Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized)
to candidate CCNA_00332 CCNA_00332 molybdenum transport system permease protein modB
Query= reanno::Smeli:SMc02872 (315 letters) >FitnessBrowser__Caulo:CCNA_00332 Length = 224 Score = 54.7 bits (130), Expect = 2e-12 Identities = 52/181 (28%), Positives = 80/181 (44%), Gaps = 13/181 (7%) Query: 121 IFLPTLLSFVIVGFIWKLILSPIWGVAPYLLDTVGLRSLFGPWLGKPDTALIAVSLISVW 180 + LP +L ++GF + L P + LL G+R+L + G L+ SLI Sbjct: 45 VALPIVLPPTVLGFYLLIALGPNSPLMA-LLQPFGVRTLAFTFEG-----LVIGSLIYSL 98 Query: 181 QYIGIPMMLIYAALLNIPDEVTEAAELDGVTGWSQFWKIKLPLILPAIGIVSILTFVGNF 240 + P+ A L I DE EAA G + FW++ LPL LP +ILTF Sbjct: 99 PFAVQPLR---NAFLAIGDEPLEAAASLGASRAETFWRVALPLALPGYVAAAILTFAHTV 155 Query: 241 NAFDLIYTVQGALAGPDKSTDILGTLLYRTFFGFQLQLGDRSMGATIAAIMFLIILAGVA 300 F ++ + G + G T +L T +YR + R + + A FL++ +A Sbjct: 156 GEFGVVMMLGGNIPG---ETTVLSTEIYRLVEALEWGEAHR-LSLLLLAFAFLVLFVLLA 211 Query: 301 L 301 L Sbjct: 212 L 212 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: 187 Number of extensions: 10 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: 315 Length of database: 224 Length adjustment: 25 Effective length of query: 290 Effective length of database: 199 Effective search space: 57710 Effective search space used: 57710 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