GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Pseudomonas stutzeri RCH2

Align MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate GFF851 Psest_0865 ABC-type maltose transport systems, permease component

Query= TCDB::Q8DT26
         (278 letters)



>FitnessBrowser__psRCH2:GFF851
          Length = 296

 Score =  133 bits (334), Expect = 5e-36
 Identities = 87/293 (29%), Positives = 150/293 (51%), Gaps = 21/293 (7%)

Query: 3   RKKQLQIGSIYALLILLSFIWLFPIIWVILTSFRGEGTAYVPYIIPKTWTLDNYIKLF-- 60
           +  + ++ + +A L+      LFP++ VI  SFR EG      + P+  TL+++      
Sbjct: 7   KSARYRLWATHAALLAFVAAILFPLLMVISISFR-EGNFATGSLFPENPTLEHWSLALGI 65

Query: 61  ---------TNSSFPFGRWFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLA 111
                    T   FP   W  N++ ++  + +L   ++   AY+ +R++F  +   LK  
Sbjct: 66  PYTHADGSVTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSM 125

Query: 112 LVLNMFPGFMSMIAVYYILKALNL------TQTLTSLVLVYSSGAALTFYIAKGFFDTIP 165
           L+  MFP  +S++A+Y +   L          +  ++++    G AL  +  KG+F++I 
Sbjct: 126 LIFQMFPPVLSLVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESID 185

Query: 166 YSLDESAMIDGATRKDIFLKITLPLSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYT 225
            SL+E+A++DGAT    F  I LP+S PI+    +LAFI    ++  A V+L D   K T
Sbjct: 186 ASLEEAAIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMD-VDKLT 244

Query: 226 VAIGLFSMLQADTINNWFMAFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278
           +++G    L     N  +  FAA +VL  +PIT +F++ QK+ V G+T G VK
Sbjct: 245 LSVGAQQYLYPQ--NYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295


Lambda     K      H
   0.330    0.142    0.428 

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: 239
Number of extensions: 15
Number of successful extensions: 4
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: 278
Length of database: 296
Length adjustment: 26
Effective length of query: 252
Effective length of database: 270
Effective search space:    68040
Effective search space used:    68040
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 (21.8 bits)
S2: 47 (22.7 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