GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Synechococcus elongatus PCC 7942

Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase

Query= reanno::pseudo1_N1B4:Pf1N1B4_774
         (244 letters)



>FitnessBrowser__SynE:Synpcc7942_1406
          Length = 368

 Score =  135 bits (339), Expect = 1e-36
 Identities = 79/208 (37%), Positives = 121/208 (58%), Gaps = 12/208 (5%)

Query: 21  STEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIVDGTSIADPKTNLPKLRSRVG 80
           S E++ GE++ + GPSG GK+TL++ +   E  Q G + + G ++A  + +LP     VG
Sbjct: 28  SFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLAGETVATAQRSLPPETRSVG 87

Query: 81  MVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEASKKALQLLERVGLSAHAKKHPGQLSGG 140
           MVFQ + LFPHL+++DN+         R ++ ++  A Q L  VGL    +++P +LSGG
Sbjct: 88  MVFQDYALFPHLTVLDNVCFGL-----RDRKGSAAVARQALALVGLEGLERRYPHELSGG 142

Query: 141 QQQRVAIARALAMDPIVMLFDEPTSALDPE----MVNEVLDVMVQLAHEGMTMMCVTHEM 196
           QQQRVA+ARALA  P ++L DEP S LD +    +  E+ D++ Q      T + VTH+ 
Sbjct: 143 QQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRDILRQAQ---ATAILVTHDQ 199

Query: 197 GFARKVADRVIFMDQGKIIEDCKKEEFF 224
             A  + DRV  M  G+  +  + EE F
Sbjct: 200 EEALSICDRVAVMRLGRFEQIGQPEELF 227


Lambda     K      H
   0.321    0.135    0.390 

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: 212
Number of extensions: 9
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: 244
Length of database: 368
Length adjustment: 27
Effective length of query: 217
Effective length of database: 341
Effective search space:    73997
Effective search space used:    73997
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 (21.9 bits)
S2: 48 (23.1 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