GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Skermanella stibiiresistens SB22

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_084164990.1 N825_RS22885 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_000576635.1:WP_084164990.1
          Length = 377

 Score =  221 bits (564), Expect = 2e-62
 Identities = 137/360 (38%), Positives = 211/360 (58%), Gaps = 23/360 (6%)

Query: 6   VKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFD 65
           ++ V+K F  G V A+ +VN+++E G+  G+LGPSG GKTT +R+IAGL   ++G +  D
Sbjct: 28  LEGVTKRFA-GDVNAVSDVNLDLERGKLLGLLGPSGCGKTTTLRMIAGLLPITSGRILVD 86

Query: 66  DRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVA 125
           D  ++     + PP  R  G+VFQ +AL+P++T  EN+AF L   ++ K E R+RV E  
Sbjct: 87  DDDIS-----LRPPHQRDFGLVFQNYALFPHMTVAENVAFGLDMRRVPKAEARRRVAEAL 141

Query: 126 KILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKE 185
           +++ +       PRE+SGGQQQRVALARALV +P +LLLDEP SNLDA++RD  R  ++E
Sbjct: 142 ELVRLPGYGERKPREMSGGQQQRVALARALVINPRILLLDEPLSNLDAKLRDEMRREIRE 201

Query: 186 VQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEIN 245
           +Q RLG+T + V+HD  +   + D VGV+  G+L Q+G PED+Y+ P S+ VA  +G  N
Sbjct: 202 IQQRLGITTVFVTHDQVEALTMCDVVGVMSGGRLAQIGTPEDIYERPASLFVADFVGRTN 261

Query: 246 ELEGKVTN-EGVVIGSLRFPVSVSSDR---AIIGIRPEDVKLS--KDVIKDDSWILVGKG 299
            L+ +V N   V +G   +  + ++ R   A + IRP  + L+  +D     +     +G
Sbjct: 262 ILDCEVLNGHRVRLGDGVYSCAATTIRPGKAKVAIRPHRINLTPHRDRALLSTSTNSAEG 321

Query: 300 KVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHS-------GEEVLVYVRKDKIKVFEK 352
           +V    Y G + +  I       ++ T    P H        G+++L   R D + VFE+
Sbjct: 322 RVLRTTYVGDIVQYDIDIGGPTLQVET----PTHGRGLAVAVGDKLLCEWRPDDMLVFER 377


Lambda     K      H
   0.319    0.139    0.390 

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: 324
Number of extensions: 9
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: 353
Length of database: 377
Length adjustment: 30
Effective length of query: 323
Effective length of database: 347
Effective search space:   112081
Effective search space used:   112081
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 (21.7 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