Align N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized)
to candidate AZOBR_RS18180 AZOBR_RS18180 sugar ABC transporter
Query= reanno::Phaeo:GFF2752 (280 letters) >FitnessBrowser__azobra:AZOBR_RS18180 Length = 273 Score = 129 bits (323), Expect = 9e-35 Identities = 83/274 (30%), Positives = 139/274 (50%), Gaps = 9/274 (3%) Query: 11 NSILAHGALITYTLIALFPVFVILVNSFKTRKAIFRD-PLGLPTSD---TFSLVGYQTVL 66 NS A++ +A FP++ +LV S + +F D P LPT T++ +T L Sbjct: 4 NSTARTLAVLVLLGVAAFPLYWMLVTSLTPSERLFDDRPNLLPTLSQIGTYAAAFTETSL 63 Query: 67 KQGDFFLYFQNSMIVTVVSLALVLLFGAMAAFALAEYRFKGNMLLGLYLALGIMIPIRIG 126 +Q + NS+IV V + L +L + A+AL+ F G +LLG L + M+P + Sbjct: 64 RQ-----WLINSLIVAVGTTVLSILLSVLPAYALSRLTFNGKLLLGFALFMTQMLPEAML 118 Query: 127 TVAILELMVDTGLVNTLTALILVYTAQGLPLAVFILSEFMKQVSDDLKNAGRIDGLSEYT 186 V + ++ L+NTL LIL TA +P+ +IL + V +++ A R+DG S Sbjct: 119 VVPLYDIFTKLSLLNTLLGLILANTAFTVPVVTWILKGAIDGVPSEIEEAARVDGCSRLG 178 Query: 187 IFFRLVLPLVRPAMATVAVFNMIPIWNDLWFPLILAPAEETKTLTLGSQVFIGQFVTDWN 246 I +V+PL+ P +A AV WN+ F + +T ++G F+G+ T + Sbjct: 179 IVLAVVVPLIAPTLAAAAVIAFFHGWNEYVFAQTFISDDALRTASVGLASFVGELSTPVH 238 Query: 247 AVLSALSMAILPVMVLYVIFSRQLIRGITSGAVK 280 V++ + LP +V Y+ R ++ G+T+G VK Sbjct: 239 TVMAVGFIYTLPAVVFYLFVQRYVVAGMTTGGVK 272 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: 213 Number of extensions: 7 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: 273 Length adjustment: 25 Effective length of query: 255 Effective length of database: 248 Effective search space: 63240 Effective search space used: 63240 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