Align Inner-membrane translocator (characterized, see rationale)
to candidate Pf1N1B4_6033 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6033 Length = 325 Score = 134 bits (337), Expect = 4e-36 Identities = 95/321 (29%), Positives = 161/321 (50%), Gaps = 10/321 (3%) Query: 52 QAGKSTSMGRYLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLS 111 ++G +G YL LA ++L + LF S +SY + + N+ + +L+ Sbjct: 10 RSGNFYGLGTYLG--LAGALLAMVALFSVLSSHFLSYD------TFSTLANQIPDLMVLA 61 Query: 112 IGMSLVIATGGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLV 171 +GM+ V+ GGIDLSVG+V+A+A + + +L S++ G+ V LAG I G + Sbjct: 62 VGMTFVLIIGGIDLSVGSVLALAASAVSVAILGWGWSVLPAALLGMAVAALAGTITGSIT 121 Query: 172 SFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGML 231 I + +L ++ RG+A + G + FA + G+ I + ++ Sbjct: 122 VAWRIPSFIVSLGVLEMARGLAYQMT-GSRTAYIGDAFAWLSNPIAFGISPSFIIALLII 180 Query: 232 TFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQ 291 +Q +L +T G ++ +G N +A R GIN K K+ + + GL A +A + + ++ Sbjct: 181 FIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLE 240 Query: 292 GSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFN 351 +D NAG LEL + AVVIGG +L GGR S+I + G LII LA + G Sbjct: 241 AADP-NAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTK 299 Query: 352 LLIKAIVILTVLLLQSAKFRR 372 +I VI+ ++L + + +R Sbjct: 300 RIITGAVIVVAVVLDTYRSQR 320 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: 311 Number of extensions: 18 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: 405 Length of database: 325 Length adjustment: 29 Effective length of query: 376 Effective length of database: 296 Effective search space: 111296 Effective search space used: 111296 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