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 Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::Q72L52 (376 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 337 bits (865), Expect = 2e-97 Identities = 190/371 (51%), Positives = 239/371 (64%), Gaps = 47/371 (12%) Query: 1 MAKVRLEHVWKRFGKVV----AVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEIS 56 MA + L ++ KR+G + N E +DGEFVV VGPSGCGK+T LRM+AGLEEIS Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 57 EGNIYIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKE 116 G + IGDR+VND+ P RDIAMVFQNYALYPHM +ENMA+GL++ + PKDEI RV + Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 117 AARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEI 176 AA+IL++ HLL RKPRELSGGQRQRVAMGRAIVR+P+VFL DEPLSNLDAKLR + R EI Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 177 AKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGS 236 KL R LG+T+++VTHDQVEAMTL R++VM G ++Q TP +Y PA FVA FIGS Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFIGS 240 Query: 237 PSMNFVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLK--GY 294 P MN ++ APG A LG+RPEHL ++ G+ Sbjct: 241 PPMNLLKN------------APG----------------AQPGTILGIRPEHLDVRSEGW 272 Query: 295 TTIPEEENVLRGEVEVVEPLGAETEIHVAVNGTLLVAKVD--GHAPVKPGDKVELLADTQ 352 VE VE LGAE I+ +NG ++ +V+ H+P +P + + Sbjct: 273 AV----------TVETVELLGAERLIYGRINGEQVIVRVEEGTHSP-EPDSVIHVQPRAD 321 Query: 353 RLHAFDLETDR 363 RLHAFD T + Sbjct: 322 RLHAFDAATGK 332 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: 403 Number of extensions: 20 Number of successful extensions: 4 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: 334 Length adjustment: 29 Effective length of query: 347 Effective length of database: 305 Effective search space: 105835 Effective search space used: 105835 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 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