Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate H281DRAFT_03232 H281DRAFT_03232 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= reanno::Phaeo:GFF2752 (280 letters) >FitnessBrowser__Burk376:H281DRAFT_03232 Length = 283 Score = 155 bits (393), Expect = 7e-43 Identities = 86/259 (33%), Positives = 142/259 (54%), Gaps = 4/259 (1%) Query: 24 LIALFPVFVILVNSFKTRKAIFRDPL-GLPTSDTFSLV-GYQTVLKQGDFFLYFQNSMIV 81 LI L P+ +LV S ++ + + G P F+L Y+ L YF NS+++ Sbjct: 26 LIWLLPMIAVLVTSIRSSEELSEGNYWGWPKH--FALFDNYREALTTSPMLHYFWNSVLI 83 Query: 82 TVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIGTVAILELMVDTGLVN 141 TV ++ + AMA FALA YRF+GN L G +P+++ + + +L + G+ N Sbjct: 84 TVPAVIGSIALAAMAGFALAIYRFRGNSSLFATFVAGNFVPVQVLMIPVRDLSLQLGVFN 143 Query: 142 TLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYTIFFRLVLPLVRPAMA 201 T++ALIL + + L F+KQ+ +L A RI+G +E+T+FFR+VLPL+RPA+A Sbjct: 144 TVSALILFHVSFQTGFCALFLRNFIKQLPFELVEAARIEGANEWTVFFRIVLPLIRPALA 203 Query: 202 TVAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIGQFVTDWNAVLSALSMAILPVMV 261 +A+ +WND ++ L L ++ +T+G GQ+ T WN V + +A LP + Sbjct: 204 ALAILVFTFVWNDYFWALCLTQGDDAAPITVGVAALKGQWTTAWNLVSAGSILAALPSVA 263 Query: 262 LYVIFSRQLIRGITSGAVK 280 ++ + + G+T GA K Sbjct: 264 MFFAMQKHFVAGLTFGATK 282 Lambda K H 0.330 0.143 0.414 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: 232 Number of extensions: 13 Number of successful extensions: 1 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: 280 Length of database: 283 Length adjustment: 26 Effective length of query: 254 Effective length of database: 257 Effective search space: 65278 Effective search space used: 65278 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