Align Putative bacterial solute-binding protein 1 family (characterized, see rationale)
to candidate SMc03061 SMc03061 alpha-glucoside ABC transporter periplasmic-binding protein
Query= uniprot:A8LLL6 (452 letters) >FitnessBrowser__Smeli:SMc03061 Length = 458 Score = 563 bits (1450), Expect = e-165 Identities = 275/459 (59%), Positives = 329/459 (71%), Gaps = 8/459 (1%) Query: 1 MRHTLHASAAALALSAGMAGAGG-----HLAFTPGE-GEFNWDSYQAFAEATDLSGQDLS 54 M+ +L AA AL AG AG G L F PGE FNW S + F + DL GQ L+ Sbjct: 1 MKRSLLIGVAAFALLAGTAGLAGTAGAADLKFKPGEDSRFNWASLEEFKKGHDLKGQTLT 60 Query: 55 IFGPWLAGEADAFSNLVAFFNEATGANATYVGSDSLEQQIVIDAEAGSAPDLTVFPQPGL 114 IFGPW + F ++ A+F EATG Y S++ EQQIVID +AGS PD+ + PQPGL Sbjct: 61 IFGPWRGEDEALFKSVYAYFVEATGVELKYSSSENYEQQIVIDTQAGSPPDVAILPQPGL 120 Query: 115 ATTMAARGFLTPLPDGTDDWLRENYAAGQSWIDLGTYADGSGNDQLYGFFFNVNVKSLVW 174 +AA+G LTPL D T WL +NYAAGQSW+DL TY G LY F + ++VKSLVW Sbjct: 121 IADLAAKGLLTPLGDETKQWLLDNYAAGQSWVDLSTYNGKDGTSALYAFPYKIDVKSLVW 180 Query: 175 YIPENFEDFDYEVPETMEEFKALMDQMVEDGQTPLCVGLGSGGATGWPATDWVEDLMLRT 234 Y+PENFED YEVP+TMEE KAL +++ EDG+ P C+GLGSGGATGWPATDWVEDLMLRT Sbjct: 181 YVPENFEDAGYEVPKTMEELKALTEKIAEDGEKPWCIGLGSGGATGWPATDWVEDLMLRT 240 Query: 235 QPPEVYDAWVSNEMPFDDPRVVAAIEEYGSFTRNDDYVVGNANDTASVDFRESPLGLFAS 294 QP E YD WV NE+PF D V A+EE+G F RND +V G A AS DFR+SP GLF+S Sbjct: 241 QPAETYDKWVKNEIPFTDAAVTGALEEFGWFARNDAFVDGGAAAVASTDFRDSPKGLFSS 300 Query: 295 PPACMMHRQASFIPAYFPEGTELGEDADFFYFPAFE-EKDLGRPVLGAGTLFAITNENPA 353 PP C +H QASFIP++FPEG +GEDADFFY P +E +K+LG PVLGAGTL IT + PA Sbjct: 301 PPKCYLHHQASFIPSFFPEGKVVGEDADFFYMPPYESKKELGNPVLGAGTLAMITKDTPA 360 Query: 354 ASAFIEFLKTPFAHEIMMAQDGFLTPFKGANPAAYASDTLRGQGEILTNATTFRFDGSDL 413 A AFIEFLKTP AHE+ MAQ FLTP+K N Y + L+ QGEIL NATTFRFDGSDL Sbjct: 361 ARAFIEFLKTPIAHEVWMAQTSFLTPYKSVNVDVYGNPPLKKQGEILLNATTFRFDGSDL 420 Query: 414 MPGGVGAGTFWTGMVDYSSGAKSAADVASEIQASWESLK 452 MPG +GAG FWTGMVD+ G KS+ADVA+ +Q +W+S+K Sbjct: 421 MPGKIGAGAFWTGMVDF-VGGKSSADVAAGVQKAWDSIK 458 Lambda K H 0.317 0.134 0.413 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: 808 Number of extensions: 45 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: 452 Length of database: 458 Length adjustment: 33 Effective length of query: 419 Effective length of database: 425 Effective search space: 178075 Effective search space used: 178075 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: 51 (24.3 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