GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Synechococcus elongatus PCC 7942

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__SynE:Synpcc7942_1680
          Length = 338

 Score =  132 bits (331), Expect = 1e-35
 Identities = 79/241 (32%), Positives = 128/241 (53%), Gaps = 19/241 (7%)

Query: 6   LKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELD 65
           +++  VSK+FG  QA+  V +T+E G +  L+GP+G+GK+T   +I GL QPD+G   L 
Sbjct: 3   IQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLT 62

Query: 66  GKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAARE 125
           G+    +    V    I   FQ+  LF  +TV +N+  G  +R               + 
Sbjct: 63  GR---DATNESVRDRQIGFVFQHYALFKHLTVRKNIAFGLELR---------------KH 104

Query: 126 EEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMN 185
            +  +R + ++LL+ V +     R    LS G ++R+ +ARALA  PQ+L LDEP   ++
Sbjct: 105 TKEKVRARVEELLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALD 164

Query: 186 ATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNP 244
           A  +  LR  L K+  E   T + + HD +  M + ++I V+++GK    G PA++  NP
Sbjct: 165 AKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNP 224

Query: 245 A 245
           A
Sbjct: 225 A 225


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: 192
Number of extensions: 10
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: 338
Length adjustment: 26
Effective length of query: 229
Effective length of database: 312
Effective search space:    71448
Effective search space used:    71448
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