Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 15367 b1247 oligopeptide transporter subunit (NCBI)
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Keio:15367 Length = 334 Score = 185 bits (469), Expect = 2e-51 Identities = 113/331 (34%), Positives = 184/331 (55%), Gaps = 32/331 (9%) Query: 3 LMELKGVSVIFEDKVGLFKKRKFY-------ALKDVSLSMNQGDLLIVLGESGAGKTTLG 55 L+E+ + V FE K G K+ F+ A+ V+L + +G+ L V+GESG GK+T Sbjct: 11 LLEIADLKVHFEIKDG---KQWFWQPPKTLKAVDGVTLRLYEGETLGVVGESGCGKSTFA 67 Query: 56 RVIVGLQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAP 115 R I+GL K T G V + G + K ++ R D+Q+I QDP ++L T+ EI+ P Sbjct: 68 RAIIGLVKATDGHVAWLGKELLGMKPDEWRAVRSDIQMIFQDPLASLNPRMTIGEIIAEP 127 Query: 116 ILRWE-KINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRI 174 + + K+++ E+R+R+ ++ V L P + +YPH+ SGGQ QR+ IAR+L + P++ Sbjct: 128 LRTYHPKMSRQEVRERVKAMMLKVGLLP--NLINRYPHEFSGGQCQRIGIARALILEPKL 185 Query: 175 IVADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFA 234 I+ DEPV+ +D S++ ++N L +++ + L+++FI HD+ + + H+ D+ +VM+ Sbjct: 186 IICDEPVSALDVSIQAQVVNLLQQLQREMGLSLIFIAHDLAVVK---HISDR--VLVMYL 240 Query: 235 GRIVERADLEEILKDPLHPYTNDLIKLTP----------SIDNLYKEINVKINYERVEKG 284 G VE +E+ +PLHPYT L+ P +I L E+ IN G Sbjct: 241 GHAVELGTYDEVYHNPLHPYTRALMSAVPIPDPDLEKNKTIQLLEGELPSPIN---PPSG 297 Query: 285 CPYRLRCPFAMDICKNEEPKL-FKYSHEVAC 314 C +R RCP A C P L + H V+C Sbjct: 298 CVFRTRCPIAGPECAKTRPVLEGSFRHSVSC 328 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: 279 Number of extensions: 17 Number of successful extensions: 4 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: 324 Length of database: 334 Length adjustment: 28 Effective length of query: 296 Effective length of database: 306 Effective search space: 90576 Effective search space used: 90576 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: 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