Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate HSERO_RS07885 HSERO_RS07885 peptide ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__HerbieS:HSERO_RS07885 Length = 335 Score = 160 bits (405), Expect = 4e-44 Identities = 104/298 (34%), Positives = 162/298 (54%), Gaps = 16/298 (5%) Query: 26 YALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFK 85 +AL V L + G+++ ++GESG GK+TLGRV GL P+ G+V+ +G + + Sbjct: 43 HALDKVDLKVLPGEVVGLVGESGCGKSTLGRVACGLLDPSDGQVLVNGRDRASLSSREEA 102 Query: 86 KYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEE 145 + R VQ+I Q+PY++L +++I+ K+ D L + L L PA Sbjct: 103 EARLQVQMIFQNPYASLNPRLRIDQIVGEAAQVNGKVEGD-LDDYVCQQLLRAGLDPA-- 159 Query: 146 FLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNL 205 +YPHQ SGGQ+QR+ IAR+L+V P+++V DE V +D S++ ILN +++ L L Sbjct: 160 LRDRYPHQFSGGQRQRIGIARALAVQPQMLVCDEAVAALDVSIQAQILNLFMDLRAELGL 219 Query: 206 TMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPSI 265 T +FI+HD+ + H+ D+ ++M+ GR+VE A + E+ P HPYT L+ P + Sbjct: 220 TYLFISHDLGVVE---HVSDR--VVIMYLGRVVESAPVAELFGQPNHPYTQALLAEVPRM 274 Query: 266 DNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEPKLFKYS--HEVACFL 316 KE I E GC + RCP A C+ E+P L + + H AC L Sbjct: 275 GARKKEFTA-IKGEIPSPLNPPTGCHFNPRCPHATQRCREEQPLLREIAPGHMSACHL 331 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: 282 Number of extensions: 14 Number of successful extensions: 5 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: 335 Length adjustment: 28 Effective length of query: 296 Effective length of database: 307 Effective search space: 90872 Effective search space used: 90872 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