Align Solute-binding protein Bpro_3107 (characterized)
to candidate Pf6N2E2_1301 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1301 Length = 339 Score = 166 bits (421), Expect = 6e-46 Identities = 111/329 (33%), Positives = 171/329 (51%), Gaps = 19/329 (5%) Query: 16 LAALLAG-------LGMGAAQATEFRSADTH----NADDYPTVAAVKYMGELLEKKSGGK 64 + LLAG LG + A E R N ++P + +LL +KSGGK Sbjct: 5 MKTLLAGACATGLLLGSVVSHADEIRERTLRFAFQNVKEHPQGQGAQKFADLLSEKSGGK 64 Query: 65 HKIKVFNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRK 124 K+++F LG + +T+ ++ G LD T +N G + A P + PFLF+++ Sbjct: 65 IKVRLFPGGTLGGDVQTVSALQGGTLDITVLNSGILAAQAPDYAMLDFPFLFNNVEEAHA 124 Query: 125 SLDGPVGDEILKSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVA 183 +DGPVG ++ +S G + L ++D G R++ +K P+ + D +GLKIRV QS +++ Sbjct: 125 VIDGPVGQKLAVQLDSKGLVALGYWDLGFRNLTNSKHPVTKLEDMQGLKIRVIQSPIYLE 184 Query: 184 LVSAMGANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEIL 243 SA+GAN PM + EVYTGL+ ID EN + K E K S T H P+ L Sbjct: 185 TFSALGANPVPMAFPEVYTGLEQHTIDGQENPFTVIEGNKFYEVQKYLSVTGHIFNPQSL 244 Query: 244 VMSKIIYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGA----EIVEVDK 299 ++S+ +++L E+ MIR+AA E+ F+R+ K A V AGA E+ +K Sbjct: 245 IISQKTWNRLNDDEKAMIRSAATEAQKFQREVTAASMDK--AKVTLAGAMTVNEVTPAEK 302 Query: 300 KSFQAVMGPVYDKFMTTPDMKRLVKAVQD 328 F+ + PV DKF + D LVK + + Sbjct: 303 DRFRERVKPVVDKFAKSLDAD-LVKTMYE 330 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: 214 Number of extensions: 6 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: 330 Length of database: 339 Length adjustment: 28 Effective length of query: 302 Effective length of database: 311 Effective search space: 93922 Effective search space used: 93922 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