GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate Pf6N2E2_2890 Glucose ABC transport system, inner membrane component 2

Query= reanno::Smeli:SMc03063
         (380 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2890
          Length = 281

 Score =  113 bits (283), Expect = 6e-30
 Identities = 71/215 (33%), Positives = 108/215 (50%), Gaps = 9/215 (4%)

Query: 167 FLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLY 226
           F NS+ + VP+ +I   I A   Y L+   F G  +   +++    +P Q  L+P     
Sbjct: 74  FWNSIKITVPAVLISTAIGALNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTL 133

Query: 227 NGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFV 286
             +G      A T  G+   H  +GL       RNY   +P  ++++AR+DGA  F IF 
Sbjct: 134 GKMGL-----ASTTTGLVFVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFR 188

Query: 287 KIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGG--NWE 344
           +IILP+S P +    I+QF   WND L  +VF  +  D   +T  L NL+ +  G   + 
Sbjct: 189 RIILPMSTPIIMVCLIWQFTQIWNDFLFGVVF--SSGDSQPITVALNNLVNTSTGAKEYN 246

Query: 345 ILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
           +  A+A I  +  L+V+    +Y VRGL AG+VKG
Sbjct: 247 VDMAAAMIAGLPTLLVYVVAGKYFVRGLTAGAVKG 281


Lambda     K      H
   0.324    0.139    0.418 

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: 252
Number of extensions: 14
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: 380
Length of database: 281
Length adjustment: 28
Effective length of query: 352
Effective length of database: 253
Effective search space:    89056
Effective search space used:    89056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 48 (23.1 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