GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Synechococcus elongatus PCC 7942

Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase

Query= TCDB::P0A9S7
         (255 letters)



>FitnessBrowser__SynE:Synpcc7942_0513
          Length = 250

 Score =  142 bits (358), Expect = 7e-39
 Identities = 90/243 (37%), Positives = 132/243 (54%), Gaps = 19/243 (7%)

Query: 15  FGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHLEGLPG 74
           +G  L VN V+L +   E+V L+GPNGAGKTT F   TG  +P  G + L +  L  LP 
Sbjct: 20  YGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLDETELTRLPM 79

Query: 75  QQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRRAQSEALDRA 134
            Q AR+G+    Q   +FR +TV+ENLL+   Q   TG+               E   R 
Sbjct: 80  TQRARLGIGYLAQEASIFRHLTVVENLLLVLQQ---TGI------------RGREQRQRV 124

Query: 135 ATWLERIGLLEHANRQASNLAYGDQRRLEIARCMVT---QPEILMLDEPAAGLNPKETKE 191
              L    L + A+ Q   ++ G++RR EIAR +      P+ L+LDEP AG++P    E
Sbjct: 125 EELLSEFRLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAVAE 184

Query: 192 LDELIAELRNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQIRNNPDVIRAY 251
           + E+IA LR      IL+ +H+++  + I+DR Y++  G  LA G+ E++ +NP V + Y
Sbjct: 185 VQEIIARLR-AQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQYY 243

Query: 252 LGE 254
           LGE
Sbjct: 244 LGE 246


Lambda     K      H
   0.320    0.137    0.395 

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: 170
Number of extensions: 8
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: 250
Length adjustment: 24
Effective length of query: 231
Effective length of database: 226
Effective search space:    52206
Effective search space used:    52206
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