GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Escherichia coli BW25113

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate 14980 b0855 ATP-binding component of putrescine transport system (VIMSS)

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__Keio:14980
          Length = 377

 Score =  121 bits (303), Expect = 2e-32
 Identities = 77/243 (31%), Positives = 130/243 (53%), Gaps = 23/243 (9%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           LL+IR+++K + G  A++ V +TI +G+I+ L+G +G GK+T   ++ G  QP  G   L
Sbjct: 19  LLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
           DG   S   P+      I   FQ+  LF  MTV +N+  G                K  +
Sbjct: 79  DGVDLSQVPPY---LRPINMMFQSYALFPHMTVEQNIAFGL---------------KQDK 120

Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184
             +A I  +  ++L  V + +FAKR    LS G ++R+ +AR+LA  P+LL LDEP   +
Sbjct: 121 LPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL 180

Query: 185 NATEKLGLR---ELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQ 241
           +  +KL  R   E++  ++  G T +++ HD +  M +  RI +++ GK +  G P ++ 
Sbjct: 181 D--KKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIY 238

Query: 242 KNP 244
           ++P
Sbjct: 239 EHP 241


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: 223
Number of extensions: 14
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: 255
Length of database: 377
Length adjustment: 27
Effective length of query: 228
Effective length of database: 350
Effective search space:    79800
Effective search space used:    79800
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