GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc02869 in Shewanella loihica PV-4

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)

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



>lcl|FitnessBrowser__PV4:5207560 Shew_0094 ABC transporter-related
           protein (RefSeq)
          Length = 369

 Score =  158 bits (399), Expect = 2e-43
 Identities = 91/232 (39%), Positives = 133/232 (57%), Gaps = 8/232 (3%)

Query: 10  CKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIGGQTVTT 69
           CK F    +  D     + GE +  VGPSG GKSTL+R+I+GL    +GEI  G     +
Sbjct: 10  CKIFQQEGIALDAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFS 69

Query: 70  TP------PAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123
           +       P +R +  V Q + L+P+++   N+  AL  +  PK E  AR  +    ++L
Sbjct: 70  SESGRYLTPQQRHLGYVPQHFGLFPNMTALANVVAAL--DHIPKAERVARAKDWLERVNL 127

Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183
               DR P+ LSGGQRQRVA+ RA+ REP++ L DEP S +D   R    LE+ARL  QL
Sbjct: 128 HGLPDRLPANLSGGQRQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQL 187

Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIG 235
           +  +I VTHD  EA+ LAD+++++  G + Q G+P E+ + P N  VA+ +G
Sbjct: 188 AIPVIMVTHDLNEALLLADRMILISQGTLLQQGSPREVLSRPRNEAVAKQMG 239


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: 273
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: 331
Length of database: 369
Length adjustment: 29
Effective length of query: 302
Effective length of database: 340
Effective search space:   102680
Effective search space used:   102680
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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