), Expect = 4e-51 Identities = 117/366 (31%), Positives = 188/366 (51%), Gaps = 22/366 (6%) Query: 34 NSVEEKTIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGIDGKQIEVVDKDNKSET 93 +S + IKIG SG+L+ YG QKG + + I +G ++++ D+KS+ Sbjct: 22 SSAQAAEIKIGVVLPLSGALSGYGQPSQKGLDI-IQSITPTLK-NGDTVKLIVIDDKSDK 79 Query: 94 AEAASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQDGLTKGQDYLF 153 EAA+ LV+ KV AV+G TS T A A + PL+S +AT D +T+ Y+ Sbjct: 80 VEAANAMQRLVSSDKVDAVIGEVTSSNTLAMTKIADDSKTPLVSSTATNDRVTRNHPYVS 139 Query: 154 IGTFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKGIAKSFRESY---KGEIVADET 210 F DSFQG + +N S L AK + D+++DY+ G+AK+FR + G I + Sbjct: 140 RVCFSDSFQGVVGANLASRDLKAKTAAIVFDSSNDYSVGLAKAFRTQFLKNGGTIPIEVQ 199 Query: 211 FVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKPIVGGDGFNGEEFV 270 G DF+A L +K K+ D I +P YY E I QA+ +G+ KP+VGGDG ++ Sbjct: 200 APGGSKDFKAQLASVKAKNVDMIYMPIYYTEGALIAVQAKQLGLSKPVVGGDGLAADQVF 259 Query: 271 QQATAEKASNIYFISGFSTTVEVSAKAK-------AFLDAYRAKYNEEPSTFAALAYDSV 323 + ++G+ TT S AK F+ A+ AKY + T+ A+A D+ Sbjct: 260 FDVGKDA------VNGYMTTDYYSPNAKEQTPAGEVFIKAWEAKYQQPTHTWGAMAADAY 313 Query: 324 HLVANAAKGAKNSGE---IKNNLAKTKDFEGVTGQTSFDADHNTVKTAYMMTMNNGKVEA 380 +++ NA + + + + TKDF+GVTG + + + +++A + + +GK+ Sbjct: 314 NVIINAMNQCSDPHDRVCVNEKIRATKDFQGVTGTLTLQ-NGDAIRSAVINEVKDGKLAF 372 Query: 381 AEVVKP 386 VV P Sbjct: 373 RTVVNP 378 Lambda K H 0.310 0.126 0.337 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: 330 Number of extensions: 15 Number of successful extensions: 4 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: 386 Length of database: 378 Length adjustment: 30 Effective length of query: 356 Effective length of database: 348 Effective search space: 123888 Effective search space used: 123888 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 (21.8 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