Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate WP_028321170.1 H567_RS0109125 branched-chain amino acid ABC transporter permease
Query= uniprot:D8IUY4 (309 letters) >NCBI__GCF_000422285.1:WP_028321170.1 Length = 308 Score = 262 bits (670), Expect = 7e-75 Identities = 140/307 (45%), Positives = 199/307 (64%), Gaps = 9/307 (2%) Query: 3 IFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVA- 61 I Q+INGL +G +YALIALGYT+VYG+L +INFAHG+I M G+ G + L + Q Sbjct: 9 ILCDQLINGLTIGGIYALIALGYTLVYGILFMINFAHGEIFMFGSFAGYAALTFLLQYGF 68 Query: 62 PGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMM 121 + ++ A + A+ V ++ ++ERIAYRPLR A RLAPLI+AIG SI LQ + ++ Sbjct: 69 TEQRPLASILAAFLAAMVVSALLGTILERIAYRPLRRASRLAPLISAIGASIFLQNVMLI 128 Query: 122 IWGRSPLPFPQVMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMRATA 181 I +P ++ I IS QIM++ + M GL + +++T+ GRAMRA A Sbjct: 129 IIKGRMQVYPDLLHETFFEIGWFNISNFQIMIILGSFFLMAGLYIFIQRTRTGRAMRAVA 188 Query: 182 ENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAAVL 241 E+ A LMG+D N++I++TF IG+ LAA AGVM Y+ MGF+PG+KAF+AAVL Sbjct: 189 EDRSAAALMGIDVNRIIMITFVIGSALAAAAGVMVGMYYTQINHMMGFIPGIKAFTAAVL 248 Query: 242 GGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPSGIM 301 GGIGN+ GAMLGG+ LGL E+ G F+ + Y+D+ AF +L++VL RP GI+ Sbjct: 249 GGIGNVPGAMLGGLFLGLAEAFGV--------LFMPAQYKDVIAFALLVLVLIFRPRGIL 300 Query: 302 GERVADR 308 GE V+++ Sbjct: 301 GEVVSEK 307 Lambda K H 0.328 0.144 0.416 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: 268 Number of extensions: 15 Number of successful extensions: 3 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: 309 Length of database: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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