Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate WP_012334425.1 M446_RS22575 branched-chain amino acid ABC transporter substrate-binding protein
Query= uniprot:Q1MDE9 (367 letters) >NCBI__GCF_000019365.1:WP_012334425.1 Length = 366 Score = 302 bits (774), Expect = 8e-87 Identities = 156/352 (44%), Positives = 226/352 (64%), Gaps = 2/352 (0%) Query: 10 LVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGILGEKVVLEL 69 ++A+L ++ AD+ +G++ P TGPVAA GDQV NG AV ++N+ GG+ GEK+VL++ Sbjct: 11 VLAALLWSTAVRADVVVGVVVPRTGPVAAIGDQVLNGVNAAVKDVNESGGVNGEKLVLDV 70 Query: 70 ADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPTATAPDLTK 129 DDA +PKQ VS AN+ + + + +VG V SG + S++ AENG +MVTP+A LT+ Sbjct: 71 QDDACDPKQAVSVANRFLQNKVGLIVGHVCSGATMAASEIYAENGDVMVTPSANVAKLTE 130 Query: 130 RGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKATLNAGGIT 189 RGL+ + R CGRDDQQ E+AA+ + + F K+VAI++D +G+GLADA K LN G+ Sbjct: 131 RGLSGIFRVCGRDDQQGELAARTIAERFPGKKVAILHDNQPFGRGLADATKTNLNRIGVK 190 Query: 190 EVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANATIIGGDGL 249 E + AITPG++D++++ TR+KS +DVVY+GGYH E G L RQ + A +A IG G+ Sbjct: 191 ESLFAAITPGERDYTSVITRLKSAGIDVVYYGGYHQEMGTLVRQASEQAYSAQWIGTSGI 250 Query: 250 SNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAAKNIPAEAFTLNAYAAVEVLKA 309 ++ EF AI AA G + T DA + ++KA D A++I E FTL Y AV+VL Sbjct: 251 ASKEFAAIAHGAADGVLMTFNPDARRRSEAKAVVDRFRAQSIEPEGFTLYGYTAVQVLAQ 310 Query: 310 GIEKAGSAEDAEAVATALKDGKEIPTAIGKVTYGETGDLTSQSFSLYKWEAG 361 A S D +AV ALK G T +G V + GD+++ + LY+W G Sbjct: 311 AARNAQST-DPKAVDRALKSG-TFGTILGNVGFDRKGDISAPGYVLYRWSNG 360 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: 342 Number of extensions: 17 Number of successful extensions: 2 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: 366 Length adjustment: 30 Effective length of query: 337 Effective length of database: 336 Effective search space: 113232 Effective search space used: 113232 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: 49 (23.5 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