Align Inner-membrane translocator (characterized, see rationale)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 165 bits (417), Expect = 2e-45 Identities = 103/271 (38%), Positives = 162/271 (59%), Gaps = 9/271 (3%) Query: 98 IDILNRSAPVALLSIGMSLVIATGGIDLSVGAVMAIAGAVCANLLL--VPDISLVTVIAA 155 ++IL + A +L+ GM+ VI T GIDLSVG+V+A++ + + L P ++ I + Sbjct: 62 MNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIFS 121 Query: 156 GLIVGLLAGCINGGLVSFLGIQPIVATLLLMVAGRGVAQLINQGQ-IITFQHPGFAAIGV 214 GL++G+ +NG +V+ L I V TL M A RG A L+ G ++ P F IG Sbjct: 122 GLVMGM----VNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGN 177 Query: 215 GQFLGLPMPVWIVIGMLTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGI 274 G FL +P +W+ + ++ S ++LRKT LG+ I A+G N +A+R GI + LF Y I Sbjct: 178 GDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSI 237 Query: 275 AGLCAALAGMISTADIQGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALII 334 +GL + LAG +S + + G++ N G ELDA+ AVV+GG +L GG S+ +VVGALII Sbjct: 238 SGLFSGLAGAMSASRLYGAN-GNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALII 296 Query: 335 QTLATTIIVSGLPAKFNLLIK-AIVILTVLL 364 + + + GL + + + K A+++L V+L Sbjct: 297 GVMNNGLTILGLSSFWQYVAKGAVIVLAVIL 327 Lambda K H 0.323 0.136 0.379 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: 300 Number of extensions: 18 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: 405 Length of database: 339 Length adjustment: 30 Effective length of query: 375 Effective length of database: 309 Effective search space: 115875 Effective search space used: 115875 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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