GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluP in Pedobacter sp. GW460-11-11-14-LB5

Align The Na+-dependent sugar transporter, HP1174 (transports glucose, galactose, mannose and 2-deoxyglucose (Psakis et al. 2009)). (most similar to 2.A.1.7.2; 49% identity) (characterized)
to candidate CA265_RS08675 CA265_RS08675 glucose/galactose MFS transporter

Query= TCDB::O25788
         (407 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS08675 CA265_RS08675
           glucose/galactose MFS transporter
          Length = 428

 Score =  192 bits (488), Expect = 2e-53
 Identities = 131/415 (31%), Positives = 202/415 (48%), Gaps = 36/415 (8%)

Query: 13  LTALFFLMGFITVLNDILIPHLKPIFDLTYFEASLIQFCFFGAYFIMGGVFGNVISKIGY 72
           + ALFF+ GF+T  N  LIP  K  F L+  +A  + F  + AYF +      ++ K+G+
Sbjct: 19  ICALFFIFGFVTWANGTLIPFFKLSFGLSNLQAFFVTFASYMAYFFLALPSSWILKKVGF 78

Query: 73  PFGVVLGFVITATGCALFYPAAHFGSYGFFLGALFILASGIVCLQTAGNPFVTLLSKGKE 132
             G+VLG VI   G  +F PAA   ++G FL  +F+  + +  LQTA NP++T++   + 
Sbjct: 79  KNGIVLGLVILGLGSLIFIPAAQTRTFGLFLTGIFVQGAALALLQTASNPYLTIIGPIES 138

Query: 133 ARNLVLVQAF-NSLGTTLGP-IFGSLLIFSTTKMGDNASLIDKLADAKS----------- 179
           A   + +    N     + P I GSL +        NAS ++K   A +           
Sbjct: 139 AAKRISIAGICNKFAGMIVPLIMGSLFL-------KNASEVEKQIKAATGAVHEQLLNDV 191

Query: 180 ---VQMPYLGLAVFSLLLALIMYLLKLPDVEKE-------MPKETTQKSLFSHKHFVFGA 229
              V MPY+ LA+   L A+ +    LP+VE E         +    KS+F   H   GA
Sbjct: 192 LGRVNMPYIVLAIVFCLFAIFIKFTNLPEVEVEEDVIDESKGEVVKHKSIFQFPHLFLGA 251

Query: 230 LGIFFYVGGEVAIGSFLVLSFEKLLNLDSQSSAHYLVYYWGGAMVGRFLGSVLMNK-IAP 288
           L IF YVG EV  G  + + + + L +  + S           ++G  +G V + K I+ 
Sbjct: 252 LCIFVYVGAEVMAGDIIGI-YGRELGISPEISGKLTSITLFSMLIGYIIGIVTIPKYISQ 310

Query: 289 NKYLAFNALSSIVLIALAIIIGGKIALFALTFVGFFNSIMFPTIFSLATLNLGHLTSKAS 348
            K L   A+  I+   L+ +I    A+  +  +G  NS+M+P IF L   +LG  T   S
Sbjct: 311 QKALRICAILGIIFTILSFVISSWFAVIFVALLGLANSLMWPAIFPLGISHLGKFTKIGS 370

Query: 349 GVISMAIVGGALIPPIQGAVTDMLTATESNLLYAYGVPLL-CYFYILFFALKGYK 402
            ++ M I GGAL+P +   + + L     N   AY + +L CY YIL+FA+KG+K
Sbjct: 371 AIMIMGIAGGALMPLLYAFLNEKL---HVNFQLAYLLTVLPCYLYILYFAIKGHK 422


Lambda     K      H
   0.328    0.144    0.423 

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: 534
Number of extensions: 28
Number of successful extensions: 5
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: 407
Length of database: 428
Length adjustment: 32
Effective length of query: 375
Effective length of database: 396
Effective search space:   148500
Effective search space used:   148500
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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