Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate PfGW456L13_2876 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2876 Length = 525 Score = 162 bits (409), Expect = 2e-44 Identities = 97/257 (37%), Positives = 160/257 (62%), Gaps = 9/257 (3%) Query: 4 LVVKNLTKIFSLG---FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60 L V NL F +G F K + AV +S ++ + + +VGESGSGK+T + ILRLL Sbjct: 269 LEVDNLQVRFPVGGGLFQRKTWLRAVDGISLNIQRGKTLGIVGESGSGKSTLGQAILRLL 328 Query: 61 PPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLE 120 + G I F+G+ + D ++ L +R+K+ VFQDPF S +P V + + + + + Sbjct: 329 D-SEGGIRFQGQAL--DGLTQKQLRPWRKKMQVVFQDPFGSLSPRMSVAQIISEGLEV-H 384 Query: 121 NKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADE 180 ++ S ++ E+I+ +L VG+DP+ +YPH+ SGGQ+QRI IAR +L+P LI+ DE Sbjct: 385 SQLSTEECNAEVIR-ALNEVGLDPQS-RHRYPHEFSGGQRQRIAIARALVLKPALILLDE 442 Query: 181 PTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPD 240 PTS +D + + ++ LL +L+E+ G + +FI+HDL + ++ ++ V+K+G++VERG Sbjct: 443 PTSALDRTVQKQVVALLRQLQEKYGLTYLFISHDLAVVRALAHDMIVIKDGKVVERGASH 502 Query: 241 KVVLEPTHEYTKLLVGS 257 +V P H YTK L+ + Sbjct: 503 EVFDSPQHPYTKELLAA 519 Score = 156 bits (395), Expect = 8e-43 Identities = 92/241 (38%), Positives = 147/241 (60%), Gaps = 10/241 (4%) Query: 26 VKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPT----SGEIYFEGKDIWKDIKDR 81 V+N+ +++ E ++LVGESGSGK+ TA IL+LLP T +G I + G+++ D Sbjct: 20 VRNLCLDIRPGECLALVGESGSGKSVTAHSILQLLPQTDTETTGSIRYRGQELVG--ADA 77 Query: 82 ESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRV 140 L + R ++ +FQ+P S NP + +E+ + + +LL +K K A I E L V Sbjct: 78 GKLRKLRGNRIAMIFQEPMTSLNPLHSIEKQIGE--TLLVHKGLAGKAAQARILELLHLV 135 Query: 141 GID-PKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEE 199 GI P++ L YPHQ+SGGQ+QR+MIA P L++ADEPT+ +D + + I+ LL+ Sbjct: 136 GIQKPEERLKAYPHQLSGGQRQRVMIAMALACEPELLIADEPTTALDVTVQRKILLLLKS 195 Query: 200 LREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSIP 259 L++ G S++ I+HDL L ++ + VMK GEIVE+ + + EP H Y+ +L+ + P Sbjct: 196 LQQRLGMSLLLISHDLNLVRSIAQRVCVMKAGEIVEQAPCETLFTEPRHPYSCILLHAEP 255 Query: 260 K 260 + Sbjct: 256 E 256 Lambda K H 0.319 0.139 0.397 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: 373 Number of extensions: 18 Number of successful extensions: 6 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: 268 Length of database: 525 Length adjustment: 30 Effective length of query: 238 Effective length of database: 495 Effective search space: 117810 Effective search space used: 117810 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 (21.7 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