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 SM_b20111 SM_b20111 oligopeptide ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Smeli:SM_b20111 Length = 546 Score = 196 bits (497), Expect = 1e-54 Identities = 114/263 (43%), Positives = 161/263 (61%), Gaps = 13/263 (4%) Query: 4 LVVKNLTKIFSL--GFFSK-RRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60 L VKN+ K ++L GFF+K R+ AVKN+SF+V E + +VGESGSGK+T A+++L L Sbjct: 281 LEVKNIDKFYTLSSGFFAKPARLHAVKNLSFDVAAGETIGIVGESGSGKSTVARVLLGLN 340 Query: 61 PPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAIS--- 117 + GE F G+D+ K DR+ L+ FRRKV VFQDP++S NP T++ +S Sbjct: 341 EASGGEALFHGRDVLK--MDRKQLLAFRRKVQMVFQDPYSSMNP----RMTVFDIVSEPW 394 Query: 118 LLENKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIV 177 + K + + E L VG++P+ +YPHQ SGGQ+QRI IAR P L+V Sbjct: 395 RIHKDILEKTRWRDRVTELLGLVGLNPEHAK-RYPHQFSGGQRQRIAIARALACDPELVV 453 Query: 178 ADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERG 237 DE S +D S + +I LL ELR+ G + IFITHDL + + +D I VMK+GEIVE Sbjct: 454 CDEAVSALDVSVQVQVIDLLAELRDRLGLAYIFITHDLPIVRHFADRIIVMKSGEIVEHA 513 Query: 238 HPDKVVLEPTHEYTKLLVGSIPK 260 +++ P H YT+ L+ + PK Sbjct: 514 TTEEIFRNPQHAYTRQLINATPK 536 Score = 164 bits (415), Expect = 4e-45 Identities = 102/263 (38%), Positives = 155/263 (58%), Gaps = 14/263 (5%) Query: 4 LVVKNLTKIF-SLGFFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL-- 60 L VK+LT F SLG A VSF V E + ++GESGSGK+ +A I+ L+ Sbjct: 7 LEVKDLTVDFLSLG----GAFRATSGVSFHVDAGETLVILGESGSGKSVSASAIMGLIDT 62 Query: 61 PP---TSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAIS 117 PP +G + + G+D+ + + E R++ +FQDP + NP Y + L + + Sbjct: 63 PPGDICAGSVAYRGRDL-SSLSEGERRDLNGRRIAMIFQDPLSHLNPVYTIGWQLEEVFT 121 Query: 118 LLENKPSNKKEALELIKESLFRVGI-DPKDVLGKYPHQISGGQKQRIMIARCWILRPLLI 176 + + ++ EA + E L RVGI +P+ + +YPHQ SGGQ+QRIMI LRP ++ Sbjct: 122 V--HGVASGAEARQRAIEILGRVGIPEPEKRIDQYPHQFSGGQRQRIMIGMAIALRPEIL 179 Query: 177 VADEPTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVER 236 +ADEPT+ +D S + I++LL++L+ E G +II ITHDL +A ++D + VMK+G IVE Sbjct: 180 IADEPTTALDVSVQAQILELLKKLQAEDGLAIIMITHDLEVAANMADRVIVMKSGRIVEE 239 Query: 237 GHPDKVVLEPTHEYTKLLVGSIP 259 G V P H YT+ L+ ++P Sbjct: 240 GEARAVFENPAHSYTRTLINALP 262 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: 396 Number of extensions: 17 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: 546 Length adjustment: 30 Effective length of query: 238 Effective length of database: 516 Effective search space: 122808 Effective search space used: 122808 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