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_012332140.1 M446_RS10800 ABC transporter substrate-binding protein
Query= TCDB::Q8DQI1 (386 letters) >NCBI__GCF_000019365.1:WP_012332140.1 Length = 378 Score = 151 bits (382), Expect = 3e-41 Identities = 119/367 (32%), Positives = 182/367 (49%), Gaps = 15/367 (4%) Query: 27 GAVNTAGNSVEEKTIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGI-DGKQIEVV 85 GAV AG + ++ +K+G +G + YG A Q+G LA+ EIN GG+ G+ + + Sbjct: 16 GAVAGAG-AQDKSPVKLGAIEILTGPNSRYGVAIQRGFDLALAEINRNGGVLGGRPLALA 74 Query: 86 DKDNKSETAEAASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQDGL 145 +D+ +A + L+ + KV ++GP S AA A + VP++ S T +G+ Sbjct: 75 YEDSAGAKEQALNAARKLIGRDKVPLILGPTLSNEMFAAGPVANERKVPIVGTSTTANGI 134 Query: 146 TKGQDYLFIGTFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKG---IAKSFRESYK 202 T Y+F + ++ + EK K+V + N + K + K+ E Sbjct: 135 TAIGPYVFRTSLPEADVIPVTLRTAKEKFGVKRVAVMYGNDDAFTKSAYDVMKAGLEKLG 194 Query: 203 GEIVADETFVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKP--IVG 260 E + ETF + DTDF A LTK+KG + DAIV+ A I QAR +GID I+G Sbjct: 195 IETLTTETFGSKDTDFSAQLTKIKGLNPDAIVLSALVEAASGIALQARQLGIDPKVFIIG 254 Query: 261 GDGFNGEEFVQQATAEKASNIYFISGFSTTVEVSAKAKAFLDAYRAKYN-EEPSTFAALA 319 G+G N + + A A I F + +AF+ A+R KY+ + P FAA A Sbjct: 255 GNGLNSPKLGEIAGAAADGTIVGSPWF--VGKKDPANQAFVAAFREKYSGDSPDQFAAQA 312 Query: 320 YDSVHLVANA--AKGAKNSGEIKNNLAKTKDFEGVTGQTSFDADHNTVKTA--YMMTMNN 375 YD++ +VA A A GA +S +IK+ L K K GV G SF + T+ ++TM Sbjct: 313 YDTLFIVAKAIDAAGAPDSEKIKDALIKVK-HSGVMGPFSFSESRDPADTSGVVVLTMKG 371 Query: 376 GKVEAAE 382 GK + E Sbjct: 372 GKFQLLE 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: 283 Number of extensions: 12 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 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