GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Synechococcus elongatus PCC 7942

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Synpcc7942_1893 Synpcc7942_1893 ATPase

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__SynE:Synpcc7942_1893
          Length = 258

 Score =  159 bits (402), Expect = 6e-44
 Identities = 99/266 (37%), Positives = 150/266 (56%), Gaps = 14/266 (5%)

Query: 10  SDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMG 69
           ++  LL+ E LS +FGGL A+ D   +   G IT LIGPNGAGK+T+F  ++ F K   G
Sbjct: 3   AESWLLEAEGLSKRFGGLQAVQDVRLQVAEGTITGLIGPNGAGKSTLFALLSNFLKADAG 62

Query: 70  MITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASG 129
            + F  ++     +E+L  +++  +  + RTFQ  R  S LTVLEN+L+    +  +   
Sbjct: 63  KVRFRGRA-----IEKLQPYQLA-QLGLVRTFQVARSLSRLTVLENMLLGGQQQRGEKFW 116

Query: 130 YTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTG 189
              L    +   +R+  E  + A   L    L  +A D AG L  G ++ LE+ARA+   
Sbjct: 117 QVWLHPQAI---RRQEQELRDRAFSLLSDVGLAAKAQDYAGSLSGGQRKLLEMARALMAQ 173

Query: 190 PELLCLDEPAAGLNPRESATLNALLKSIRA--ETGTSILLIEHDMSVVMEISDHVVVLEY 247
           P+L+ LDEPAAG+NP   A +  +   I+   + G S L+IEH+M V+M + D V VL  
Sbjct: 174 PQLVLLDEPAAGVNP---ALIEKICDHIQTWNQQGISFLIIEHNMDVIMSLCDRVWVLAE 230

Query: 248 GQKISDGTPDHVKNDPRVIAAYLGVE 273
           G+ + DG P  ++ D +V+AAYLG+E
Sbjct: 231 GKNLVDGPPAQIQQDEQVLAAYLGLE 256


Lambda     K      H
   0.318    0.136    0.386 

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: 191
Number of extensions: 11
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: 292
Length of database: 258
Length adjustment: 25
Effective length of query: 267
Effective length of database: 233
Effective search space:    62211
Effective search space used:    62211
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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