Align Inner-membrane translocator (characterized, see rationale)
to candidate BPHYT_RS16055 BPHYT_RS16055 sugar ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__BFirm:BPHYT_RS16055 Length = 335 Score = 161 bits (407), Expect = 2e-44 Identities = 102/298 (34%), Positives = 167/298 (56%), Gaps = 12/298 (4%) Query: 16 LLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVIALSGV 75 LL + +V F D F SG + N+LR + I A+GMT VI++GGIDLSVG+V+AL+G Sbjct: 43 LLVVCIVMVFASDSFLSGANIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMALAGT 102 Query: 76 VTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARGLATTL 135 + + L+ + + A + + +G FGA G + + P IVTLA M +ARGLA Sbjct: 103 LAAGLMVAGM-NAVAALAIGIAVGLGFGAANGFFVAFAGMPPIIVTLATMGIARGLALIY 161 Query: 136 SEESIAIDHPFYDAVAEMSIALPGNGAL---DLSSLIFILFFVIIAVVMHYTRFGTNVYA 192 + +P D + + ++ G+G + +I + +VI V++ FG VYA Sbjct: 162 TG-----GYPI-DGLPDW-VSFFGSGKILGVQAPVVIMAVIYVIAWVLLERMPFGRYVYA 214 Query: 193 IGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDAIAAV 252 IGGN+ + L G+ +A+ + +Y I+ + A IV T SG +G ELDAIAAV Sbjct: 215 IGGNEQATRLSGVRVARVKLIVYTIAGLTSAFAAIVLTARLMSGQPNAGVGFELDAIAAV 274 Query: 253 VIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILLQK 310 V+GGT ++GG G ++GT++G +L+GV+ + G ++ + ++ G ++ I + + Sbjct: 275 VMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVG-VNPYVQNVIKGGIILLAIYISR 331 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: 370 Number of extensions: 23 Number of successful extensions: 5 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: 335 Length adjustment: 28 Effective length of query: 292 Effective length of database: 307 Effective search space: 89644 Effective search space used: 89644 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