Align ABC transporter for D-Trehalose, permease component 1 (characterized)
to candidate WP_086510782.1 BZY95_RS15415 sugar ABC transporter permease
Query= reanno::Smeli:SM_b20326 (328 letters) >NCBI__GCF_002151265.1:WP_086510782.1 Length = 310 Score = 133 bits (335), Expect = 5e-36 Identities = 99/319 (31%), Positives = 153/319 (47%), Gaps = 28/319 (8%) Query: 5 SLADRPAALAHGGRIGSDLQAQRVRSAWL---FLAPTFLVLALVAGWPLIRTIYFSFTNA 61 S A RP A + R S L AWL LAP+ + ++ T S TN+ Sbjct: 5 SSAARPTAGSTARRSHSGLL-----QAWLPKLVLAPSAAISLFFVYGFMLWTFVLSLTNS 59 Query: 62 SLTNLSGAEFVGFANYLSWITLKSGRTIYRGLLADPAWWNAVWNTLKFTVLSVSIETALG 121 + L EFVGFA Y L+A+ WW A N + F L V+I ALG Sbjct: 60 RM--LPSYEFVGFAQYAR-------------LMANDRWWVASTNLVVFGGLFVAICLALG 104 Query: 122 LIVALVLNAQFPGRGLVRAAILIPWAIPTIVSAKMWAWMLNDQFGILNDMLIGLGLIGEK 181 L++A++L+ + G +R L P A+ IV+ +W W+LN GI M+ G + Sbjct: 105 LVLAILLDQRIRQEGALRTIYLYPMALSFIVTGVVWKWLLNPGLGI-QAMVRSWGFENFR 163 Query: 182 IAWTASPDTAMIAELIVDVWKTTPFMALLILAGLQMVPGDIYEAAKIDGVHPVRVFWRVT 241 W PD A+ +I VW+ + F+ L LAGL+ + I +AA++DG R++WRV Sbjct: 164 FDWLVDPDMAVYTLVIAAVWQASGFVMALFLAGLRGIDDSILKAAQLDGASLPRIYWRVV 223 Query: 242 LPLIRPALMVAVIFRMLDALRIFDLIYVLT---PNNAQTKTMSVMARENLFDFDKFAYGA 298 +P +RP + AV+ A++ FDL+ LT P A + M + F + G+ Sbjct: 224 IPCLRPVVFSAVMILSHIAIKSFDLVVALTGGGPGYASDLPATFM-YAHAFTRAQIGLGS 282 Query: 299 AASTMLFLIIATITILYMW 317 A++ ++ + I I Y++ Sbjct: 283 ASAMLMLGGVLAILIPYLY 301 Lambda K H 0.328 0.140 0.438 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: 330 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: 328 Length of database: 310 Length adjustment: 28 Effective length of query: 300 Effective length of database: 282 Effective search space: 84600 Effective search space used: 84600 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 24 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