Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF2021 Psest_2064 ABC-type uncharacterized transport system, duplicated ATPase component
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__psRCH2:GFF2021 Length = 553 Score = 136 bits (342), Expect = 1e-36 Identities = 82/260 (31%), Positives = 148/260 (56%), Gaps = 10/260 (3%) Query: 3 LMELKGVSVIFEDKVGLFKKRKFY--ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVG 60 L+E+ + V F K GL ++ + A+ V+ S+ +G L ++GESG+GK+TLG I+ Sbjct: 279 LLEVDDLRVWFPIKKGLLRRTVDHIKAVDGVNFSLPKGQTLGIVGESGSGKSTLGLAILR 338 Query: 61 LQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWE 120 L + GE+ + G ++ ++ + R+ +Q++ QDP+ +L +V +I+ + Sbjct: 339 LLG-SRGEIRFQGQHLQSMSQRQVRPLRRQMQVVFQDPFGSLSPRMSVGQIVGEGLHIHR 397 Query: 121 KINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEP 180 N E + +I L V L P E +YPH+ SGGQ+QR++IAR+L + P +I+ DEP Sbjct: 398 MGNAKEQEQAIIEALVEVGLDP--ETRHRYPHEFSGGQRQRIAIARALVLKPALILLDEP 455 Query: 181 VTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVER 240 + +D +++ ++ L ++ + NLT +FI+HD+ + R H +V+ G++VE+ Sbjct: 456 TSALDRTVQRQVVELLRSLQAKYNLTYLFISHDLAVVRALSH-----QMMVVKQGQVVEQ 510 Query: 241 ADLEEILKDPLHPYTNDLIK 260 +I P HPYT L++ Sbjct: 511 GAAADIFAAPQHPYTQQLLE 530 Score = 133 bits (334), Expect = 1e-35 Identities = 75/243 (30%), Positives = 138/243 (56%), Gaps = 11/243 (4%) Query: 28 LKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGL-----QKPTSGEVVYDGYNIWKNKRK 82 ++ V+ + +G+ L ++GESG+GK+ I+ L + G++++ G ++ K K Sbjct: 30 VEGVTFDIRKGETLALVGESGSGKSVTAHSILRLLPYPLARHPQGQILFHGQDLLKADEK 89 Query: 83 IFKKYRKD-VQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLT 141 +K R + + ++ Q+P ++L TV + + + + + R + LLELV + Sbjct: 90 AMRKIRGNRIAMVFQEPMTSLNPLHTVGKQINEVLEIHKGLRGKAATARTLELLELVGIP 149 Query: 142 PAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKN 201 + + YPH+LSGGQ+QR+ IA +L+ P +++ADEP T +D ++++ IL L E++ Sbjct: 150 EPRKRIRAYPHELSGGQRQRVVIAMALANEPELLIADEPTTALDVTVQLKILELLKELQA 209 Query: 202 RLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKL 261 RL + ++ I+HD+ + R H VM GR+VE+A E++ + P HPYT +L+ Sbjct: 210 RLGMALLLISHDLNLVRRIAH-----RVCVMQRGRVVEQALCEDLFRAPQHPYTQELLAA 264 Query: 262 TPS 264 PS Sbjct: 265 EPS 267 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: 483 Number of extensions: 25 Number of successful extensions: 8 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: 553 Length adjustment: 32 Effective length of query: 292 Effective length of database: 521 Effective search space: 152132 Effective search space used: 152132 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: 50 (23.9 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