GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Phaeobacter inhibens BS107

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein

Query= TCDB::G3LHY9
         (356 letters)



>FitnessBrowser__Phaeo:GFF1915
          Length = 363

 Score =  209 bits (532), Expect = 9e-59
 Identities = 119/330 (36%), Positives = 190/330 (57%), Gaps = 8/330 (2%)

Query: 25  LKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNIA 84
           LK ++ +   G    LLG SGCGK+TLLN I+GL + + G+I  + ++VT    + R +A
Sbjct: 28  LKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEATEGQIWINDENVTWREPKDRGLA 87

Query: 85  QVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTADQ 144
            VFQ   +Y  MTV  NLAF LR   V +A+ D+ V +   ++ L     R+   L+  Q
Sbjct: 88  MVFQSYALYPKMTVRGNLAFGLRMNKVPKAEADKLVDEAARVLQLEELLDRRPGELSGGQ 147

Query: 145 KQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTEA 204
           +Q++++GR LVR  V+  LFDEPL+ +D  ++  LR +LKRLH++ G TM+YVTHDQ EA
Sbjct: 148 RQRVAIGRALVRK-VDVFLFDEPLSNLDAKLRAELRVELKRLHQELGATMIYVTHDQVEA 206

Query: 205 LTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARI-EGSTVKVGDE 263
           LT A+++ VM DG + Q+ +P E++ RP++ +V  F+G P MNF+   + E   ++  D 
Sbjct: 207 LTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVGLPSMNFVNGVVTESGAIQTEDF 266

Query: 264 TLTLEYAPKTSGTA---KTELGIRPEFIR-LGREGMPITISKVEDIGRQKIVRARFADQP 319
            L L+     S  A   + E+GIRPE +      G  + +  VE +G ++++  +  +  
Sbjct: 267 ELALDQCNLASTPAPGTEVEIGIRPEHVHPANAGGFMLDVGMVELLGSERLIWGKVGNTS 326

Query: 320 IAIVVPEDADIPA--DARVTFDPSAISIYA 347
           I +    D  I +    R+   P A S+++
Sbjct: 327 IVMRDDPDTTIRSGDQVRINLKPGAFSVFS 356


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: 285
Number of extensions: 15
Number of successful extensions: 2
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: 363
Length adjustment: 29
Effective length of query: 327
Effective length of database: 334
Effective search space:   109218
Effective search space used:   109218
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