GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas fluorescens FW300-N2E3

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 AO353_25130 AO353_25130 ABC transporter

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25130
          Length = 381

 Score =  336 bits (861), Expect = 7e-97
 Identities = 184/367 (50%), Positives = 245/367 (66%), Gaps = 21/367 (5%)

Query: 1   MAKVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNI 60
           M K++L++V K+ G V  ++D +LE   GEFVVFVGPSGCGK+T LR+IAGL+ I  G++
Sbjct: 1   MIKLKLDNVNKQLGGVRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAGDL 60

Query: 61  YIGDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARI 120
            I +R VND+ P++R + MVFQ+YALYPHM+VY+N++FGL+L +  K  +  RV   A+I
Sbjct: 61  LIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTAQI 120

Query: 121 LKIEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQ 180
           L+++ LL RKP+ELSGGQRQRVAMGRA+ REP + L DEPLSNLDA LRV+MR EIA+L 
Sbjct: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180

Query: 181 RRLGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMN 240
            RLG T IYVTHDQVEAMTL  +IVV+  G ++QV +P  LY+ PA+RFVAGF+GSP MN
Sbjct: 181 ARLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240

Query: 241 FVRAGVEVQGEKVYLVAPGFRIRANAVLGSALKPY------AGKEVWLGVRPEHLGLKGY 294
           F+ A +   GE   +  P        VLG    P+      A   + LGVRPEH+ LK  
Sbjct: 241 FLAARLHAPGETSLVDTP--------VLGMTSLPFDSSNLAADTPLSLGVRPEHVSLKA- 291

Query: 295 TTIPEEENVLRGEVEVVEPLGAETEIHVAV-NGTLLVAKVDGHAPVKPGDKVELLADTQR 353
                 +  +   V  VE LG+ET +H+       L+ + + +A  + GD+VEL  D   
Sbjct: 292 -----ADGTVGVIVTGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVGDRVELQLDIGN 346

Query: 354 LHAFDLE 360
           LH FD +
Sbjct: 347 LHLFDAD 353


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: 420
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: 381
Length adjustment: 30
Effective length of query: 346
Effective length of database: 351
Effective search space:   121446
Effective search space used:   121446
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: 50 (23.9 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