Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate SMc02033 SMc02033 periplasmic binding protein
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__Smeli:SMc02033 Length = 395 Score = 48.9 bits (115), Expect = 2e-10 Identities = 74/290 (25%), Positives = 120/290 (41%), Gaps = 58/290 (20%) Query: 1 MIKNTIAIACSTL--LLAAAAQPAMAADKPLKSVGVTVG----DLANPFFVA--IAKGAE 52 + K+++ A +T+ L A PA+A D +++ VT+G D+ F A + A Sbjct: 5 LAKSSLFAAAATIAVLPMLGAVPAVAQDG--ENIDVTIGWVPPDITGVFKTATNFFELAA 62 Query: 53 SGAHKINPDAKVTVVS--SKYDLNTQVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQK 110 A+K + KV S S QV IE+ I KVDLI ++ A+ + PA+ +A Sbjct: 63 EDANKNGFNVKVLTKSPTSPTAFAEQVSIIEDMIQRKVDLIAVSPAEVATIKPALARATA 122 Query: 111 AGIVVVAVDVAAA--GADVT--VMSDNTMAGAESCKF----------------------- 143 AGI VV V++ G DV+ + DNT GAE + Sbjct: 123 AGIPVVVVNLLEPIDGVDVSSYIGFDNTQ-GAEVSAYSVVDYFGGPGVLGTGDKVDVEPG 181 Query: 144 ----------LAEKLQGKGNVVI-VNGPPVSAVMD------RVTGCKAEFKKSPGIKILS 186 +A KL + I G + V R+ G + ++ PGI+I+ Sbjct: 182 TYLDLKFWEDIASKLSAEDKAKIKARGAIIEGVAGGFYSTARLEGFRKVLEQFPGIEIVG 241 Query: 187 DNQNAGGSRDGGMTTMSNLLAA-QPKIDAVFAINDPTAIGAELAIRQAKR 235 +R+ G ++L A Q +D ++A ++ +GA L R Sbjct: 242 GTCAGDWNREKGTRCAEDILQANQGNLDFIWAASNEMGLGAMLVAGSQNR 291 Lambda K H 0.314 0.129 0.360 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: 240 Number of extensions: 12 Number of successful extensions: 1 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: 316 Length of database: 395 Length adjustment: 29 Effective length of query: 287 Effective length of database: 366 Effective search space: 105042 Effective search space used: 105042 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (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