GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0211 in Pseudomonas fluorescens FW300-N2C3

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 AO356_28585 AO356_28585 ABC transporter

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28585
          Length = 379

 Score =  335 bits (860), Expect = 9e-97
 Identities = 188/381 (49%), Positives = 250/381 (65%), Gaps = 26/381 (6%)

Query: 3   KVRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYI 62
           K++L++V K+ G    ++D +LE   GEFVVFVGPSGCGK+T LR+IAGL+ I  G++ I
Sbjct: 3   KLKLDNVNKQLGGARILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLI 62

Query: 63  GDRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILK 122
             R VND+ P++R + MVFQ+YALYPHM+VY+N++FGL+L +  K  +  RV + A+IL+
Sbjct: 63  DGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQILQ 122

Query: 123 IEHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRR 182
           ++ LL RKPRELSGGQRQRVAMGRA+ REP + L DEPLSNLDA LRV+MR EIA+L  R
Sbjct: 123 LDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGR 182

Query: 183 LGVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFV 242
           LG T IYVTHDQVEAMTL  +IVV+  G I+QV +P  LY+ PA+RFVAGF+GSP MNF+
Sbjct: 183 LGSTMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYERPASRFVAGFLGSPRMNFL 242

Query: 243 RAGVEVQGEKVYLVAPGFRIRANAVLGSALKPY------AGKEVWLGVRPEHLGLKGYTT 296
            A +   GE   +         + VLG    P+      A  ++ LG+RPEH+ LK    
Sbjct: 243 AAFLHTPGETSQV--------ESLVLGMTSLPFDSSGLAANTQLSLGIRPEHIALKA--- 291

Query: 297 IPEEENVLRGEVEVVEPLGAETEIHVAV-NGTLLVAKVDGHAPVKPGDKVELLADTQRLH 355
               +      V  VE LG+ET +H+       +V + + +A  + GD+VEL  D   LH
Sbjct: 292 ---AQGTAGIAVSGVEYLGSETYVHLDTGQDDPMVCRCEVNAGWRVGDRVELQLDIDNLH 348

Query: 356 AFDLETDRTIGHAQERAAVAR 376
            FD     T G A +R A+ R
Sbjct: 349 VFD-----THGTALQRHAIDR 364


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: 405
Number of extensions: 24
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: 379
Length adjustment: 30
Effective length of query: 346
Effective length of database: 349
Effective search space:   120754
Effective search space used:   120754
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