GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for Glycerol, permease component 2 (characterized)
to candidate Pf1N1B4_4848 Various polyols ABC transporter, permease component 2

Query= reanno::acidovorax_3H11:Ac3H11_794
         (270 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4848
          Length = 276

 Score =  144 bits (363), Expect = 2e-39
 Identities = 83/272 (30%), Positives = 136/272 (50%), Gaps = 8/272 (2%)

Query: 4   KRFQKRTLFLIAYLLFALL--PIYWMVNMSFKTNAEILST---FSFFPQHFTWDNYKTIF 58
           +R Q   L  +A+ +  L+  PI+WMV  SFKT  +  +T   F F P   T +NY  I 
Sbjct: 7   RRLQSLLLGTLAWAIAILIFFPIFWMVLTSFKTEIDAFATPPQFIFTP---TLENYLHIN 63

Query: 59  TDESWYSGYINSLIYVSINMVITLTVALPAAYAFSRYSFLGDKHVFFWLLTNRMTPPAVF 118
               ++S   NS++       + L +A+PAAY+ + Y     K    W+L+ +M PP   
Sbjct: 64  ERSDYFSFAWNSVVISFSATALCLLIAVPAAYSMAFYETQRTKGTLLWMLSTKMLPPVGV 123

Query: 119 LLPFFQLYTTVGLMDTHIAVALAHLLFSVPLAVWILEGFMSGIPREIDETAYIDGYSFPR 178
           L+P + L  + GL+DT IA+ + + L ++P+ VW++  +   IP++I E A +DG +  +
Sbjct: 124 LMPIYLLAKSFGLLDTRIALIVIYTLINLPIVVWMIYTYFKDIPKDILEAARLDGATLWQ 183

Query: 179 FFMTIFLPLIKAGVGVAAFFCFMFSWVELLLARTLTSVNAKPIVATMTRTVSASGMDWAT 238
             + + LP+ K G+        +  W E   +  LTS  A P+ A +    S  G+ WA 
Sbjct: 184 EMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLTSSQAAPLTALIASYSSPEGLFWAK 243

Query: 239 LAAAGVLTIVPGAIVIWFVRHYIAKGFAMGRV 270
           L+A   L   P  I  W  +  + +G + G V
Sbjct: 244 LSAVSTLACAPILIFGWISQKQLVRGLSFGAV 275


Lambda     K      H
   0.332    0.141    0.451 

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: 17
Number of successful extensions: 1
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: 270
Length of database: 276
Length adjustment: 25
Effective length of query: 245
Effective length of database: 251
Effective search space:    61495
Effective search space used:    61495
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 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