Align Sugar ABC transporter permease (characterized, see rationale)
to candidate 15432 b1312 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:A0A165KQ00 (289 letters) >FitnessBrowser__Keio:15432 Length = 280 Score = 120 bits (302), Expect = 3e-32 Identities = 83/282 (29%), Positives = 139/282 (49%), Gaps = 10/282 (3%) Query: 10 SVGRFLVYAVLALATAFFLLPLYAMLVTSFKYAEEIRSTSLLALPGSLNWSAWGTAWQSA 69 ++ R Y LAL L P + ML+TSFK A+E S LP W Sbjct: 7 TLSRIGFYCGLALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLP-----QQWTLEHYVD 61 Query: 70 CTGVDCNGLRPFFMNSVAMAVPAVLISTVWGALNGYVLSLWKFRGSDALFGMLLFGVFMP 129 +F NS+ ++V + +++ G L Y LS +F+G + + V+M Sbjct: 62 IFNPMIFPFVDYFRNSLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTI-NASFYTVYMF 120 Query: 130 FQVVLL-PMSQVLGWLGLSSSITGLVLVHCLAGLAGTTLFFRNYYAAIPKELVNAARMDG 188 ++L+ P+ +++ LG+ + L++ L ++Y+ IP E+ AA MDG Sbjct: 121 SGILLVVPLFKIITALGIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDG 180 Query: 189 ASFFQIFWRIVLPLSTPIVMVTLIWQFTNIWNDFLFGVVF-SGTDSKPVTVGLNNLANTS 247 + QI +RI +PL+ ++ ++ F WND+LF +F S + + VGLN L +T Sbjct: 181 LNRLQIIFRITVPLAMSGLISVFVYCFMVAWNDYLFASIFLSSASNFTLPVGLNALFSTP 240 Query: 248 SSVKAYNVDMAAAIIAGLPTMVIYVLAGKFFVRGLTAGAVKG 289 + + MAA+++ LP +++Y L+ +F GLTAG VKG Sbjct: 241 DYI--WGRMMAASLVTALPVVIMYALSERFIKSGLTAGGVKG 280 Lambda K H 0.327 0.139 0.436 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: 201 Number of extensions: 10 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: 289 Length of database: 280 Length adjustment: 26 Effective length of query: 263 Effective length of database: 254 Effective search space: 66802 Effective search space used: 66802 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