GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_2123 Echvi_2123 ABC-type spermidine/putrescine transport systems, ATPase components

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__Cola:Echvi_2123
          Length = 318

 Score =  149 bits (377), Expect = 8e-41
 Identities = 89/241 (36%), Positives = 147/241 (60%), Gaps = 9/241 (3%)

Query: 1   MAKVRLEHVWKRFGK-VVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGN 59
           M+ +++  V KR+    +A++DF+L+ + G  V  VG SG GK++ LR+IAGLE  S G 
Sbjct: 1   MSYLKVSEVSKRYDAGSLALEDFSLQVKRGGVVSMVGESGSGKSSLLRIIAGLEVQSAGV 60

Query: 60  IYIGDRLVND-----VPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRV 114
           +++GD+ + +     VP  D +I ++ Q Y LYP+  V EN+A  L L  Y K     R 
Sbjct: 61  VHLGDQKILNPAQKLVPGYD-EIQLIHQEYKLYPNSTVEENIARPLLL--YDKAYQKERT 117

Query: 115 KEAARILKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRA 174
            E   +L +    ++KPR+LSGGQ+Q+VA+GRA+  EP+V L+DEP S+LDA  + ++  
Sbjct: 118 AEILELLSLRAFKDKKPRQLSGGQQQKVAIGRALSIEPEVLLLDEPFSSLDAIQKRDLIE 177

Query: 175 EIAKLQRRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFI 234
           E+ ++   L VT I+VTHD  +A+ +   +++++ G++ Q      ++  PA+ +VA   
Sbjct: 178 ELKEIFDALEVTVIFVTHDVDDALLMSEELLIIQKGKLLQQGNVREVFRKPASAYVARLF 237

Query: 235 G 235
           G
Sbjct: 238 G 238


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: 234
Number of extensions: 10
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: 318
Length adjustment: 29
Effective length of query: 347
Effective length of database: 289
Effective search space:   100283
Effective search space used:   100283
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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