GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Geotalea uraniireducens Rf4

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011939016.1 GURA_RS10785 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_000016745.1:WP_011939016.1
          Length = 250

 Score =  232 bits (592), Expect = 5e-66
 Identities = 115/248 (46%), Positives = 166/248 (66%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           +L +R +++RFGG+ AL  V  +I +  I G+IGPNGAGKTT FN++TG+Y P +G+  L
Sbjct: 1   MLSVRQITQRFGGITALEDVSFSIGKDLITGIIGPNGAGKTTLFNIVTGIYTPTSGSVLL 60

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
             K  S     + A  G+ RTFQNI LFG+MTVLENVMVG H ++        F+     
Sbjct: 61  GDKDISRLPSEKRAYLGMVRTFQNIELFGKMTVLENVMVGLHSKSSSGFLACAFKMPWHL 120

Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184
            EE  IR+ + + L+F GI   A++ A +L +G  R LEIARALA +P++L +DEPAAG+
Sbjct: 121 REERRIRDNAMRWLEFTGIADLAQQEAANLPFGKGRLLEIARALALEPKILLMDEPAAGL 180

Query: 185 NATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNP 244
           N+ E   L  L+ KI+  G T++L+EHD++L+M +C+ I VL+ G+ +AEG P ++Q+NP
Sbjct: 181 NSKETHELSLLIRKIREMGVTVVLVEHDMELVMDICDSIVVLNLGRKLAEGTPREIQENP 240

Query: 245 AVIEAYLG 252
            V+ AYLG
Sbjct: 241 EVVAAYLG 248


Lambda     K      H
   0.320    0.138    0.394 

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: 171
Number of extensions: 5
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: 255
Length of database: 250
Length adjustment: 24
Effective length of query: 231
Effective length of database: 226
Effective search space:    52206
Effective search space used:    52206
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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