GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS08675
          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.

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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