Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate H281DRAFT_03731 H281DRAFT_03731 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= reanno::pseudo5_N2C3_1:AO356_00015 (277 letters) >FitnessBrowser__Burk376:H281DRAFT_03731 Length = 270 Score = 143 bits (360), Expect = 5e-39 Identities = 79/259 (30%), Positives = 128/259 (49%), Gaps = 6/259 (2%) Query: 21 VTALLLFFPIFWMVLTSFKTE---IDAFATPPQFIFMPTLENYLHIQERSDYFHFAWNSV 77 V L P++WM+ S +T + FAT PQ + T ENY I ++ NS+ Sbjct: 15 VYMLFALIPLYWMLSISLRTNEETMSTFATLPQHV---TFENYKIIFTDPSWYWGYINSI 71 Query: 78 LISFSATALCMLIAVPAAYSMAFYETKRTKQTLLWMLSTKMLPPVGVLMPIYLLAKGAGL 137 + T + +L+A+PAAY+ + Y K W+L+ +M PP L+P + L GL Sbjct: 72 IYVLMNTVMSVLVALPAAYAFSRYRFLGDKHMFFWLLTNRMTPPAVFLLPFFQLYSSVGL 131 Query: 138 LDTRIALIVIYTLINLPIVVWMIYTYFKDIPREILEAARLDGATLGQEMLRVLLPISKGG 197 DT IA+ + + L N+P+ VW++ + + REI E A +DG T +++ LP+ K G Sbjct: 132 TDTYIAVALAHMLFNVPLAVWILEGFMSGVSREIDETAYIDGYTFPAFFVKIFLPLIKSG 191 Query: 198 LASTMLLSMILCWNEAFWSLNLTSSSAAPLTALIASYSSPEGLFWAKLSAVSTLACAPIL 257 + T + W E + LTS +A P+ A++ S G+ W LSA L P Sbjct: 192 VGVTAFFCFMFSWVELLLARTLTSVNAKPIAAVMTRTVSAAGMDWGVLSAAGVLTIVPGA 251 Query: 258 IFGWISQKQLVRGLSFGAV 276 + + + + +G + G V Sbjct: 252 LVIYFVRNYIAKGFAMGRV 270 Lambda K H 0.327 0.137 0.423 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: 247 Number of extensions: 14 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: 277 Length of database: 270 Length adjustment: 25 Effective length of query: 252 Effective length of database: 245 Effective search space: 61740 Effective search space used: 61740 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: 47 (22.7 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