Align ABC transporter substrate-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_013075699.1 BTUS_RS08490 ABC transporter substrate-binding protein
Query= TCDB::Q8DQI1 (386 letters) >NCBI__GCF_000092905.1:WP_013075699.1 Length = 391 Score = 292 bits (748), Expect = 1e-83 Identities = 160/397 (40%), Positives = 253/397 (63%), Gaps = 19/397 (4%) Query: 1 MKKKFALSFVALASVALLAACGEVKSGAVNTAGNSVEEKTIKIGFNFEESGSLAAYGTAE 60 MKK +++ L ALL ACG SG+ T S TI +G N E SG ++AYG++ Sbjct: 1 MKKPWSVVTALLLGSALLTACG---SGSGTTGAGS---DTINLGANLELSGQVSAYGSSA 54 Query: 61 QKGAQLAVDEINAAGGIDGKQIEVVDKDNKSETAEAASVTTNLVTQSKVSAVVGPATSGA 120 + G QLAVDEIN AGG+ GK++ ++ DN+S+T ++ ++ L+ Q KV A++GPAT+G Sbjct: 55 KDGMQLAVDEINQAGGVLGKKLNLIALDNQSDTTQSTTIAQKLIEQ-KVVAILGPATTGN 113 Query: 121 TAAAVANATKAGVPLISPSATQDGLT------KGQDYLFIGTFQDSFQGKIISNYVSEKL 174 T A + AT A +P+I+P+ T +T K +Y F F D FQG + +++ + L Sbjct: 114 TMAELNVATDAKIPIITPTGTAAKITVDPNTGKVNEYAFRTCFIDPFQGTVGADFARKDL 173 Query: 175 NAKKVVLYTDNASDYAKGIAKSFRESYK---GEIVADETFVAGDTDFQAALTKMKGKDFD 231 NAK VLY SDYAKG+A +F++ ++ G+++ E + + D+DF+A LT++KG + D Sbjct: 174 NAKTAVLYVAQDSDYAKGLADAFKKEFEKQGGKVIDSEQYTSTDSDFRATLTRIKGMNPD 233 Query: 232 AIVVPGYYNEAGKIVNQARGMGIDKPIVGGDGFNGEEFVQQATAEKASNIYFISGFSTTV 291 + +P YY + GKI+ QAR +G+++PI+GGDG++ + VQ A A+ +N++F + +S+ Sbjct: 234 LLYIPNYYQDVGKIIKQARELGMNQPILGGDGYDSDTLVQIAGAKNTNNVFFTNHYSSD- 292 Query: 292 EVSAKAKAFLDAYRAKYNEEPSTFAALAYDSVHLVANAAK--GAKNSGEIKNNLAKTKDF 349 + K + F+ ++ KYN +P FAAL YD+V LVA+A K G+ + +IK+ LA+TK+F Sbjct: 293 DPDQKIQDFVKKFQEKYNRKPDGFAALGYDTVRLVADAIKRAGSTDPVKIKDALAQTKNF 352 Query: 350 EGVTGQTSFDADHNTVKTAYMMTMNNGKVEAAEVVKP 386 + VTG S DA+HN VK A ++ M +GK ++P Sbjct: 353 DAVTGTMSIDAEHNPVKAAVVIEMKDGKQVFRTKIQP 389 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: 405 Number of extensions: 26 Number of successful extensions: 6 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: 391 Length adjustment: 30 Effective length of query: 356 Effective length of database: 361 Effective search space: 128516 Effective search space used: 128516 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 24 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