GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Shewanella oneidensis MR-1

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__MR1:200449
          Length = 378

 Score =  225 bits (574), Expect = 1e-63
 Identities = 107/233 (45%), Positives = 159/233 (68%)

Query: 4   LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63
           L++  V K F  V  + D++LT+  GE    +G SG GKSTLLR+++G E  T+G I + 
Sbjct: 21  LKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIYLD 80

Query: 64  GQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123
           G+ +T  PP +R I M+FQSYAL+PH++V +N+A  LKQ++ PK EI  RV E  +++ +
Sbjct: 81  GEDITDLPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLKLVHM 140

Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183
           E Y  R+P +LSGGQRQRVA+ R++ + PKL L DEP+  LD  LR   +LE+  +  ++
Sbjct: 141 EQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERV 200

Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGA 236
             + + VTHDQ EAMT+A +I ++ DG I Q G+PM++Y +P +R +AEFIG+
Sbjct: 201 GVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYESPNSRMIAEFIGS 253


Lambda     K      H
   0.320    0.137    0.391 

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: 8
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: 331
Length of database: 378
Length adjustment: 29
Effective length of query: 302
Effective length of database: 349
Effective search space:   105398
Effective search space used:   105398
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