Align Inner-membrane translocator (characterized, see rationale)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 160 bits (406), Expect = 3e-44 Identities = 102/312 (32%), Positives = 172/312 (55%), Gaps = 22/312 (7%) Query: 15 LLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSG 74 ++ ++LV + GF S N+LRD A + I A MTL+IISG ID+SVG ++A Sbjct: 32 VIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDVSVGPMVAFVS 91 Query: 75 VVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLA--------GMF 126 V + L+ +++ +A +++L LG L G L G + V+ + F+ TL G+F Sbjct: 92 VCLAFLL-QFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATLGLWSALRGMGLF 150 Query: 127 LARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRF 186 + L + E + D + + +P +S+LI I+ F + + T F Sbjct: 151 MTNALPVPIDENEVL------DWLGGQFLGVP------VSALIMIVLFALFVFISRKTAF 198 Query: 187 GTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVEL 246 G +V+A+GGN +A+L GI++ + I I+ +S LA + GI+ SG A A G+E Sbjct: 199 GRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGLEF 258 Query: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFI 306 D IAAVV+GGT L+GG G + GT+LGV+++ +I + G ++S++ ++V G+++ + Sbjct: 259 DVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLG-INSFFQQVVRGVIIVVAV 317 Query: 307 LLQKLLNGRKTQ 318 L LL R ++ Sbjct: 318 LANILLTQRSSK 329 Lambda K H 0.330 0.145 0.424 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: 327 Number of extensions: 19 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: 320 Length of database: 332 Length adjustment: 28 Effective length of query: 292 Effective length of database: 304 Effective search space: 88768 Effective search space used: 88768 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: 48 (23.1 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