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_2493 Synpcc7942_2493 ATPase

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__SynE:Synpcc7942_2493
          Length = 253

 Score =  231 bits (588), Expect = 1e-65
 Identities = 122/250 (48%), Positives = 171/250 (68%), Gaps = 1/250 (0%)

Query: 4   TLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63
           +LL++  V++RFGGL A+N V   +E G+I+GLIGPNGAGKTT FN+ITGL     G   
Sbjct: 2   SLLQLEQVTRRFGGLVAVNQVSFKVEVGEIFGLIGPNGAGKTTLFNLITGLQPLSGGEIC 61

Query: 64  LDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAA 123
             G       P ++A+ GIARTFQN+RLF +++V ENV+V  H + + +++  +     A
Sbjct: 62  FQGDRLDRQRPDQIAQRGIARTFQNLRLFNQLSVFENVLVARHRQARTSLWDELIGSSRA 121

Query: 124 REEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183
             +    R + Q+LL+ + +   A + A  L+YGD+RRLEIARALA +PQLL LDEPAAG
Sbjct: 122 TRQSRGDRRRVQELLELLELSDQADQPAASLAYGDRRRLEIARALALEPQLLLLDEPAAG 181

Query: 184 MNATEKLGLRELLVKIQAEGK-TILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242
           +N  EK  L + +  I+ + + T++LIEH V L+MGLC+RI VLD+G+ IA G PA V++
Sbjct: 182 LNPREKQDLSDRIRAIREQFQLTVVLIEHHVPLVMGLCDRIAVLDFGQLIALGDPATVRQ 241

Query: 243 NPAVIEAYLG 252
           +PAVIEAYLG
Sbjct: 242 DPAVIEAYLG 251


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: 204
Number of extensions: 9
Number of successful extensions: 2
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: 253
Length adjustment: 24
Effective length of query: 231
Effective length of database: 229
Effective search space:    52899
Effective search space used:    52899
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: 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