Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate SM_b20970 SM_b20970 sugar uptake ABC transporter permease
Query= uniprot:A3DHA3 (284 letters) >FitnessBrowser__Smeli:SM_b20970 Length = 319 Score = 136 bits (342), Expect = 7e-37 Identities = 88/275 (32%), Positives = 150/275 (54%), Gaps = 7/275 (2%) Query: 7 LAGYLFSSPYLAGFLIFFAIPSAMSVYYCFTRG--VGSFEFAGLDNFKSVIASN-SYRLA 63 LA +LF SP++ GFL F P S+ F VG F GLDN++S+ + +R + Sbjct: 25 LAPFLFISPWILGFLFFTLGPLCFSLTMSFFDWPVVGERTFVGLDNYRSMFMEDPQFRES 84 Query: 64 VKNTLIFNSVSVPVIMIVSLLLAMLLNKALRGARYFRMFFVLPLVIPVASIILVWQITFN 123 + T+ F ++ VP +++S LLA+LL+ A + +FR F LP VI +++ +W ++ Sbjct: 85 LWITVKFAAIYVPFNIVMSFLLALLLHHATFASGFFRTVFYLPSVISGVALVTIWSWIYS 144 Query: 124 -EFGVLNNLLNHFGIAGVEWLNS-KWSIAVLVLLYVWKNCGYNIILFTAGLNSIPKDYYD 181 E+G+LN +L+ GI G WL ++ +++ +W G +IL T GL +IPK+ Y+ Sbjct: 145 REYGLLNFMLSLVGIDGPNWLGDPSLALVAIIVASLWGLGGTMLILLT-GLKAIPKELYE 203 Query: 182 AASIDGAGGFKCFTSITLPLLVPTIFFVFIISIINSFKVFREAYLLCGNYPPLNMYML-Q 240 AA++ G G+ ITLP+L P + F FI SII++F+ A LL P + Y Sbjct: 204 AATVSGVPGWAQMVFITLPMLGPMLIFTFITSIISAFQQLTIALLLTKGGPLGSTYFFAM 263 Query: 241 HFMNNNFNNLNYQRLSTASLLMELFIVAIVFLMYK 275 + +N F + + S +M + ++ + ++ + Sbjct: 264 YIYDNAFKYFDMGYAAAGSWVMFVIVLTLSLVVMR 298 Lambda K H 0.331 0.144 0.444 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: 222 Number of extensions: 17 Number of successful extensions: 4 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: 284 Length of database: 319 Length adjustment: 27 Effective length of query: 257 Effective length of database: 292 Effective search space: 75044 Effective search space used: 75044 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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