Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate BWI76_RS03135 BWI76_RS03135 sugar ABC transporter permease
Query= reanno::Smeli:SMc02872 (315 letters) >FitnessBrowser__Koxy:BWI76_RS03135 Length = 290 Score = 114 bits (286), Expect = 2e-30 Identities = 78/256 (30%), Positives = 124/256 (48%), Gaps = 24/256 (9%) Query: 17 RRWHILVFLLPALVVYTAVMILPLFETLRQSFYNT--VDGQLTFVGLGNFKVLFGDPRWA 74 + W + L P+L+ PL ++ S ++T V +VGL NF LF D Sbjct: 3 KTWLPWLILSPSLLFLLLFTWFPLGRSVYDSLFDTRMVSDGGQYVGLENFSRLFAD---- 58 Query: 75 ADFWNALKNNFVFFLIHMAVQNPIGIALAAMLSVPKL---RFGAFYRTAIFLPTLLSFVI 131 + FW +L NN ++ L+ + G+ LA +L+V R + RTA F P ++ V Sbjct: 59 SVFWQSLVNNLLYILLTVVP----GVTLALLLAVALTENHRVNRWLRTAFFFPMIIPMVS 114 Query: 132 VGFIWKLILSPIWGVAPYLLDTVGLRSLFGP----WLGKPDTALIAVSLISVWQYIGIPM 187 +W I P G+ + L LFGP WLG+ ++AL+A++LI VW++ G M Sbjct: 115 AAALWLFIFMPGLGLLDHYL-----AKLFGPMNNNWLGRSNSALLALALIGVWKFAGYYM 169 Query: 188 MLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSILTFVGNFNAFDLIY 247 + A L +IP EAA ++G T F+K+ LPL+ P + V + + D + Sbjct: 170 LFFLAGLQSIPASTREAAIMEGATRTQVFFKVTLPLLRPTLSFVITTALIYSITQIDHVA 229 Query: 248 TVQGALAGPDKSTDIL 263 + GPD +T +L Sbjct: 230 VM--TRGGPDNATTVL 243 Lambda K H 0.331 0.146 0.461 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: 278 Number of extensions: 15 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 315 Length of database: 290 Length adjustment: 27 Effective length of query: 288 Effective length of database: 263 Effective search space: 75744 Effective search space used: 75744 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: 48 (23.1 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