GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Gallaecimonas xiamenensis 3-C-1

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_156804435.1 B3C1_RS03280 polyamine ABC transporter ATP-binding protein

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



>NCBI__GCF_000299915.1:WP_156804435.1
          Length = 375

 Score =  225 bits (574), Expect = 1e-63
 Identities = 109/236 (46%), Positives = 158/236 (66%)

Query: 4   LQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEISIG 63
           L +  V K FG V+ + +++L +  GE    +G SG GKSTLLR+++G E  ++G I I 
Sbjct: 17  LTIEGVSKFFGQVKAVDNVSLEIRKGEIFALLGGSGSGKSTLLRMLAGFEQPSSGRIFID 76

Query: 64  GQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRMLSL 123
           GQ +T  PP KR I M+FQSYAL+PH++V +N+A  LKQ+  PK EI  RV E  R++ +
Sbjct: 77  GQDITELPPYKRPINMMFQSYALFPHMTVAQNIAYGLKQDGLPKAEIGPRVDEMLRLVRM 136

Query: 124 EDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLHRQL 183
            DY  R+P +LSGGQRQRVA+ R++ + PKL L DEP+  LD  LR   +LE+ ++   +
Sbjct: 137 TDYAQRKPQQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLELVQIIESV 196

Query: 184 SASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAM 239
             + + VTHDQ EAMT+A +I ++ +G I Q GTP+++Y +P +R  AEFIG+  M
Sbjct: 197 GVTCVMVTHDQEEAMTMAQRIAIMNEGWIVQQGTPLDIYESPNSRMTAEFIGSVNM 252


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: 305
Number of extensions: 11
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: 375
Length adjustment: 29
Effective length of query: 302
Effective length of database: 346
Effective search space:   104492
Effective search space used:   104492
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 24 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