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 SMa1434 SMa1434 ABC transporter ATP-binding protein
Query= TCDB::Q9WXN4 (268 letters) >FitnessBrowser__Smeli:SMa1434 Length = 550 Score = 181 bits (459), Expect = 3e-50 Identities = 110/260 (42%), Positives = 157/260 (60%), Gaps = 7/260 (2%) Query: 4 LVVKNLTKIFSLG---FFSKRRIEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL 60 L V +L+K + LG F KR AV +VSF ++ E V +VGESGSGK++ A+M+LRL Sbjct: 282 LQVAHLSKHYKLGSGPFSPKREFRAVDDVSFTLRRGETVGIVGESGSGKSSIARMLLRLN 341 Query: 61 PPTSGEIYFEGKDIWKDIKDRESLVEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLE 120 PTSG F G+DI+ ++K + +L FRR+V VFQDPF S NP V R++ + Sbjct: 342 EPTSGAALFAGEDIF-ELKGK-ALDGFRRRVQMVFQDPFGSMNPRMNV-RSIISEPWAIH 398 Query: 121 NKPSNKKEALELIKESLFRVGIDPKDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADE 180 ++ E + E L VG+ + ++PHQ SGGQ+QRI IAR P LIV DE Sbjct: 399 RDILPRERWNERVVELLELVGLKAEHA-ARHPHQFSGGQRQRIAIARALASEPELIVCDE 457 Query: 181 PTSMIDASSRGGIIKLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPD 240 S +D S + +I+LL +LR+ G S +FITHDL + +D I VM+ G IVE G + Sbjct: 458 AVSALDVSIQMQVIELLADLRQRLGLSYVFITHDLPIVRQFADRILVMQRGRIVEEGETE 517 Query: 241 KVVLEPTHEYTKLLVGSIPK 260 + + P HEYT+ L+ ++P+ Sbjct: 518 ALFVSPQHEYTQALLRAVPQ 537 Score = 159 bits (401), Expect = 2e-43 Identities = 95/245 (38%), Positives = 146/245 (59%), Gaps = 13/245 (5%) Query: 23 IEAVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLL--PP---TSGEIYFEGKDIWKD 77 + AV +VSF+V E + ++GESGSGK+ + ++ L+ PP SG + F+G D+ + Sbjct: 25 VRAVDDVSFDVCPGETLVILGESGSGKSVSTGTVMGLIDCPPGDIVSGSLVFDGTDLSR- 83 Query: 78 IKDRESLVEFR-RKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEAL-ELIKE 135 D E E R++ +FQDP A NP Y V R Q + E+ + A+ + + Sbjct: 84 -LDDEGRRELNGRRIAMIFQDPLAYLNPVYTVGR---QIAEVFESHGEGEGGAVRDKVVR 139 Query: 136 SLFRVGIDPKDV-LGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGII 194 L RVGI D + YPHQ SGGQ+QR+MIA L+P +++ADEPT+ +D S + I+ Sbjct: 140 LLERVGIPEADERIDYYPHQFSGGQRQRVMIAMAIALKPDILIADEPTTALDVSVQAQIL 199 Query: 195 KLLEELREEQGTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLL 254 +LL +L+ E G ++I ITHDL +A ++D I VM G++VE G + V P+H YT+ L Sbjct: 200 ELLRDLQRETGMALIMITHDLEVAAAMADRIIVMNGGKVVESGKAEDVFTNPSHAYTRRL 259 Query: 255 VGSIP 259 + ++P Sbjct: 260 MSAVP 264 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: 408 Number of extensions: 20 Number of successful extensions: 7 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: 550 Length adjustment: 30 Effective length of query: 238 Effective length of database: 520 Effective search space: 123760 Effective search space used: 123760 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