Align ABC transporter for D-Glucosamine Hydrochloride, permease component 2 (characterized)
to candidate WP_109969962.1 DK846_RS15735 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_2052 (220 letters) >NCBI__GCF_003173355.1:WP_109969962.1 Length = 225 Score = 113 bits (282), Expect = 3e-30 Identities = 63/206 (30%), Positives = 110/206 (53%), Gaps = 1/206 (0%) Query: 14 FDTLLAGLGLGLSLALVSIAIGCVIGLAMAFALLSKHRVLRVLASVYVTVIRNTPILVLI 73 F LL+G+ + + L V++ IG ++GL MA + ++R + S+YV R P+LVL+ Sbjct: 11 FPYLLSGIFITVGLVAVALLIGIILGLPMALGQVYGKHLIRSVISIYVWFFRGLPVLVLL 70 Query: 74 LLIYFAL-PSLGIRLDKLPSFVITLSLYAGAYLTEVFRGGLLSIHKGQREAGLAIGLGEW 132 L YF + P LG+ L + L L AY +++FRG + SI +GQ A ++G+ Sbjct: 71 FLFYFGIFPGLGLDLPAFVVGAVVLGLRGAAYQSQIFRGAIQSIAEGQMTAARSLGMSRA 130 Query: 133 QVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARKINVESYRVIETWL 192 Q + +P +R LP SN + + ++S+ AI V EL + +I ++Y + +L Sbjct: 131 QAIRSIILPQAMRIALPGWSNEYPEILTESSICYAIGVAELLTRSSQIVSQTYVTMPIYL 190 Query: 193 VTTALYVAACYLIAMLLRYFEQRLAI 218 +++ Y L++ E+R+AI Sbjct: 191 ACAVMFILLSYAGTHLIQRLEKRIAI 216 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: 152 Number of extensions: 12 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: 225 Length adjustment: 22 Effective length of query: 198 Effective length of database: 203 Effective search space: 40194 Effective search space used: 40194 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: 45 (21.9 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