Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized)
to candidate SMc01979 SMc01979 sugar transport system permease ABC transporter protein
Query= reanno::Smeli:SMc02871 (279 letters) >FitnessBrowser__Smeli:SMc01979 Length = 277 Score = 157 bits (396), Expect = 3e-43 Identities = 86/277 (31%), Positives = 155/277 (55%), Gaps = 2/277 (0%) Query: 3 KARASFMRTGAVHAALIAYTLIALFPVFLTIVNSFKSRNAIFREPLAVPTPETFSLIGYE 62 +A+ +F+ T A A++AY ALFP+F + + + ++ E + + P SL ++ Sbjct: 2 RAKQAFL-TIAHRLAVLAYIAFALFPLFWLLKVAVTPNDLLYSEGIRL-WPSRASLEHFD 59 Query: 63 TVLKQGDFIGYFQNSIIVTVVSIALVLLFGAMAAFALSEYRFRGNTLMGLYLALGIMIPI 122 VL+ F +F+NS+IV+ + +V + +++ +ALS +RFRG + + L M P+ Sbjct: 60 FVLRHSAFPVFFRNSLIVSGSTAVIVTILASLSGYALSRFRFRGKYWLVTLMLLTQMFPL 119 Query: 123 RLGTVAILQGMVATGLVNTLTALILVYTAQGLPLAVFILSEFMRTVSDDLKNAGRIDGLS 182 + I + + GL N+LT L++VYTA +P A F++ F + DL+ A IDG + Sbjct: 120 VMLVAPIFKILSPLGLTNSLTGLVVVYTAFNVPFATFLMQSFFDGIPKDLEEAAMIDGAT 179 Query: 183 EYAIFLRLVLPLIRPAMATVAVFTMIPIWNDLWFPLILAPAEATKTVTLGSQIFIGQFVT 242 ++ F +++LPL P +A F W++L F L+L A T +G F+ +F Sbjct: 180 QFVAFRQIILPLTLPGIAATLGFVFTAAWSELLFSLMLISGNAQATFPVGLLSFVSKFSV 239 Query: 243 NWNAVLSALSLAIFPVLVLYVIFSRQLIRGITAGAVK 279 ++ +++A LA+ P + +++ R L++G+TAGAVK Sbjct: 240 DFGQMMAAGVLALIPACLFFLLIQRYLVQGLTAGAVK 276 Lambda K H 0.330 0.142 0.409 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: 235 Number of extensions: 11 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: 279 Length of database: 277 Length adjustment: 25 Effective length of query: 254 Effective length of database: 252 Effective search space: 64008 Effective search space used: 64008 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 (21.8 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