GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Dechlorosoma suillum PS

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= TCDB::G3LHY9
         (356 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  163 bits (413), Expect = 6e-45
 Identities = 91/241 (37%), Positives = 143/241 (59%), Gaps = 7/241 (2%)

Query: 24  SLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNI 83
           +L +V      G   ALLGPSGCGKTTLL II+G+     G+++F+G + T+L  + R +
Sbjct: 17  ALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGSEATHLHARERQV 76

Query: 84  AQVFQFPVIYDTMTVYDNLAFPLR----NRGVAEADVDRRVRDILEMIDLASWARRKAQG 139
             VFQ   ++  M V++N+AF LR         E+++ +RV D+L ++ L   A R    
Sbjct: 77  GFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLSLVQLDWLADRYPTQ 136

Query: 140 LTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTH 199
           L+  Q+Q+I+L R L   +   +L DEP   +D  ++  LR  L+RLH +   + V+VTH
Sbjct: 137 LSGGQRQRIALARALAV-EPKVLLLDEPFGALDTKVRKELRRWLRRLHDEMHISSVFVTH 195

Query: 200 DQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIEGSTVK 259
           DQ EAL  A++VVVM  G+I Q+G+P E++  P+  FV  F+G+  +N   +R+ G+  +
Sbjct: 196 DQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN--VNVFHSRVHGAWAE 253

Query: 260 V 260
           V
Sbjct: 254 V 254


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: 279
Number of extensions: 9
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: 360
Length adjustment: 29
Effective length of query: 327
Effective length of database: 331
Effective search space:   108237
Effective search space used:   108237
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