Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate GFF1646 PGA1_c16690 binding protein-dependent transport system, inner membrane component
Query= reanno::acidovorax_3H11:Ac3H11_2942 (279 letters) >FitnessBrowser__Phaeo:GFF1646 Length = 283 Score = 129 bits (325), Expect = 5e-35 Identities = 82/252 (32%), Positives = 133/252 (52%), Gaps = 2/252 (0%) Query: 30 FPLGWLFLTAFKTELQAIAVPP-LFVFTPTLENFHEVQERSDYLLYAKNSVITSVLSTVL 88 FPL WL A + + + T ENF V +++L Y +NS+ S+ + Sbjct: 31 FPLYWLMKIAITPDALIFSEGTRMLPSAVTFENFATVLFETEFLAYFRNSLTVSLGTAFF 90 Query: 89 GLMLAAPAAYAMAFFKGKYTKDILMWMLSTKMMPAVGALVPIYVLAQKSHLLDTQLALII 148 ++AA A YA + F + I+ ML T+M P + + PIY + LL++ +LI+ Sbjct: 91 TTLIAAGAGYAFSRFVFAGKRIIIAVMLITQMFPLLMIIAPIYKIVADLGLLNSLTSLIV 150 Query: 149 VFALSNLPIMVWMLYSHFKDIPHEILEAARMDGATLWQEVRLVLLPLGMGGLASTGLLCL 208 V+ N+P +++ S F IP ++ EAA MDG + +Q +R V+ PL + GL +T Sbjct: 151 VYTAFNIPFATFLMQSFFDGIPKDLEEAAMMDGCSRFQALRTVVFPLTLPGLGATLGFVF 210 Query: 209 VLSWNEAFWSLNL-SAAKAGTLATLIASYSSPEGLFWAKLSAASLMAIAPIVVFGWFSQK 267 +W+E ++L L S A T + ++ S + W ++ AA ++A+ P +F F Q+ Sbjct: 211 TAAWSELLFALMLISKNDAMTFPVGLLTFVSKFSVDWGQMMAAGVLALVPSCLFFIFIQR 270 Query: 268 QLVQGLTFGAVK 279 LVQGLT GAVK Sbjct: 271 YLVQGLTSGAVK 282 Lambda K H 0.327 0.137 0.420 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: 186 Number of extensions: 6 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: 279 Length of database: 283 Length adjustment: 26 Effective length of query: 253 Effective length of database: 257 Effective search space: 65021 Effective search space used: 65021 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 (21.7 bits) S2: 47 (22.7 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