Align Inner-membrane translocator (characterized, see rationale)
to candidate HSERO_RS05185 HSERO_RS05185 ABC transporter permease
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__HerbieS:HSERO_RS05185 Length = 340 Score = 326 bits (835), Expect = 6e-94 Identities = 168/305 (55%), Positives = 222/305 (72%), Gaps = 5/305 (1%) Query: 11 ITASLLLTMFLVGTFQFDGFASGRVVTNLLRDNAFLLITALGMTLVIISGGIDLSVGAVI 70 +T LL+ M + G +DGF S +V+ NLL DNAFLL+ A+GMT VI+SGGIDLSVG+V+ Sbjct: 20 VTVVLLVVMLVAGALGYDGFLSPQVMLNLLIDNAFLLVVAIGMTFVILSGGIDLSVGSVL 79 Query: 71 ALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLARG 130 AL+ +V + L+ + WHPLL V +L +G FGA MG +IH +KLQ FIVTLAGMFLARG Sbjct: 80 ALTTMVAAFLLQNWHWHPLLVIVTVLLMGAGFGAAMGAMIHYFKLQAFIVTLAGMFLARG 139 Query: 131 LATTLSEESIAIDHPFYDAVAEMSIALPGNGALDLS-SLIFILFFVIIAVVM-HYTRFGT 188 L +S SI ID P + +++ + L G L +S S++ LF + +A+ M H TRFG Sbjct: 140 LCYLISINSITIDDPLFTTLSQTRLELAG---LFISPSVVIALFMLALAIWMAHCTRFGR 196 Query: 189 NVYAIGGNQHSAELMGISIAKTTISIYAISSFLATLAGIVFTFYTFSGYALGAIGVELDA 248 VYAIGGN++SA LMG+ + +T + +YA S A +AG++F+FY SGY L A GVELDA Sbjct: 197 AVYAIGGNENSALLMGLPVGRTKVLVYAFSGLCAAVAGVLFSFYMLSGYGLHAQGVELDA 256 Query: 249 IAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLLFFFILL 308 IAAVVIGGTLLTGG G+V GT+ GV+++GVIQT I FDG+LSSWWTKI IG LLF F + Sbjct: 257 IAAVVIGGTLLTGGYGYVAGTLTGVLILGVIQTLIAFDGTLSSWWTKIFIGALLFVFCVA 316 Query: 309 QKLLN 313 Q++++ Sbjct: 317 QRVIS 321 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: 408 Number of extensions: 16 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: 340 Length adjustment: 28 Effective length of query: 292 Effective length of database: 312 Effective search space: 91104 Effective search space used: 91104 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: 49 (23.5 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