Align ABC transporter permease (characterized, see rationale)
to candidate 8501893 DvMF_2608 inner-membrane translocator (RefSeq)
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Miya:8501893 Length = 302 Score = 269 bits (688), Expect = 5e-77 Identities = 136/294 (46%), Positives = 201/294 (68%), Gaps = 11/294 (3%) Query: 11 GLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGAPGWVIL 70 GL GS+YALIALGYTMVYGII+LINFAHGEV M+GA T+ G + + G P IL Sbjct: 13 GLTRGSIYALIALGYTMVYGIIELINFAHGEVYMMGAFTALIVAGAL--GIYGFPALAIL 70 Query: 71 LLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWKPNYKPY 130 ++A ++A + A +EK+AY+PLR +PRL+PLI+AIGMSI LQ ++ ++ P+ Sbjct: 71 IIAAVVAVIYCAAYGLTLEKIAYKPLRDAPRLSPLISAIGMSIFLQNYVILAQTSDFMPF 130 Query: 131 PTMLPSSPF-EIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENPRVASL 189 P ++P F E + +++LI+ +A+++A+L + +T +G+AMRATA+N ++A L Sbjct: 131 PNLVPQPDFLEPIAHIMGASEVLIIVTSAISMAALTLFIKYTRMGKAMRATAQNRKMAML 190 Query: 190 MGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGIGNLAG 249 +G+ D VIS TF+IG+ LAA+ G++ AS+ G +GF+ G+KAFTAAV GGIG++ G Sbjct: 191 LGIDADKVISLTFVIGSSLAAVGGVLIASHVGQVNFAIGFIAGIKAFTAAVLGGIGSIPG 250 Query: 250 AVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGE 303 A++GG++LG E+ +GYI S Y D AF +L++IL RPSG+LG+ Sbjct: 251 AMLGGLVLGWCESFATGYI--------SSDYEDALAFALLVLILIFRPSGILGK 296 Lambda K H 0.327 0.142 0.419 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: 266 Number of extensions: 17 Number of successful extensions: 6 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