Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Ac3H11_694 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
Query= TCDB::Q97VF4 (324 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_694 Length = 341 Score = 173 bits (438), Expect = 6e-48 Identities = 105/301 (34%), Positives = 175/301 (58%), Gaps = 20/301 (6%) Query: 27 ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDG----YNIWKNKRK 82 A+ DVS ++++G+ L ++GESG+GK+T+GR++ L PTSG++ Y G ++ + + Sbjct: 39 AVDDVSFTIHRGETLGLVGESGSGKSTIGRLLTRLVDPTSGQMRYHGGAAPQDLAQLSQS 98 Query: 83 IFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELR-KRLINLLELVKLT 141 ++ R +Q+I QDPY++L + ++L A L + K R R+ LLE V L Sbjct: 99 QYRPLRSQIQIIFQDPYASLNPRMRIRDVL-AEALDTHGLAKGAARLPRIHQLLEQVGLR 157 Query: 142 PAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKN 201 P E ++PH+ SGGQ+QR+ IAR+L+V P+ IVADEP++ +D S++ ++N L E+K Sbjct: 158 P--EHAERFPHEFSGGQRQRIGIARALAVEPQFIVADEPLSALDVSIQAQVVNLLGELKE 215 Query: 202 RLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKL 261 +L LT++FI+HD+ + Y L D+ +V++ GR++E A E + P HPYT L+ Sbjct: 216 QLGLTLLFISHDLDVVEY---LCDR--VVVLYLGRVMEIAPTEALYAQPQHPYTQALLAA 270 Query: 262 TPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFAMDICKNEEPKLFKYS--HEVAC 314 P D + + + GC +R RCP A C + + +L + + H AC Sbjct: 271 APIPDPAQRRSIALLQGDLPSPANPPSGCVFRTRCPQAEARCASADMQLREVAPGHLHAC 330 Query: 315 F 315 + Sbjct: 331 W 331 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: 301 Number of extensions: 16 Number of successful extensions: 5 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: 341 Length adjustment: 28 Effective length of query: 296 Effective length of database: 313 Effective search space: 92648 Effective search space used: 92648 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