Align CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate HSERO_RS15500 HSERO_RS15500 ABC transporter permease
Query= TCDB::Q9X9R5 (276 letters) >FitnessBrowser__HerbieS:HSERO_RS15500 Length = 276 Score = 133 bits (334), Expect = 5e-36 Identities = 91/264 (34%), Positives = 144/264 (54%), Gaps = 16/264 (6%) Query: 19 VFALVSLAPLV---WTAI--AASRTNHRLAETPPPLWFGGNLFKNLEAAWEQAGLGTAML 73 V AL+ L PL+ WTA AA T L + P L +N AW+ A L Sbjct: 22 VLALLWLLPLLYALWTAFHPAAFATRFTL-DAPLTL-------QNFVNAWQAAPFPRYFL 73 Query: 74 NSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMMIPPQLAVVPLYLWMSD 133 N+ ++ I + ++ +TLA +AFA+ FR S ++ +L + +M+ P + +V Y M+ Sbjct: 74 NTFLLVTMILAAQLVLATLAAYAFARFTFRGSNVMFMLVLLQLMVMPDILIVENYQTMNL 133 Query: 134 LGWSNQLHTVILPSLVTAFGTFFMRQYLVQALPTELIEAARVDGASSLRIVWHVVFPAAR 193 LG + + ++ LP +AFG F +RQ + +P EL EAA V+GAS+ +I+ V P AR Sbjct: 134 LGLRDTILSIGLPYFASAFGIFLLRQ-TFKTVPRELDEAATVEGASAWQILMQVYVPLAR 192 Query: 194 PAMAVLGLLTFVFAWNDFLWPIIALNQ-QNPTVQVGPEL-ARHRVLPDQAVIMAGALLGT 251 P GL++ WN+FLWP+I N ++ + VG ++ + D ++I A L+ + Sbjct: 193 PIYIAFGLVSVSTHWNNFLWPLIVTNSVESRPLTVGLQVFSSTDQGVDWSIITAATLMTS 252 Query: 252 LPLLVAFLLFGKQIVGGIMQGAIK 275 PLL+AFLLF +Q V M+ I+ Sbjct: 253 APLLLAFLLFQRQFVQSFMRAGIR 276 Lambda K H 0.327 0.140 0.434 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: 225 Number of extensions: 16 Number of successful extensions: 3 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: 276 Length of database: 276 Length adjustment: 25 Effective length of query: 251 Effective length of database: 251 Effective search space: 63001 Effective search space used: 63001 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 47 (22.7 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