Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate SM_b20111 SM_b20111 oligopeptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Smeli:SM_b20111 Length = 546 Score = 195 bits (495), Expect = 2e-54 Identities = 107/267 (40%), Positives = 170/267 (63%), Gaps = 17/267 (6%) Query: 3 LMELKGVSVIFEDKVGLFKK-RKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGL 61 ++E+K + + G F K + +A+K++S + G+ + ++GESG+GK+T+ RV++GL Sbjct: 280 ILEVKNIDKFYTLSSGFFAKPARLHAVKNLSFDVAAGETIGIVGESGSGKSTVARVLLGL 339 Query: 62 QKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEK 121 + + GE ++ G ++ K RK +R+ VQ++ QDPYS++ TV +I+ P W + Sbjct: 340 NEASGGEALFHGRDVLKMDRKQLLAFRRKVQMVFQDPYSSMNPRMTVFDIVSEP---W-R 395 Query: 122 INKDELRK-----RLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIV 176 I+KD L K R+ LL LV L P E +YPHQ SGGQ+QR++IAR+L+ +P ++V Sbjct: 396 IHKDILEKTRWRDRVTELLGLVGLNP--EHAKRYPHQFSGGQRQRIAIARALACDPELVV 453 Query: 177 ADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGR 236 DE V+ +D S+++ +++ LAE+++RL L +FITHD+PI R+F IVM +G Sbjct: 454 CDEAVSALDVSVQVQVIDLLAELRDRLGLAYIFITHDLPIVRHF-----ADRIIVMKSGE 508 Query: 237 IVERADLEEILKDPLHPYTNDLIKLTP 263 IVE A EEI ++P H YT LI TP Sbjct: 509 IVEHATTEEIFRNPQHAYTRQLINATP 535 Score = 130 bits (328), Expect = 6e-35 Identities = 89/275 (32%), Positives = 145/275 (52%), Gaps = 24/275 (8%) Query: 3 LMELKGVSVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQ 62 L+E+K ++V F G F+ A VS ++ G+ L++LGESG+GK+ I+GL Sbjct: 6 LLEVKDLTVDFLSLGGAFR-----ATSGVSFHVDAGETLVILGESGSGKSVSASAIMGLI 60 Query: 63 KPTSGE-----VVYDGYNIWKNKRKIFKKYRKD-----VQLIPQDPYSTLPFNKTVEEIL 112 G+ V Y G ++ + + R+D + +I QDP S L T+ L Sbjct: 61 DTPPGDICAGSVAYRGRDL----SSLSEGERRDLNGRRIAMIFQDPLSHLNPVYTIGWQL 116 Query: 113 VAPILRWEKINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNP 172 + E R+R I +L V + E+ + +YPHQ SGGQ+QR+ I ++++ P Sbjct: 117 EEVFTVHGVASGAEARQRAIEILGRVGIPEPEKRIDQYPHQFSGGQRQRIMIGMAIALRP 176 Query: 173 RIIVADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVM 232 I++ADEP T +D S++ IL L +++ L ++ ITHD+ +A ++ D+ IVM Sbjct: 177 EILIADEPTTALDVSVQAQILELLKKLQAEDGLAIIMITHDLEVAA---NMADR--VIVM 231 Query: 233 FAGRIVERADLEEILKDPLHPYTNDLIKLTPSIDN 267 +GRIVE + + ++P H YT LI P D+ Sbjct: 232 KSGRIVEEGEARAVFENPAHSYTRTLINALPHADD 266 Lambda K H 0.321 0.141 0.410 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: 470 Number of extensions: 25 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 324 Length of database: 546 Length adjustment: 32 Effective length of query: 292 Effective length of database: 514 Effective search space: 150088 Effective search space used: 150088 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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