GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Klebsiella michiganensis M5al

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BWI76_RS05980 BWI76_RS05980 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Koxy:BWI76_RS05980
          Length = 260

 Score =  239 bits (609), Expect = 6e-68
 Identities = 133/253 (52%), Positives = 171/253 (67%), Gaps = 3/253 (1%)

Query: 6   NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65
           N+V+L+V  ++ +FGGL+A+  V   +   +++GLIGPNGAGKTT FNVIT  Y P +G+
Sbjct: 4   NKVILEVQDVTMQFGGLRAIDSVSFHVDEAEIFGLIGPNGAGKTTMFNVITANYKPTSGS 63

Query: 66  FELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRT- 124
             LAGK  +    + V  AGIARTFQNIRLF  MT LENVMVG    +   L  A     
Sbjct: 64  VTLAGKSLKGLKPNRVVNAGIARTFQNIRLFNSMTVLENVMVGLDSASRYSLLEAALHIG 123

Query: 125 KGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEP 184
           + F AE AA AK A  +LD +GI  FAD +A  LSYG+QR++EIARALAT P+L+ LDEP
Sbjct: 124 RYFPAERAAKAK-AMAILDDIGIAHFADVQATNLSYGNQRKVEIARALATSPKLLLLDEP 182

Query: 185 AAGMNATEKVQLRELIDRIRNDNR-TILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAE 243
           AAGMN  E  +L +LI R+RND R ++LLIEHD+  V  LC+RV VL+YGK +  G  +E
Sbjct: 183 AAGMNPKETEELADLIFRMRNDYRLSVLLIEHDMPFVNKLCERVMVLEYGKPLFSGLMSE 242

Query: 244 VQKNEKVIEAYLG 256
             ++  VI AYLG
Sbjct: 243 AIQDPDVISAYLG 255


Lambda     K      H
   0.319    0.137    0.384 

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: 232
Number of extensions: 11
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: 260
Length of database: 260
Length adjustment: 24
Effective length of query: 236
Effective length of database: 236
Effective search space:    55696
Effective search space used:    55696
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: 47 (22.7 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