GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Shewanella oneidensis MR-1

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)

Query= TCDB::G3LHY9
         (356 letters)



>FitnessBrowser__MR1:200449
          Length = 378

 Score =  160 bits (405), Expect = 5e-44
 Identities = 91/269 (33%), Positives = 155/269 (57%), Gaps = 11/269 (4%)

Query: 33  NDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNIAQVFQFPVI 92
           N G  +ALLG SG GK+TLL +++G  +P+ GRI  DG+D+T+L    R I  +FQ   +
Sbjct: 44  NKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIYLDGEDITDLPPYERPINMMFQSYAL 103

Query: 93  YDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTADQKQKISLGR 152
           +  MTV  N+AF L+   + +A++++RV+++L+++ +  + +RK   L+  Q+Q+++L R
Sbjct: 104 FPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLKLVHMEQYGKRKPHQLSGGQRQRVALAR 163

Query: 153 GLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTEALTFAEKVV 212
            L +     +L DEP+  +D  ++  ++ ++  + ++ G T V VTHDQ EA+T A ++ 
Sbjct: 164 SLAKRP-KLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRIS 222

Query: 213 VMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIEGSTV-----KVGD--ETL 265
           +M DG I Q G+P +++E P+   +  FIGS  +N     IE   V     K  D   + 
Sbjct: 223 IMSDGWIAQTGSPMDIYESPNSRMIAEFIGS--VNLFSGEIEVDEVDHLIIKPNDLARSF 280

Query: 266 TLEYAPKTS-GTAKTELGIRPEFIRLGRE 293
            + Y   TS    +  L +RPE   + RE
Sbjct: 281 YVGYGVTTSLEDKRVWLAVRPEKTIISRE 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: 292
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: 378
Length adjustment: 30
Effective length of query: 326
Effective length of database: 348
Effective search space:   113448
Effective search space used:   113448
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