Align ABC transporter substrate-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 208250 DVU2744 high-affinity branched-chain amino acid ABC transporter, perisplasmic amino acid binding protein
Query= TCDB::Q8DQI1 (386 letters) >MicrobesOnline__882:208250 Length = 385 Score = 177 bits (448), Expect = 6e-49 Identities = 116/365 (31%), Positives = 182/365 (49%), Gaps = 20/365 (5%) Query: 40 TIKIGFNFEESGSLAAYGTAEQKGAQLAVDEINAAGGID--GKQ--IEVVDKDNKSETAE 95 TIKIGF+ +G + G A + A++ DEINA GG++ GK+ +E V +DN+S+ Sbjct: 23 TIKIGFDIPLTGDIPKVGEASKFAAEMLRDEINAKGGLEVGGKKYMLEFVYEDNESKPES 82 Query: 96 AASVTTNLVTQSKVSAVVGPATSGATAAAVANATKAGVPLISPSATQDGLTKGQDYLFIG 155 A + L+ + +V A+VGP +S A A PLISP +T TKG+ ++F Sbjct: 83 AVNAALKLIERDQVLAIVGPNSSKQAVPAGGVADDNETPLISPWSTNPDTTKGRPWVFRA 142 Query: 156 TFQDSFQGKIISNYVSEKLNAKKVVLYTDNASDYAKGIAKSFRESY-----KGEIVADET 210 F D FQ ++ N+ S++ AK + D ++DY+KG+A FR + KG +VA E+ Sbjct: 143 AFLDPFQAPVVVNFASKQFGAKTAAVMFDVSNDYSKGLADIFRVKWEEKHGKGTVVAFES 202 Query: 211 FVAGDTDFQAALTKMKGKDFDAIVVPGYYNEAGKIVNQARGMGIDKPIVGGDGFNGEEFV 270 D DF A LTK+ D I +P YN IV QA +G P +G D + E + Sbjct: 203 HGTKDQDFSAQLTKLLAAKPDFIFLPENYNIVALIVKQAHDLGWKGPFMGSDAWGSAELM 262 Query: 271 QQATAEKASNIYFISGFSTTVEVSAKAKAFLDAYRAKYNEEPSTFAALAYDSVHLVANAA 330 + F S + K F+D Y +Y P AAL +D+ +V A Sbjct: 263 TLCGKDCVGQ--FFSTHYAAAGATGATKEFIDKYTNRYGYIPDDVAALTWDATRIVLTAI 320 Query: 331 KGA--------KNSGEIKNNLAKTKDFEGVTGQTSFDADHNTVKTAYMMTMNN-GKVEAA 381 + K I++N++ F+G+TG+ FDA+ + +K A ++ +++ G+ Sbjct: 321 QNGGKVEKDVRKMRKLIRDNISAITTFDGITGKMKFDAEGDPIKCAVVVKISDKGEFVFT 380 Query: 382 EVVKP 386 E V P Sbjct: 381 ESVCP 385 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: 337 Number of extensions: 18 Number of successful extensions: 5 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: 385 Length adjustment: 30 Effective length of query: 356 Effective length of database: 355 Effective search space: 126380 Effective search space used: 126380 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