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 WP_007693924.1 C447_RS11155 ABC transporter ATP-binding protein
Query= TCDB::Q72L52 (376 letters) >NCBI__GCF_000336675.1:WP_007693924.1 Length = 368 Score = 314 bits (804), Expect = 3e-90 Identities = 184/372 (49%), Positives = 238/372 (63%), Gaps = 25/372 (6%) Query: 1 MAKVRLEHVWKRF----GKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEIS 56 M ++ + + K + +VAV+D +L EDGEF+VFVGPSGCGK+TTLR IAGLE ++ Sbjct: 1 MTQIEINELTKEYDTGDSAIVAVEDLDLSIEDGEFIVFVGPSGCGKSTTLRCIAGLESVT 60 Query: 57 EGNIYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLR-RYPKDEIDRRVK 115 +G I D +VND+ P+DRD+AMVFQNYALYPHM V +NM+FGL+L + EID RV Sbjct: 61 DGEIRFDDEVVNDLRPRDRDVAMVFQNYALYPHMTVKQNMSFGLKLSSQLSSGEIDSRVT 120 Query: 116 EAARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAE 175 +AA ++ I+ LL ++P ELSGGQ+QRVA+GR+IVREP VFLMDEPLSNLDAKLR MR E Sbjct: 121 DAAEMMGIDDLLGKRPGELSGGQQQRVALGRSIVREPGVFLMDEPLSNLDAKLRAGMRTE 180 Query: 176 IAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIG 235 I +LQ L VTTIYVTHDQ EAM +G RI V+ G +QQ P LY P N FVA FIG Sbjct: 181 IQELQNELDVTTIYVTHDQTEAMAMGDRIAVLNGGVLQQAAVPEELYRNPVNEFVADFIG 240 Query: 236 SPSMNFVRAGVEVQGEKVYLVAP-GFRIRANAV-LGSALKPYAGKEVWLGVRPEHLGLKG 293 SPS+N V V+G + L P GF R + LG +GVRPE L Sbjct: 241 SPSINLF--DVTVEGTR--LAGPGGFTYRLSGFDLGER------SHARMGVRPEDL---- 286 Query: 294 YTTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVDGHAPVKPGDKVELLADTQR 353 I E + L V VVE +G E I+ + G +VA+ D +P D+V L + + Sbjct: 287 --AIDERGDDL--TVTVVEKMGNENFIYGELGGQEVVARTDSSIRPEPDDEVGLAFEEEA 342 Query: 354 LHAFDLETDRTI 365 ++ F+ ++ R I Sbjct: 343 VYFFEPDSGRAI 354 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: 396 Number of extensions: 19 Number of successful extensions: 3 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: 368 Length adjustment: 30 Effective length of query: 346 Effective length of database: 338 Effective search space: 116948 Effective search space used: 116948 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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