Align Maltose transport system permease protein malG aka TT_C1629, 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_008412465.1 DESHY_RS10040 carbohydrate ABC transporter permease
Query= TCDB::Q72H66 (280 letters) >NCBI__GCF_000315365.1:WP_008412465.1 Length = 279 Score = 180 bits (457), Expect = 3e-50 Identities = 97/274 (35%), Positives = 149/274 (54%), Gaps = 4/274 (1%) Query: 6 RLLGRLFFYLLVVFVVVYSVFPFYWAVISSFKPSDALFSPDPSFLPVPFTLEHYENVFLQ 65 +L+ + Y + +V+++ P W V+SS K +FS P F P T Y +F + Sbjct: 10 KLIATVLIYTALAIAMVWALLPIIWMVLSSLKTEANMFSMPPKFTFKP-TFSTYAFMFTE 68 Query: 66 ANFGRNLLNSLIVAGGATLLSLVLGVLAAYALGRLPFPPKNAVMYIVLSMTMFPQIAVLG 125 NFG L NS+I A +T ++L+LG L YAL R + + + ++S M P A + Sbjct: 69 GNFGSFLKNSMIAAFSSTAIALILGTLGGYALARGNYRRGKDIAFWIISTRMTPVAAAIV 128 Query: 126 GLFLLLRQTGLFNTHLGLILTYLLFTLPFTVWVLVGYFRGLPRELEEAAYVDGATPLQTL 185 L+++ + L T GL+ Y F LPF +W+++ +F LP ++E AA VDGAT Q Sbjct: 129 PLYIIFAKFNLIGTTFGLVFAYTTFNLPFALWMMMTFFAELPPDMEHAAMVDGATKFQAF 188 Query: 186 LKVMLPLTGPGLVTTGLLAFIAAWNEYLFALTFTVGDSVKTVPPAIASFGGATPFEIPWG 245 ++ LP PGLV TG+L + AWN++ FA FT S +T+P A + T I WG Sbjct: 189 YRIALPQVTPGLVATGILCLMFAWNDFAFASVFT-SHSNQTIPVAASLLVSQT--GIAWG 245 Query: 246 SIMAASVVVTVPLVVLVLVFQQRIVAGLTAGAVK 279 MA V+ P+++ L ++ +V GL+ GAVK Sbjct: 246 QAMATGTVIITPMLIAGLAVRKYLVRGLSMGAVK 279 Lambda K H 0.329 0.145 0.439 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: 155 Number of extensions: 11 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: 280 Length of database: 279 Length adjustment: 26 Effective length of query: 254 Effective length of database: 253 Effective search space: 64262 Effective search space used: 64262 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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