GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Synechococcus elongatus PCC 7942

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Synpcc7942_1893 Synpcc7942_1893 ATPase

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__SynE:Synpcc7942_1893
          Length = 258

 Score =  187 bits (476), Expect = 1e-52
 Identities = 98/248 (39%), Positives = 150/248 (60%)

Query: 9   VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68
           +L+  G+SKRFGGLQA+ DV + +  G + GLIGPNGAGK+T F +++     DAG    
Sbjct: 7   LLEAEGLSKRFGGLQAVQDVRLQVAEGTITGLIGPNGAGKSTLFALLSNFLKADAGKVRF 66

Query: 69  AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128
            G+  E    +++A+ G+ RTFQ  R  + +T LEN+++G   + G   +      +  +
Sbjct: 67  RGRAIEKLQPYQLAQLGLVRTFQVARSLSRLTVLENMLLGGQQQRGEKFWQVWLHPQAIR 126

Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188
            +E  +  RA  LL  VG+   A   A +LS G ++ LE+ARAL   PQL+ LDEPAAG+
Sbjct: 127 RQEQELRDRAFSLLSDVGLAAKAQDYAGSLSGGQRKLLEMARALMAQPQLVLLDEPAAGV 186

Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248
           N     ++ + I        + L+IEH++ ++M LCDRV VL  GK + +G PA++Q++E
Sbjct: 187 NPALIEKICDHIQTWNQQGISFLIIEHNMDVIMSLCDRVWVLAEGKNLVDGPPAQIQQDE 246

Query: 249 KVIEAYLG 256
           +V+ AYLG
Sbjct: 247 QVLAAYLG 254


Lambda     K      H
   0.319    0.137    0.384 

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: 187
Number of extensions: 8
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: 260
Length of database: 258
Length adjustment: 24
Effective length of query: 236
Effective length of database: 234
Effective search space:    55224
Effective search space used:    55224
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 (21.7 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