Align Solute-binding protein Bpro_3107 (characterized)
to candidate SM_b20036 SM_b20036 ABC transporter substrate-binding protein
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__Smeli:SM_b20036 Length = 338 Score = 172 bits (435), Expect = 1e-47 Identities = 102/319 (31%), Positives = 177/319 (55%), Gaps = 9/319 (2%) Query: 1 MTNRTPRISAIRSAALAALLAGLGMGAA--QATEFRSADTHNADDYPTVAAVKYMGELLE 58 M +R +++ + LA + AG + Q +F SA N +P V ++ EL++ Sbjct: 1 MFDRLTKLTLGLAVPLALMTAGPALAEIRDQTVKFASA---NNKGHPQVTGMEKFAELVK 57 Query: 59 KKSGGKHKIKVFNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSS 118 +KSGGK ++K+F LG + +T+ ++ G ++ T +N G + + +PFLF S Sbjct: 58 EKSGGKIEVKLFPGGTLGGDVQTVSALQGGVIEMTVLNAGILASNVKEFGAVDLPFLFDS 117 Query: 119 IAHMRKSLDGPVGDEILKSCESAGFIGLAFYDSGARSIYAKK-PIRTVADAKGLKIRVQQ 177 K +DGP G +++ + G +G+A+++ G R++ + P+ + D KGLKIR Q Sbjct: 118 GEEADKVMDGPFGTSLMERLPATGLVGVAYWELGFRNLTNNRHPVTKLEDIKGLKIRTIQ 177 Query: 178 SDLWVALVSAMGANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHS 237 S + V L +A+GANA P+PY E+YT L+TG +D EN + AK E K + T H Sbjct: 178 SPIPVELFNALGANAVPLPYTELYTALETGTVDGQENPSANIINAKFYEVQKYMTLTRHQ 237 Query: 238 MAPEILVMSKIIYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEV 297 P+I+++SK +D L E+ +++ AA E+ F+R+ EQ+A +L ++ G E+ E+ Sbjct: 238 YNPQIVLVSKKFWDGLNDEEKTVLQQAAVEARDFQRKVSREQDAAALEEIRKTGMEVSEL 297 Query: 298 DKKSFQAV---MGPVYDKF 313 + Q + + P+ +KF Sbjct: 298 SAEETQKLRDAVKPMIEKF 316 Lambda K H 0.316 0.130 0.362 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: 206 Number of extensions: 6 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: 330 Length of database: 338 Length adjustment: 28 Effective length of query: 302 Effective length of database: 310 Effective search space: 93620 Effective search space used: 93620 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 (21.6 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