Align ABC transporter for Lactose, permease component 2 (characterized)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)
Query= reanno::Smeli:SM_b21654 (272 letters) >FitnessBrowser__Dyella79:N515DRAFT_3133 Length = 273 Score = 168 bits (426), Expect = 1e-46 Identities = 91/267 (34%), Positives = 150/267 (56%), Gaps = 3/267 (1%) Query: 9 AMAATYGFLGLMAFLSVFPFIWM--VLGATNSSIDIIKGKLLPGAAFATNVANFFTLVNV 66 A A G L ++VFP +WM V + LLP A N F + Sbjct: 6 AKALVNGLLIGSTLVAVFPLLWMLSVSFMRPGEASALPPPLLPTHATLANYHELFERAGM 65 Query: 67 PLVFWNSAKIAIVATVLTLAVSSLAGYGFEMFRSRRRERVYRAMLLTLMIPFAALMIPLF 126 NS ++ T+L+LA + +AGY F R RER+++ +L L+IP M+PLF Sbjct: 66 GRYLLNSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLF 125 Query: 127 VMMGKAGLINTHLAVVLPSIGSAFVIFYFRQSTKAFPSELRDAAKVDGLKEWQIFLFIYV 186 +++ GL+N++ AVV+P++ + F IF RQ + P +L +AA++DG E +IF+ I + Sbjct: 126 LLLKYLGLVNSYAAVVVPAMATIFGIFLVRQYARGIPDDLMEAARIDGAGELRIFVQIVL 185 Query: 187 PVMRSTYAAAFVIVFMTAWNNYLWPLIVLQTNETKTITLVISSLASAYYPDYGVVMVGTI 246 P+++ + F+TAWN+++WPLI L E T+ + ++SL+ + D ++M G++ Sbjct: 186 PLLKPIMVTLAIFTFLTAWNDFMWPLIALTGQEHYTLPIALASLSREHVQDSELMMAGSV 245 Query: 247 LATLPTLAVFFFMQRQFVQG-MLGSVK 272 + LP L +F +QR ++QG +LGSVK Sbjct: 246 VTVLPVLVLFLALQRYYLQGLLLGSVK 272 Lambda K H 0.331 0.141 0.422 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: 13 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: 272 Length of database: 273 Length adjustment: 25 Effective length of query: 247 Effective length of database: 248 Effective search space: 61256 Effective search space used: 61256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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