GapMind for catabolism of small carbon sources

 

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

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component

Query= TCDB::G3LHY9
         (356 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4847
          Length = 367

 Score =  208 bits (530), Expect = 2e-58
 Identities = 118/293 (40%), Positives = 183/293 (62%), Gaps = 13/293 (4%)

Query: 25  LKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNIA 84
           +K +D E ND      +GPSGCGK+TLL +I+GL + S G I  DG+D+T +S   R++A
Sbjct: 19  IKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDITEVSPAKRDLA 78

Query: 85  QVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTADQ 144
            VFQ   +Y  M+V  N++F L   GVA+A+V+++V +   +++L     RK + L+  Q
Sbjct: 79  MVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVGEAARILELGPMLERKPKQLSGGQ 138

Query: 145 KQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTEA 204
           +Q++++GR +VRN     LFDEPL+ +D  ++  +R +L RLHK+   TM+YVTHDQ EA
Sbjct: 139 RQRVAIGRAIVRNP-KIFLFDEPLSNLDAALRVQMRLELLRLHKELQATMIYVTHDQVEA 197

Query: 205 LTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMP---ARIEGSTVKVG 261
           +T A+KVVV+  G+I Q+G+P +L+ +P++ FV  F+G+P M F+     R+ G + +V 
Sbjct: 198 MTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKMGFLKGKVTRVNGQSCEVL 257

Query: 262 DE-----TLTLEYAPKTSGTAKTELGIRPEFIRLGREG---MPITISKVEDIG 306
            +     TL L  A  + G A T LGIRPE + L + G   + +T    E +G
Sbjct: 258 LDAGTRITLPLSGANLSVGGAVT-LGIRPEHLELAQPGDCTLQVTADVSERLG 309


Lambda     K      H
   0.321    0.137    0.405 

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: 291
Number of extensions: 13
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: 356
Length of database: 367
Length adjustment: 29
Effective length of query: 327
Effective length of database: 338
Effective search space:   110526
Effective search space used:   110526
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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