Align ABC transporter for D-Glucosamine Hydrochloride, permease component 2 (characterized)
to candidate PP_0656 PP_0656 putative Amino acid ABC transporter, permease protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_2052 (220 letters) >FitnessBrowser__Putida:PP_0656 Length = 273 Score = 141 bits (355), Expect = 1e-38 Identities = 82/226 (36%), Positives = 131/226 (57%), Gaps = 14/226 (6%) Query: 1 MNYQLNFAAVWRDFDTL----------LAGLGLGLSLALVSIAIGCVIGLAMAFALLSKH 50 +++ L FA + F L L G L L L L S+ + ++G A A A LS Sbjct: 42 LSFDLKFAIILEKFPNLAGFKLGPNGFLQGAALTLFLCLCSMVVSVLLGFAAALARLSNS 101 Query: 51 RVLRVLASVYVTVIRNTPILVLILLIYFALPSLGIRLDKLPSFVITLSLYAGAYLTEVFR 110 VL +AS Y + R TP+L+ ILLIY LP +G+ + + +I LSL GAYL+E+FR Sbjct: 102 AVLVGVASFYTSFFRGTPLLIQILLIYLGLPQVGLVPGAISAGIIALSLNYGAYLSEIFR 161 Query: 111 GGLLSIHKGQREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAV 170 G+L + +GQREA LA+G+ Q+ ++ +P +R ++P +N FIS+ KD+SL + + V Sbjct: 162 AGILGVARGQREAALALGMRTPQIFCHIILPQAMRVIIPPTANQFISMLKDSSLISVMGV 221 Query: 171 PELTYYARKINVESYRVIETWLVTTALYVAACYLIAMLLRYFEQRL 216 E+ + A+ SYR +E ++TTA + +++++LL + RL Sbjct: 222 WEVMFLAQSYGRSSYRYLE--MLTTAAVI--YWVLSILLELLQARL 263 Lambda K H 0.330 0.142 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: 140 Number of extensions: 5 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: 220 Length of database: 273 Length adjustment: 24 Effective length of query: 196 Effective length of database: 249 Effective search space: 48804 Effective search space used: 48804 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: 46 (22.3 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