Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate PfGW456L13_1210 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1210 Length = 374 Score = 246 bits (628), Expect = 7e-70 Identities = 147/352 (41%), Positives = 202/352 (57%), Gaps = 16/352 (4%) Query: 14 GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIGDRLVNDVPPK 73 G+ + VKD NL+ GEF+ +GPSG GKTT+L M+AG E + G I + R +N+VPP Sbjct: 26 GENLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLAGRAINNVPPH 85 Query: 74 DRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKIEHLLNRKPRE 133 RDI MVFQNYAL+PHM V EN+AF L +R K ++ RVK +++++ R P + Sbjct: 86 KRDIGMVFQNYALFPHMTVAENLAFPLTVRGMNKSDVSARVKRVLSMVQLDAFAQRYPAQ 145 Query: 134 LSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRLGVTTIYVTHD 193 LSGGQ+QRVA+ RA+V EP++ LMDEPL LD +LR M+ EI L +RLGVT +YVTHD Sbjct: 146 LSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQRLGVTVVYVTHD 205 Query: 194 QVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVRAGVEVQGEKV 253 Q EA+T+ R+ V GEIQQ+ P LY+ P N FVA FIG + R + + Sbjct: 206 QGEALTMSDRVAVFHQGEIQQIAPPRTLYEEPKNTFVANFIGENNRLNGRLHSQTGDRCI 265 Query: 254 YLVAPGFRIRANAV-LGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEEENVLRGEVEVVE 312 + G ++ A AV +G G+ V L +RPE + L G + + N G VE Sbjct: 266 VELGRGEKVEALAVNVGQ-----TGEPVTLSIRPERVSLNG--SSDQCVNRFSGRVEEFI 318 Query: 313 PLGAETEIHVAVNGTL------LVAKVDGHAPVKPGDKVELLADTQRLHAFD 358 LG + + V G +A++D V GD V L + + A D Sbjct: 319 YLGDHVRVRMEVCGKTDFFVKQPIAELDPSLAV--GDVVPLGWQVEHVRALD 368 Lambda K H 0.320 0.139 0.400 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: 384 Number of extensions: 15 Number of successful extensions: 1 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: 376 Length of database: 374 Length adjustment: 30 Effective length of query: 346 Effective length of database: 344 Effective search space: 119024 Effective search space used: 119024 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: 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