Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate SM_b20706 SM_b20706 amino acid uptake ABC transporter substrate-binding protein precursor
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__Smeli:SM_b20706 Length = 258 Score = 124 bits (310), Expect = 2e-33 Identities = 82/260 (31%), Positives = 137/260 (52%), Gaps = 27/260 (10%) Query: 3 LRRNLLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFVEN-GKRTGFDIELVEAIAK 61 +R+ +L +LA A ++ A+ L++GT+ +PP FV++ GK GFD+E+ A+ + Sbjct: 1 MRKLILALALAGTALSSSAVAAEK--LKIGTEGAYPPFNFVDSSGKIGGFDVEIGLALCE 58 Query: 62 TMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKAD 121 M + E V D+ G+IPGL++K++DM +++++IT+ERKK V FT+ YY L M A Sbjct: 59 RMKVECEVVAQDWDGIIPGLLAKKYDMIIASMFITEERKKQVAFTNPYY---LAAMTHAA 115 Query: 122 NKAINKLA----DLDGKKVSVQVGTKSVSYLTEKFP----KVQRVEVEKNQEMFNLVDIG 173 K A L GK + Q GT Y+ +P K+ + E N +M N G Sbjct: 116 PKGAGISAFSNEALQGKVIGAQSGTTQADYIAAVYPDAEIKLYPTQDEANLDMVN----G 171 Query: 174 RADAAVTGKPAAFQYVRTRP---------GLRVLDEQLTTEEYGMALRKDTPELTKAVNG 224 R D V +V G + D++ + G+A+R++ E+ + +N Sbjct: 172 RLDLQVGDMLPLLDWVTKNDDGKGCCELVGEPITDKKFVGDGVGIAVRQEDNEMREKLNK 231 Query: 225 AITKLKADGTYAAIVKKWFS 244 A+ +++ADGTY I K+F+ Sbjct: 232 ALDEIRADGTYKKINDKYFT 251 Lambda K H 0.317 0.133 0.369 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: 160 Number of extensions: 7 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: 249 Length of database: 258 Length adjustment: 24 Effective length of query: 225 Effective length of database: 234 Effective search space: 52650 Effective search space used: 52650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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