Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate BPHYT_RS31740 BPHYT_RS31740 ABC transporter permease
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__BFirm:BPHYT_RS31740 Length = 316 Score = 404 bits (1039), Expect = e-117 Identities = 205/316 (64%), Positives = 252/316 (79%), Gaps = 7/316 (2%) Query: 1 MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQV 60 MDIFIQQIINGLVLGS+YA+IALGYTMVYG+L +INFAHGD+LMVGAMV LS + V+Q Sbjct: 1 MDIFIQQIINGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAITVLQDH 60 Query: 61 APGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAM 120 P L + L+IA++ A VC +V IE++AYRPLR APRLAPLITAIGVSILLQT AM Sbjct: 61 FPELGHVPTLLIALILAAAVCAMVGYTIEKVAYRPLRRAPRLAPLITAIGVSILLQTAAM 120 Query: 121 MIWGRSPLPFPQVMPSDPVHIA-------GALISPTQIMLLALAVLAMVGLVLIVEKTKM 173 +IWGR+PL FPQ++P+ P+++ GA+IS T+I ++ +A M GL+L+V +TK+ Sbjct: 121 IIWGRNPLAFPQLLPTAPLNLIQASENHPGAVISLTEIAIVVVAFFVMAGLLLLVHRTKL 180 Query: 174 GRAMRATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGL 233 GRAMRA AENP +A LMGV+ VI TF IG+ LAA+AGVM A+ Y A F MGF+PGL Sbjct: 181 GRAMRAIAENPNVASLMGVNPGFVISATFMIGSALAALAGVMIASEYGNAHFYMGFIPGL 240 Query: 234 KAFSAAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVL 293 KAF+AAVLGGIGN+ GAM+GG++LGL+E LGAGYIG LTG GSNYQD+FAF+VLI VL Sbjct: 241 KAFTAAVLGGIGNLGGAMVGGVILGLVEQLGAGYIGTLTGGVFGSNYQDVFAFVVLIAVL 300 Query: 294 TLRPSGIMGERVADRA 309 RPSG++GERVADRA Sbjct: 301 VFRPSGLLGERVADRA 316 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: 360 Number of extensions: 14 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: 316 Length adjustment: 27 Effective length of query: 282 Effective length of database: 289 Effective search space: 81498 Effective search space used: 81498 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 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