GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Pseudomonas fluorescens FW300-N2E2

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate Pf6N2E2_808 Various polyols ABC transporter, permease component 2

Query= reanno::psRCH2:GFF851
         (296 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_808
          Length = 276

 Score =  102 bits (255), Expect = 7e-27
 Identities = 89/288 (30%), Positives = 131/288 (45%), Gaps = 23/288 (7%)

Query: 12  RLWATHAALLAFVAAIL--FPLLMVISISFRE--GNFATGSLFPENPTLEHWSLALGIPY 67
           RL +     LA+  AIL  FP+  ++  SF+     FAT   F   PTLE+        Y
Sbjct: 8   RLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTPTLEN--------Y 59

Query: 68  THADGSVTQPPFPVLLWLWNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLI 127
            H +       F      WNSV I+F ++ L LL++  +AY+ A          L  ML 
Sbjct: 60  LHINERSNYFSFA-----WNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLS 114

Query: 128 FQMFPPVLSLVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDAS 187
            +M PPV  L+ IY L  Q G   + L +     +++ +L  + + +W I  YF+ I   
Sbjct: 115 TKMLPPVGVLMPIYLLAKQFGLLDTRLAL-----IVIYTLINLPIVVWMIYTYFKDIPRD 169

Query: 188 LEEAAIVDGATTWQAFFHILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSV 247
           + EAA +DGAT WQ    +LLP++   LA   +L+ I    E    S+ L       L+ 
Sbjct: 170 ILEAARLDGATLWQEMVRVLLPIAKGGLASTVLLSLILCWNE-AFWSLNLTSSKAAPLTA 228

Query: 248 GAQQYLYPQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295
               Y  P+   W   +A + L+  PI       QK +V GL+ G VK
Sbjct: 229 LIASYSSPEGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276


Lambda     K      H
   0.327    0.139    0.433 

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: 249
Number of extensions: 20
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: 296
Length of database: 276
Length adjustment: 26
Effective length of query: 270
Effective length of database: 250
Effective search space:    67500
Effective search space used:    67500
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: 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