Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate WP_042615044.1 ABB28_RS00970 carbohydrate ABC transporter permease
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896 (281 letters) >NCBI__GCF_001431535.1:WP_042615044.1 Length = 278 Score = 117 bits (292), Expect = 4e-31 Identities = 82/268 (30%), Positives = 137/268 (51%), Gaps = 15/268 (5%) Query: 21 LLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGW--IKAWDVVGGYFWNSV 78 LL+ A V L PL+ M+ S + T P+ + + + A +G F NS+ Sbjct: 19 LLVLALVSLAPLLWMVSVSVMPAGEATTFPPPLTPSHVTFANYHELFARTGMGVNFANSL 78 Query: 79 KITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLGKFGL 138 ++V L S + M GY + RF G F +L+ +P Q +LP + + GL Sbjct: 79 LVSVAITLGSLLLNTMAGYAFAKLRFVGRDRLFQVLMAALVIPAQVAMLPLFLLMKQLGL 138 Query: 139 ANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLKILLPMSIPI 198 N+ G+++ + F R Y SIPD L++AAR+DGAG IF +I+LPM P+ Sbjct: 139 VNSFGGVIVPALA--TVFGIFLVRQYARSIPDELLEAARMDGAGEMRIFFQIVLPMLKPV 196 Query: 199 VMVCLIWQFTQIWNDFLFG-VVFASGDAQPITVALNNLVNTSTGAKEYNVD----MAAAM 253 ++ I+ F WNDF++ +V + + VAL +T ++E+ +D MA A+ Sbjct: 197 LVTLSIFTFMGAWNDFMWPLIVLTDQEHYTLPVAL------ATLSREHIMDVEMMMAGAV 250 Query: 254 IAGLPTLLVYIFAGKYFLRGLTSGAVKG 281 + +P L +++ +Y+++GL G+VKG Sbjct: 251 VTVIPVLALFLLLQRYYIQGLMLGSVKG 278 Lambda K H 0.329 0.143 0.447 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: 198 Number of extensions: 12 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: 281 Length of database: 278 Length adjustment: 26 Effective length of query: 255 Effective length of database: 252 Effective search space: 64260 Effective search space used: 64260 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: 47 (22.7 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