GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG 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:Q1MCU3
         (247 letters)



>FitnessBrowser__SynE:Synpcc7942_1893
          Length = 258

 Score =  130 bits (326), Expect = 3e-35
 Identities = 79/248 (31%), Positives = 137/248 (55%), Gaps = 17/248 (6%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           LL+  G+   +G ++A+  V + V +G I  LIG NGAGKSTL   +    +A  G V F
Sbjct: 7   LLEAEGLSKRFGGLQAVQDVRLQVAEGTITGLIGPNGAGKSTLFALLSNFLKADAGKVRF 66

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHF----------- 119
            GR I ++  +++A+L + ++ +  R   R+TVLEN+ +G      + F           
Sbjct: 67  RGRAIEKLQPYQLAQLGLVRTFQVARSLSRLTVLENMLLGGQQQRGEKFWQVWLHPQAIR 126

Query: 120 ---AEDVEKIFTLFP--RLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGL 174
               E  ++ F+L     L  +     G+LSGG++++L + RALMA+P+L+LLDEP+ G+
Sbjct: 127 RQEQELRDRAFSLLSDVGLAAKAQDYAGSLSGGQRKLLEMARALMAQPQLVLLDEPAAGV 186

Query: 175 APLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLAN 234
            P +++ I + I+  N+ +G++  ++E N    + L  R +V+  GK  + G   ++  +
Sbjct: 187 NPALIEKICDHIQTWNQ-QGISFLIIEHNMDVIMSLCDRVWVLAEGKNLVDGPPAQIQQD 245

Query: 235 PEVRAAYL 242
            +V AAYL
Sbjct: 246 EQVLAAYL 253


Lambda     K      H
   0.320    0.137    0.387 

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: 159
Number of extensions: 13
Number of successful extensions: 3
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: 247
Length of database: 258
Length adjustment: 24
Effective length of query: 223
Effective length of database: 234
Effective search space:    52182
Effective search space used:    52182
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 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