GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3974 ABC transporter, ATP-binding protein

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974
          Length = 341

 Score =  266 bits (680), Expect = 6e-76
 Identities = 154/362 (42%), Positives = 218/362 (60%), Gaps = 27/362 (7%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           MA V+LE++ KR+G++ AV   NL  E GEFV  +GPSGCGKTTTL+MIAG  E+S G I
Sbjct: 1   MAFVQLENLGKRYGEIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVSSGRI 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            +  R +    P  R + +VFQ+YAL+PHM V +N+AFGLR+R+ P DE+ +RV    ++
Sbjct: 61  VLDGRDITHAKPASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQQRVDRVLKL 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           +++     R PRELSGGQRQRVA+ RA+V EP V L+DEPLSNLDA LR EM+ EI ++Q
Sbjct: 121 VRLNQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
           R +G+TT+ VTHDQ EA+++  R+VVM+ G I Q+D P  LY+ P   F++GF+G  ++ 
Sbjct: 181 REVGITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFISGFVGKANL- 239

Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAGKEVWLGVRPEHLGLKGYTTIPEE 300
                            PG R  A  V    +      E+ L +RPE + L+        
Sbjct: 240 ----------------LPGERDSAGVV---QVCNRDNGELTLSLRPEKIDLRDVGL---- 276

Query: 301 ENVLRGEVEVVEPLGAETEIHVAVN-GTL-LVAKVDGHAPVKPGDKVELLADTQRLHAFD 358
              L+G++     LG++    V+ + G L +V + DG AP+  G  V L  DT  L    
Sbjct: 277 -GRLQGKIVSRFFLGSQWLYGVSTSLGELSVVRRNDGSAPLIEGTAVGLDWDTALLRVLS 335

Query: 359 LE 360
           ++
Sbjct: 336 VD 337


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: 359
Number of extensions: 16
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: 341
Length adjustment: 29
Effective length of query: 347
Effective length of database: 312
Effective search space:   108264
Effective search space used:   108264
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