GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Desulfovibrio vulgaris Hildenborough

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 209035 DVU0105 glutamine ABC transporter, ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>MicrobesOnline__882:209035
          Length = 244

 Score =  161 bits (408), Expect = 1e-44
 Identities = 95/244 (38%), Positives = 147/244 (60%), Gaps = 20/244 (8%)

Query: 20  LQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQID 79
           ++++ + K++G H VL+GIDL V+ GE V+ +GPSG GKST LR I  LE+ TSG++ +D
Sbjct: 5   IEIRNLHKSYGDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGTIIVD 64

Query: 80  G-------VEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAK 132
           G        ++ HV   +    MVFQ + L+PH++V +N+ +G     V    +  + A+
Sbjct: 65  GYDLYDPKTDINHV---RTEAGMVFQQFNLFPHMSVLENVTIG----PVKVRRMARQEAQ 117

Query: 133 AAGMLSLEPY-LARR----PAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVN 187
           A G+  LE   LA +    P +LSGGQ+QRVAI R++  +PK+ LFDEP S LD  L V 
Sbjct: 118 ALGLALLEKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPEL-VG 176

Query: 188 TRLEIARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVA 247
             LE+ +       TM+ VTH+   A  +AD+++ ++ G+I++ G P EL+  P N  + 
Sbjct: 177 EVLEVMKQLAREGMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFADPKNPRLR 236

Query: 248 GFIG 251
            F+G
Sbjct: 237 EFLG 240


Lambda     K      H
   0.320    0.137    0.393 

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: 225
Number of extensions: 11
Number of successful extensions: 4
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: 352
Length of database: 244
Length adjustment: 26
Effective length of query: 326
Effective length of database: 218
Effective search space:    71068
Effective search space used:    71068
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: 48 (23.1 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