Align NatB aka SLR0559, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate SMc01946 SMc01946 leucine-specific binding protein
Query= TCDB::Q55387 (454 letters) >FitnessBrowser__Smeli:SMc01946 Length = 372 Score = 91.3 bits (225), Expect = 5e-23 Identities = 98/360 (27%), Positives = 144/360 (40%), Gaps = 47/360 (13%) Query: 72 PATGDLSSIGQNMPLAVQLAVDTINACGGVNGQDVTVVIEDDQTDPTAGVSAMTKLAEAD 131 P TG ++ G + + A + INA GG+NG+ + VV+ DD +DP GVS K AD Sbjct: 32 PLTGPNAAFGAQLQKGAEQAAEDINAAGGINGEQIKVVLGDDVSDPKQGVSVAQKFV-AD 90 Query: 132 QVAGVVGSFASSVSSAAVPIAVRNNIMMISPGSTSPVFTDQAKKGEFKGFW--ARTAPPD 189 V VVG F S VS A I N I+ ++P ST+P FT+ +G W RT D Sbjct: 91 GVKFVVGHFNSGVSIPASEIYAENGILQVTPASTNPQFTE-------RGLWNTFRTCGRD 143 Query: 190 TYQAQALAALAKKQGFTDAATVVINN--DYGVGFEKVFVESFTADGGNVTNKDNPVRYDP 247 Q A+A F DA VI++ YG G +S G + D Sbjct: 144 DQQG-AVAGAYIAANFKDAKVAVIHDKTPYGQGLADETKKSMNEAGVTEALYEGINTGDK 202 Query: 248 KAATLDTEAAQGFANSPDAVAAILYADTGSVLVQSAYRQGLMDGVTLLLTDGVYSPDFVE 307 + L + Q A L+ + G ++ Q QGL T++ DG+ S + Sbjct: 203 DFSALIAKMKQ--AGVSIVYYGGLHTEAGLIMRQMK-DQGLK--ATMMSGDGIVSNELAS 257 Query: 308 KVGKDANGVSLLSGALGTVPGADGKSLEAFTAQWKDATGGKDVTAFVPHTYDATVLMMLA 367 G + G L T KS A K G + A+ + Y A ++ Sbjct: 258 IAG------DAVDGTLMTFAPDPRKSPAAKDLVEKFRAAGFEPEAYTLYAYAALQVIAEG 311 Query: 368 AEAAKSNTGAGIQSKIRDVSNGPGEEVTDACEAIAMVREGKDINYQGASGNVDIDENGDV 427 A+AA + + I+ + GP ++ A G + DE GD+ Sbjct: 312 AKAAGNTDPQAVAEAIK--AKGP---------------------FKTAIGELGFDEKGDI 348 Lambda K H 0.313 0.131 0.374 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: 430 Number of extensions: 21 Number of successful extensions: 2 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: 454 Length of database: 372 Length adjustment: 31 Effective length of query: 423 Effective length of database: 341 Effective search space: 144243 Effective search space used: 144243 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 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