GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcU in Pseudomonas fluorescens FW300-N1B4

Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate Pf1N1B4_594 Glucose ABC transport system, inner membrane component 2

Query= TCDB::Q97UY9
         (287 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_594
          Length = 281

 Score =  128 bits (321), Expect = 2e-34
 Identities = 79/273 (28%), Positives = 137/273 (50%), Gaps = 10/273 (3%)

Query: 15  YLALAIVSVIWLIPVYAMLINGFKSNFEVLSTPVLVPPTKITFEAYVSVLLSLAKPLINS 74
           Y  L + + I+LIP+  ML+  FKS  ++ +  +L  P  I    ++    S+     NS
Sbjct: 18  YATLLLAAAIYLIPLVVMLLTSFKSPEDIRTGNLLSLPQVIDGIGWIKAWDSVGSYFWNS 77

Query: 75  LIIVIPTSFISAFLGAMGAYFFYTLSYSFSRASSAISDVLFSLISLATFIPQEATLLPLT 134
           + I +P   IS F+GAM  Y      +  S+       + F L+    F+P +  LLP +
Sbjct: 78  VKITVPAVLISTFIGAMNGYVLSMWRFRGSQ-------LFFGLLLFGCFLPFQTVLLPAS 130

Query: 135 RLIVSMGLLDSYIGIIFALLIFYIPTGALLMSMFISVIPRSLIEAAKMDGTGDLKIFMKI 194
             +  +GL ++  G++   +++ +    L    +   IP +L++AA++DG G   IF KI
Sbjct: 131 FTLGKIGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFWKI 190

Query: 195 VFPLSMPGFISTLIFIIIQAWNNFFIPLVLVTTPGMKLT-SIAVLSYSGAYGTLYNDTFA 253
           + P+S+P  +  LI+   Q WN+F   +V  +     +T ++  L  +      YN   A
Sbjct: 191 LLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTSTGAKEYNVDMA 250

Query: 254 AGMVASIIPLAIFVFLGRYFIRGLMALGGGGKG 286
           A M+A +  L +++F G+YF+RGL +  G  KG
Sbjct: 251 AAMIAGLPTLLVYIFAGKYFLRGLTS--GAVKG 281


Lambda     K      H
   0.330    0.144    0.417 

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: 242
Number of extensions: 17
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: 287
Length of database: 281
Length adjustment: 26
Effective length of query: 261
Effective length of database: 255
Effective search space:    66555
Effective search space used:    66555
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