Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF3696 PGA1_262p01000 dipeptide transport ATP-binding protein DppF
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__Phaeo:GFF3696 Length = 344 Score = 197 bits (500), Expect = 4e-55 Identities = 112/334 (33%), Positives = 188/334 (56%), Gaps = 32/334 (9%) Query: 3 LMELKGVSVIFEDKVGLFK------------KRKFYALKDVSLSMNQGDLLIVLGESGAG 50 L+ELK + FE G + KR +A+ +VSLS ++G+ L ++GESG G Sbjct: 11 LLELKNLEKRFELDKGFLETIKLRGGRITREKRAVHAVNNVSLSADRGEALCIVGESGCG 70 Query: 51 KTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEE 110 K+T+ R++ GL P+ GE+ YDG I R RK +Q+I Q+PY++L T+++ Sbjct: 71 KSTVARLVAGLLAPSGGEIHYDGERIDDRSRGEMMPLRKKMQMIFQNPYASLNPRMTIQQ 130 Query: 111 ILVAPILRWE-KINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLS 169 L P+ +++ E+R ++ ++ V + P+ + +YPH+ SGGQ+QR++IAR+L+ Sbjct: 131 ALEEPVRHHNPSLSRGEVRDKVSEVMRSVGVDPS--WSSRYPHEFSGGQRQRIAIARALT 188 Query: 170 VNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNT 229 V+P I+ADEP++ +D S++ +LN + E K++ LT FITHD+ + +F Sbjct: 189 VDPEFIIADEPISALDVSIQAQVLNLMLEAKDQRGLTYFFITHDLSVVEHF-----GTRV 243 Query: 230 IVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPSIDN-------LYKEINVKINYERVE 282 V++ G + E AD + + ++P HPYT L+ P + + L EI IN + Sbjct: 244 AVLYLGTLCELADTQTLFENPKHPYTKALLSAVPQLKDQGQNHIRLQGEIPTPIN---LP 300 Query: 283 KGCPYRLRCPFAMDICKNEEPKLFKYS--HEVAC 314 +GCP++ RC FA C+ P+ + + VAC Sbjct: 301 QGCPFQTRCAFANARCRESRPRPLRQADGSTVAC 334 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: 281 Number of extensions: 14 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: 344 Length adjustment: 28 Effective length of query: 296 Effective length of database: 316 Effective search space: 93536 Effective search space used: 93536 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