Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate HSERO_RS07880 HSERO_RS07880 peptide ABC transporter substrate-binding protein
Query= TCDB::Q97VF5 (362 letters) >FitnessBrowser__HerbieS:HSERO_RS07880 Length = 330 Score = 194 bits (492), Expect = 4e-54 Identities = 112/323 (34%), Positives = 185/323 (57%), Gaps = 20/323 (6%) Query: 44 MILEVHNLNVIY--DEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIR 101 + LEV NL + EG ++ AV+DVS V +G ILG++GESGSGK+ +IL + Sbjct: 4 LTLEVRNLRTHFFTPEG---VLPAVDDVSLSVGRGRILGLVGESGSGKSVTGFSILGMVD 60 Query: 102 PPGKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAIS 161 PG+I+ G+++F G D+ M R+L I+ + Q LNPVL + ++ Sbjct: 61 APGRIVGGEILFQGRDLVRMDKTSLRELQGNRIAMIFQDPMMTLNPVLKVEAQMVDAVLA 120 Query: 162 HGEADKKRVIERASELLKLVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMD 220 H + +++ E A + L ++G+ P L+ YP QLSGGM+QRV IA+++L P LI+ D Sbjct: 121 HSKVSRQQARELARDTLGMMGIASPEERLQAYPHQLSGGMRQRVAIAIAMLHKPDLIIAD 180 Query: 221 EPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKT 280 EPT+ALD+ Q +L ++ + ++ G ++++THD+ +A +A+ + VMY G ++E+G Sbjct: 181 EPTTALDVTIQAQILSEVQKLARQHGTALIWITHDLSVVAGLADEVAVMYAGRIVEQGSV 240 Query: 281 EEIIKSPLNPYTSLLVSSIPS-LKGEVKVINVPLDEP-LVSKEKGCPFLARCSKAFGRC- 337 + ++ +PL+PYT L+ S+PS + ++ +P P L+ C F ARC + +C Sbjct: 241 DAVLDAPLHPYTQGLIGSLPSNNRRGARLRQIPGMTPNLLHLPPTCAFAARCERLSQQCL 300 Query: 338 -----KEELPEIRLVYDRKVRCH 355 E LP +VRC+ Sbjct: 301 VAPAISEPLPA------HRVRCY 317 Lambda K H 0.319 0.138 0.391 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: 224 Number of extensions: 10 Number of successful extensions: 2 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: 362 Length of database: 330 Length adjustment: 29 Effective length of query: 333 Effective length of database: 301 Effective search space: 100233 Effective search space used: 100233 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