Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate 8501893 DvMF_2608 inner-membrane translocator (RefSeq)
Query= uniprot:D8IUY4 (309 letters) >FitnessBrowser__Miya:8501893 Length = 302 Score = 270 bits (691), Expect = 2e-77 Identities = 142/305 (46%), Positives = 208/305 (68%), Gaps = 19/305 (6%) Query: 4 FIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAPG 63 F + GL GS+YALIALGYTMVYG++ LINFAHG++ M+GA L + + G Sbjct: 6 FWELFFGGLTRGSIYALIALGYTMVYGIIELINFAHGEVYMMGAFTALIVAGALGIY--G 63 Query: 64 LPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMMIW 123 P + L+IA V A+ C L +E+IAY+PLR+APRL+PLI+AIG+SI LQ ++ Sbjct: 64 FPALAILIIAAVVAVIYCAAYGLTLEKIAYKPLRDAPRLSPLISAIGMSIFLQNYVILAQ 123 Query: 124 GRSPLPFPQVMPS----DPV-HIAGALISPTQIMLLALAVLAMVGLVLIVEKTKMGRAMR 178 +PFP ++P +P+ HI GA ++++++ + ++M L L ++ T+MG+AMR Sbjct: 124 TSDFMPFPNLVPQPDFLEPIAHIMGA----SEVLIIVTSAISMAALTLFIKYTRMGKAMR 179 Query: 179 ATAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSA 238 ATA+N ++A L+G+DA+KVI +TF IG+ LAA+ GV+ A++ FA+GF+ G+KAF+A Sbjct: 180 ATAQNRKMAMLLGIDADKVISLTFVIGSSLAAVGGVLIASHVGQVNFAIGFIAGIKAFTA 239 Query: 239 AVLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFLGSNYQDIFAFIVLIIVLTLRPS 298 AVLGGIG+I GAMLGG++LG ES GYI S+Y+D AF +L+++L RPS Sbjct: 240 AVLGGIGSIPGAMLGGLVLGWCESFATGYI--------SSDYEDALAFALLVLILIFRPS 291 Query: 299 GIMGE 303 GI+G+ Sbjct: 292 GILGK 296 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: 304 Number of extensions: 19 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: 309 Length of database: 302 Length adjustment: 27 Effective length of query: 282 Effective length of database: 275 Effective search space: 77550 Effective search space used: 77550 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