Align Sugar ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_2942 Various polyols ABC transporter, permease component 2
Query= uniprot:A0A161ZE72 (280 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2942 Length = 279 Score = 137 bits (344), Expect = 3e-37 Identities = 85/261 (32%), Positives = 135/261 (51%), Gaps = 5/261 (1%) Query: 20 GVLLLYAVFPFYYAIVTSLKPS-SALFEVSYWIENPDFSNYAAVLNQASFLRAIGNSLVV 78 GV LL FP + +T+ K A+ ++ P N+ V ++ +L NS++ Sbjct: 23 GVALLL-FFPLGWLFLTAFKTELQAIAVPPLFVFTPTLENFHEVQERSDYLLYAKNSVIT 81 Query: 79 ALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVAVLSGLFEVIRALGLYN 138 ++ L L L+ AAYA+ K + +LM +L M P V L ++ + + L + Sbjct: 82 SVLSTVLGLMLAAPAAYAMAFFKGKYTKDILMWMLSTKMMPAVGALVPIYVLAQKSHLLD 141 Query: 139 TSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPWVTLTRVLLPLLWPALV 198 T ALI+ + + LP VW+L + +PHE+ EAA MDGA+ W + VLLPL L Sbjct: 142 TQLALIIVFALSNLPIMVWMLYSHFKDIPHEILEAARMDGATLWQEVRLVLLPLGMGGLA 201 Query: 199 TTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHELPWGLLMAASVVVTVPL 258 +TGLL + +WNE ++L + + +A + S SP L W L AAS++ P+ Sbjct: 202 STGLLCLVLSWNEAFWSLNLS---AAKAGTLATLIASYSSPEGLFWAKLSAASLMAIAPI 258 Query: 259 VILVLIFQRRIVSGLTAGALK 279 V+ Q+++V GLT GA+K Sbjct: 259 VVFGWFSQKQLVQGLTFGAVK 279 Lambda K H 0.329 0.141 0.433 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: 215 Number of extensions: 7 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: 280 Length of database: 279 Length adjustment: 26 Effective length of query: 254 Effective length of database: 253 Effective search space: 64262 Effective search space used: 64262 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 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