Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Pf6N2E2_3426 Peptide ABC transporter, ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3426 Length = 323 Score = 179 bits (453), Expect = 1e-49 Identities = 110/297 (37%), Positives = 173/297 (58%), Gaps = 15/297 (5%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86 A+ VSLS+ G++L ++GESG+GK+TLGR I+ L + ++G++++DG ++ + KR ++ Sbjct: 30 AVNGVSLSLAPGEVLGLVGESGSGKSTLGRAILRLTEVSAGQILFDGVDMAQGKRIDIER 89 Query: 87 YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWE-KINKDELRKRLINLLELVKLTPAEE 145 R + +I QDPY+ L ++ + L A +LR I +R+R+ LL LV L P E Sbjct: 90 LRHETAMIFQDPYTALNPRMSIGDTL-AEVLRVRCAIPASLIRQRVDELLNLVGLRP--E 146 Query: 146 FLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNL 205 + P LSGGQ QR+ IAR+L++ PR+I+ADE V +D S++ I+N L E++ R+NL Sbjct: 147 LADRKPGSLSGGQCQRVGIARALAIEPRLIIADECVAALDVSIQGQIINLLLELRQRMNL 206 Query: 206 TMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPSI 265 ++FI HD+ I R L D+ VM+ G IVE+ E + +P HPYT LI+ P I Sbjct: 207 AILFIAHDLAIVR---RLCDR--VAVMYLGEIVEQGPTEAVFSNPRHPYTVALIQSIPHI 261 Query: 266 DNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEPKLFKYS-HEVACFL 316 D ++ + E + GC + RC +A IC P + + H +C L Sbjct: 262 DPTRPLLSAPLPGEPPSPLNLPSGCAFHPRCRYAQPICAKTPPPIHDINGHRYSCVL 318 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: 295 Number of extensions: 12 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: 323 Length adjustment: 28 Effective length of query: 296 Effective length of database: 295 Effective search space: 87320 Effective search space used: 87320 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: 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