Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_086508118.1 BZY95_RS00870 ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >NCBI__GCF_002151265.1:WP_086508118.1 Length = 766 Score = 198 bits (503), Expect = 4e-55 Identities = 104/286 (36%), Positives = 170/286 (59%), Gaps = 10/286 (3%) Query: 18 GLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIW 77 G K RK +A+ +S + +G++L + GESG+GKTT G ++V L T GE+ ++G +I Sbjct: 384 GRNKDRKVHAVDGISFDLREGEILGLAGESGSGKTTTGEMLVRLLDVTEGEIRFEGADIA 443 Query: 78 KNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLEL 137 + + K +R+ Q+I QDPY TL T+ +I+ P++ + LR++++ LE Sbjct: 444 QLTGRELKTFRRRAQMIFQDPYQTLNPRFTIFDIVAEPLIIHRLAEGEALRQKVVVALER 503 Query: 138 VKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLA 197 L PAE + ++PH+LSGGQ+QR++IAR++ + PR IVADEPV+M+D S+R G+LN + Sbjct: 504 AGLKPAEVYAERFPHELSGGQRQRVAIARAIVLEPRFIVADEPVSMLDVSIRAGVLNLMH 563 Query: 198 EIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTND 257 +N L ++ V+++HD+P RY T +M+ G IVE E+++++ HPYT Sbjct: 564 RFRNELGISFVYVSHDLPTIRYV-----ADRTAIMYLGEIVEVGPTEQVVRERKHPYTQL 618 Query: 258 LIKLTPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDIC 298 L++ +P D + ++ E GC + RCP AM C Sbjct: 619 LLEASPEPDPAVVKPPLESAGEIPSAVEPPNGCHFHTRCPRAMAHC 664 Score = 132 bits (333), Expect = 2e-35 Identities = 85/294 (28%), Positives = 142/294 (48%), Gaps = 16/294 (5%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTS----GEVVYDGYNIWKNKRK 82 A+ + + G+ L ++GESG GKTT + ++ L P G + +DG ++ + Sbjct: 25 AVDGIHFDLRPGEALGLVGESGCGKTTAAKAMLRLLPPNGEVPRGRIDFDGRDLVALDEE 84 Query: 83 IFKKYR-KDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLT 141 +K R K++ I Q + L TV + ++ + KI++ L V + Sbjct: 85 SMRKVRWKEIAWISQAAMNALDPVYTVGDQILEAMNAHIKIDRKTAWAHAEELFRAVGID 144 Query: 142 PAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKN 201 P L YPH++SGG KQR IA +L+++P++I+ADEP T +D + IL L++++ Sbjct: 145 PGR--LSAYPHEMSGGMKQRAVIAMALALDPKLIIADEPTTALDVVTQAQILARLSKLRR 202 Query: 202 RLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKL 261 + ++FITHDI + + VM+ G I+E + E+ P HPYT L Sbjct: 203 ERGMGLLFITHDISVV-----VQTCDRVAVMYGGHIMETGPVREVFGTPFHPYTMGLTNA 257 Query: 262 TPSIDNLYKEI----NVKINYERVEKGCPYRLRCPFAMDICKNEEPKLFKYSHE 311 P+++ +E+ + GC + RCPFA + C E P L E Sbjct: 258 FPTLEGAQRELISIPGSPPDLLNPPSGCRFAERCPFATERCVRETPPLHPVGEE 311 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: 564 Number of extensions: 26 Number of successful extensions: 7 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: 766 Length adjustment: 34 Effective length of query: 290 Effective length of database: 732 Effective search space: 212280 Effective search space used: 212280 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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