Align Solute-binding protein Bpro_3107 (characterized)
to candidate SMc00271 SMc00271 periplasmic binding protein
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__Smeli:SMc00271 Length = 325 Score = 162 bits (411), Expect = 8e-45 Identities = 99/306 (32%), Positives = 162/306 (52%), Gaps = 3/306 (0%) Query: 16 LAALLAGLGMGAAQATEFRSADTHNADDYPTVAAVKYMGELLEKKSGGKHKIKVFNKQAL 75 L A + L G A A ++ + A + VA++K+ EL+E+KS G+ KI V Sbjct: 7 LTAAVLSLCAGPAAAQTYQLSHNAAAGNPKDVASLKF-AELVEQKSEGRLKIDVGGSAQF 65 Query: 76 GSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIAHMRKSLDGPVGDEIL 135 G + ETI +++G + F+ + G +A+ P + +PFLF + +DGPVGD+I Sbjct: 66 GDDAETITNMRLGTIAFSANSQGTTSAVVPEIALLGLPFLFQDLKQAEAVMDGPVGDKIA 125 Query: 136 KSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSDLWVALVSAMGANATP 194 + E G + LA++++G R +K+ I +D G+KIR + V + +A+GA+ TP Sbjct: 126 AAAEQQGLVVLAWWNNGIRETSNSKRQITAPSDLAGMKIRTPPDQMTVDIFTALGASPTP 185 Query: 195 MPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMAPEILVMSKIIYDKLP 254 M + E+Y L+ G++D EN + + ++K E S T H + SKI++D L Sbjct: 186 MAFSELYIALQQGVVDGQENPLINIHSSKLHEVQPYISMTNHKYESTPFLASKIVFDALL 245 Query: 255 KAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEVDKKSFQAVMGPVYDKFM 314 +Q +IR AA+E+ RQ EQ + ++AAG +I +VD F VYDK+ Sbjct: 246 PEDQQIIRDAAREAGQLNRQMVGEQTTRLRGELEAAGVKINDVDPAPFVQATQSVYDKWR 305 Query: 315 TT-PDM 319 PD+ Sbjct: 306 AQYPDL 311 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: 210 Number of extensions: 12 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: 325 Length adjustment: 28 Effective length of query: 302 Effective length of database: 297 Effective search space: 89694 Effective search space used: 89694 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: 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