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 Pf1N1B4_5629 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5629 Length = 524 Score = 160 bits (406), Expect = 4e-44 Identities = 96/257 (37%), Positives = 154/257 (59%), Gaps = 9/257 (3%) Query: 4 LVVKNLTKIFSLG---FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60 L V NL F++G F K + AV +S V+ + + +VGESGSGK+T + ILRLL Sbjct: 270 LEVDNLQVHFAIGGGLFQRKTYLRAVDGISLNVQRGKTLGIVGESGSGKSTLGQAILRLL 329 Query: 61 PPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLE 120 + G I F+G+ + D ++ L +R+K+ VFQDPF S +P V + + + + + Sbjct: 330 D-SEGSIRFQGEAL--DGLTQKQLRPWRKKMQVVFQDPFGSLSPRMSVAQIISEGLEVHS 386 Query: 121 NKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADE 180 ++ EA + L VG+DP+ +YPH+ SGGQ+QRI IAR +L+P LI+ DE Sbjct: 387 QSTPDECEAQVI--RVLEEVGLDPQS-RHRYPHEFSGGQRQRIAIARALVLKPALILLDE 443 Query: 181 PTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPD 240 PTS +D + + ++ LL +L+E+ G + +FI+HDL + ++ ++ V+K+G++VE G Sbjct: 444 PTSALDRTVQKQVVALLRQLQEKYGLTYLFISHDLAVIRALAHDMIVIKDGKVVESGASH 503 Query: 241 KVVLEPTHEYTKLLVGS 257 V P H YTK L+ + Sbjct: 504 DVFDSPQHPYTKELLAA 520 Score = 156 bits (395), Expect = 8e-43 Identities = 95/242 (39%), Positives = 149/242 (61%), Gaps = 12/242 (4%) Query: 26 VKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPT----SGEIYFEGKD-IWKDIKD 80 V+N+ +++ E ++LVGESG GK+ TA IL+LLP T +G I + G++ I DIK Sbjct: 21 VRNLCLDIRPGECLALVGESGCGKSVTAHSILQLLPETGTETTGSIRYRGQELIGTDIK- 79 Query: 81 RESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFR 139 +L E R ++ +FQ+P S NP + VE+ + + +LL ++ K A I E L Sbjct: 80 --TLRELRGNRIAMIFQEPMTSLNPLHSVEKQIGE--TLLLHRGLGGKAAQARILELLQL 135 Query: 140 VGID-PKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLE 198 VGI P++ L YPHQ+SGGQ+QR+MIA P L++ADEPT+ +D + + I+ LL+ Sbjct: 136 VGIQKPEERLKAYPHQLSGGQRQRVMIAMALACEPELLIADEPTTALDVTVQRKILLLLK 195 Query: 199 ELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSI 258 L++ G S++ I+HDL L ++ + VMK GEIVE+ + + EP H Y+ +L+ + Sbjct: 196 SLQQRLGMSLLLISHDLNLVRSIAQRVCVMKAGEIVEQAPCETLFTEPKHPYSCVLLHAE 255 Query: 259 PK 260 P+ Sbjct: 256 PE 257 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: 371 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: 524 Length adjustment: 30 Effective length of query: 238 Effective length of database: 494 Effective search space: 117572 Effective search space used: 117572 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