Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_106712916.1 CU102_RS20280 carbohydrate ABC transporter permease
Query= uniprot:A3DHA2 (303 letters) >NCBI__GCF_003010955.1:WP_106712916.1 Length = 316 Score = 91.3 bits (225), Expect = 3e-23 Identities = 64/210 (30%), Positives = 100/210 (47%), Gaps = 12/210 (5%) Query: 103 FLNSAIMTIPIVIIQVIVGVFAAYAFAKLRFPLRDKLFFVFIVVMLMPLQVTLVPNYILL 162 F NS + +P VI+ +I+ YA + RF + F I +P QV L P I+ Sbjct: 109 FFNSMKILVPSVILSIIIASVNGYALSNWRFKGSELFFTALIFGAFIPYQVMLYPLVIIT 168 Query: 163 RKLDMIGSFLSVILPGGFSAFGV----VLLRQYMRGIPDECCEAAMIDGAGYLKTFTKII 218 R+L + G+ VI+ + FG+ +L R Y +P E +AA +DGAG+ + F +I+ Sbjct: 169 RQLGIFGTLTGVIVI--HTIFGMPILTLLFRNYFVSLPPELFKAARVDGAGFWRIFLQIM 226 Query: 219 LPQCKSIIASLAILAFIDNWNMVEQPLIFLSDSAKYPLSVYLAYINEGDLGLA-----FA 273 LP I IL WN +IF + + +P++V L I G+ A Sbjct: 227 LPMSLPIFVVAVILQVTGIWNDFLFGVIF-AGTKNFPMTVQLNNIVNSTQGVKEYNVNMA 285 Query: 274 SGVLYMIPTVLIYLYGEKYFVEGIQLTGIK 303 + +L +L+Y + KYFV GI +K Sbjct: 286 ATILTGAVPLLVYFFSGKYFVRGIAAGAVK 315 Lambda K H 0.331 0.147 0.425 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: 226 Number of extensions: 14 Number of successful extensions: 3 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: 303 Length of database: 316 Length adjustment: 27 Effective length of query: 276 Effective length of database: 289 Effective search space: 79764 Effective search space used: 79764 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 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