Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate 8502038 DvMF_2751 inner-membrane translocator (RefSeq)
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__Miya:8502038 Length = 301 Score = 264 bits (674), Expect = 2e-75 Identities = 140/311 (45%), Positives = 207/311 (66%), Gaps = 14/311 (4%) Query: 1 MDIFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKV--VQ 58 M+ F QQ+ NGL +G +YALIALGYTMVYGVL LINFAHGD+ +GA +G +L + Sbjct: 1 MEEFFQQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTLFTAFGLS 60 Query: 59 QVAPGLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTL 118 G G++ +++ ++G + + + L+ER+AYRPLR++ RL+ +++A+G SI Q Sbjct: 61 GFVSGPGGVLLVLVMVMGLVAL---IGFLLERVAYRPLRSSSRLSAVVSALGASIFFQNA 117 Query: 119 AMMIWGRSPLPFPQ-VMPSDPVHIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAM 177 M+I+G +P + PS + I G + +IM++A ++ M+ L ++T++G A+ Sbjct: 118 VMLIYGAKFQVYPNDIRPSYVLSIMGIDVPLVRIMMIAASLGLMLALYWFTQRTRIGAAI 177 Query: 178 RATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFS 237 RATA + A LMG+D N+VI + F IG L +AGVM Y F MG+V GLKAF+ Sbjct: 178 RATAIDQGAAKLMGIDVNRVISLVFMIGPALGGVAGVMVGLYYGQVDFTMGWVYGLKAFT 237 Query: 238 AAVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRP 297 AA+LGGIGNI GAM+GG+LLG+IE+LGA YI ++D AF+VLI++L +RP Sbjct: 238 AAILGGIGNIPGAMVGGLLLGVIEALGAAYI--------SIAWKDAIAFLVLILILIIRP 289 Query: 298 SGIMGERVADR 308 +G++GERVAD+ Sbjct: 290 TGLLGERVADK 300 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: 289 Number of extensions: 19 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: 309 Length of database: 301 Length adjustment: 27 Effective length of query: 282 Effective length of database: 274 Effective search space: 77268 Effective search space used: 77268 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