Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_085979178.1 SACCYDRAFT_RS14750 sugar ABC transporter permease YjfF
Query= uniprot:A0KWY7 (320 letters) >NCBI__GCF_000244975.1:WP_085979178.1 Length = 310 Score = 306 bits (785), Expect = 3e-88 Identities = 154/311 (49%), Positives = 218/311 (70%), Gaps = 1/311 (0%) Query: 7 IPLWITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSV 66 +P+ T +L L F VG ++DGFASG+VV NL DNAFL++ A+GMT VI++GGIDLSV Sbjct: 1 MPILTTFALFLATFGVGAVRYDGFASGQVVANLFVDNAFLIVLAVGMTFVILTGGIDLSV 60 Query: 67 GAVIALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMF 126 G+V+ALS +V + + + W L V +L LG FG L G +IH + +QPFI TLAGMF Sbjct: 61 GSVVALSTMVAASTL-QAGWPAPLVIVAVLVLGAGFGLLTGLVIHHFDVQPFIATLAGMF 119 Query: 127 LARGLATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLSSLIFILFFVIIAVVMHYTRF 186 LARGL + ESI+I + +A I LPG+ + ++ +L + V+H TRF Sbjct: 120 LARGLCFLIDVESISIKDDTFRDLATGVIELPGDIRITYGVVVALLVVAVAVYVLHRTRF 179 Query: 187 GTNVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVEL 246 G VYA+GG++HSA LMG++ + + +Y IS + L G++F Y SGY L A+G+EL Sbjct: 180 GRTVYAVGGSEHSAMLMGLATGRVKVGVYVISGLCSALGGLLFALYMLSGYGLHAVGMEL 239 Query: 247 DAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFI 306 DAIAAVVIGGT+L+GG+G+V+G+VLGV+++G IQT I+F+G+LSSWWTKIV+G LL FI Sbjct: 240 DAIAAVVIGGTVLSGGAGYVVGSVLGVLMLGTIQTIISFEGTLSSWWTKIVVGALLLVFI 299 Query: 307 LLQKLLNGRKT 317 ++Q+ + R++ Sbjct: 300 VMQRAIVRRRS 310 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: 393 Number of extensions: 21 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: 320 Length of database: 310 Length adjustment: 27 Effective length of query: 293 Effective length of database: 283 Effective search space: 82919 Effective search space used: 82919 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 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