Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_035131541.1 Q763_RS04180 ABC transporter ATP-binding protein
Query= TCDB::Q97VF4 (324 letters) >NCBI__GCF_000769915.1:WP_035131541.1 Length = 562 Score = 166 bits (420), Expect = 1e-45 Identities = 94/263 (35%), Positives = 154/263 (58%), Gaps = 9/263 (3%) Query: 3 LMELKGVSVIFEDKVGLFKKR-KFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGL 61 L+E+ V + GLF + KF A+ +VS + +G+ L ++GESG GK+TLG I+ L Sbjct: 304 LLEVINVEKEYVSSSGLFGRDVKFKAVNNVSFKIYEGETLGLVGESGCGKSTLGNAILQL 363 Query: 62 QKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEK 121 K T+G ++Y G ++ K ++ RK++Q+I QDPYS+L TV + ++ P+ Sbjct: 364 DKATAGSILYKGQDLTKLSASAIRELRKEIQIIFQDPYSSLNPRITVGKAIMEPMKVHGL 423 Query: 122 INKD-ELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEP 180 D E R++ I +L+ V L EE +YPH+ SGGQ+QR+ IAR++++ P++IV DE Sbjct: 424 YKNDRERREKTIEILKRVGL--GEEHFNRYPHEFSGGQRQRVGIARTIALQPKLIVCDES 481 Query: 181 VTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVER 240 V+ +D S++ +LN L E+K T +FI+HD+ + +Y +VM G+I E Sbjct: 482 VSALDISVQAQVLNLLNELKENFGFTYIFISHDLAVVKYM-----SDQVLVMNKGQIEEM 536 Query: 241 ADLEEILKDPLHPYTNDLIKLTP 263 + + + + P YT LI+ P Sbjct: 537 NEADALYEHPEKEYTKKLIEAIP 559 Score = 137 bits (345), Expect = 6e-37 Identities = 81/253 (32%), Positives = 143/253 (56%), Gaps = 19/253 (7%) Query: 30 DVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQ-----KPTSGEVVYDGYNIWKNKRKIF 84 D + ++ Q ++L ++GESG+GK+ ++GL + T G + ++G +I + + Sbjct: 27 DSTFTLEQNEILGIVGESGSGKSVTSLAVMGLLPKGILQVTQGSIAFEGRDISQLTTREM 86 Query: 85 KKYR-KDVQLIPQDPYSTL-PFNKT---VEEILVAPILRWEKINKDELRKRLINLLELVK 139 + R D+ +I Q+P S+L P K VEEI ++K E++ +++L E VK Sbjct: 87 RNIRGNDIAMIFQEPMSSLNPSLKCGYQVEEIFK----EHTSLSKREIKATVLSLFEKVK 142 Query: 140 LTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEI 199 L E+ +YPH++SGGQKQR+ IA +++ P+I++ADEP T +D +++ I+ L E+ Sbjct: 143 LPNPEKIYNRYPHEISGGQKQRVMIAMAIACKPKILIADEPTTALDVTVQKEIILLLKEL 202 Query: 200 KNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259 + ++++FI+HD+ + +VM+ G IVE+ EI ++P H YT LI Sbjct: 203 QQETKMSIIFISHDLSLVSEI-----ANRVLVMYKGNIVEQGVATEIFENPKHTYTKALI 257 Query: 260 KLTPSIDNLYKEI 272 PS+D K + Sbjct: 258 NSRPSLDVRLKRL 270 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: 492 Number of extensions: 25 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: 562 Length adjustment: 32 Effective length of query: 292 Effective length of database: 530 Effective search space: 154760 Effective search space used: 154760 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: 51 (24.3 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