Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_00475 (220 letters) >NCBI__GCF_003217355.1:WP_110804905.1 Length = 262 Score = 130 bits (326), Expect = 3e-35 Identities = 78/220 (35%), Positives = 116/220 (52%), Gaps = 14/220 (6%) Query: 14 FDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLI 73 F TL G+G+ + + L + A V+GL +A A LS+H + R LA Y VIR PI+V++ Sbjct: 37 FATLSKGIGITVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVML 96 Query: 74 LLIYFAL-------------PSLGIR-LDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKG 119 L + FAL P +R L V+ L L A+L EVFR GLLS+ +G Sbjct: 97 LYVAFALVPAVVAGWNALGLPEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVERG 156 Query: 120 QREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARK 179 Q EA A+GL W + P R VLP L N+F+++ KD+SL + + V ++T + Sbjct: 157 QIEAAKALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKV 216 Query: 180 INVESYRVIETWLVTTALYVAACYLIAMVLRYFEQRLAIR 219 ++R ET+ V +Y+A +++ LR E L R Sbjct: 217 TAAGNFRYFETYNVVALIYLAMTVTLSLALRKLEAHLRKR 256 Lambda K H 0.329 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: 175 Number of extensions: 15 Number of successful extensions: 2 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: 262 Length adjustment: 23 Effective length of query: 197 Effective length of database: 239 Effective search space: 47083 Effective search space used: 47083 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 24 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