GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Synechococcus elongatus PCC 7942

Align Inositol transport system ATP-binding protein (characterized)
to candidate Synpcc7942_2492 Synpcc7942_2492 ATPase

Query= reanno::Phaeo:GFF717
         (261 letters)



>FitnessBrowser__SynE:Synpcc7942_2492
          Length = 237

 Score =  111 bits (278), Expect = 1e-29
 Identities = 71/234 (30%), Positives = 123/234 (52%), Gaps = 10/234 (4%)

Query: 3   MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62
           MS+PL+++  I  ++G+V+AL  +++++FPGE   L+G NGAGKST ++ +S +    +G
Sbjct: 1   MSEPLLQLSQIAVNYGAVVALTDLTLEIFPGEIVALIGANGAGKSTTLRAISRLVPLQQG 60

Query: 63  DILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIR-KIGPLKLFDH 121
            I ++ Q L        +  G+A   +   ++   SV  N  +G    R +IG     + 
Sbjct: 61  RIYYDQQDLGLIPAPQLVGRGLAHCPEGRRVLARQSVRINLELGAYCRRDRIGIQTDLEL 120

Query: 122 DYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGV 181
            +     + E +         +Q  GTLSGGE+Q +AIARA+    ++L+LDEP+  L  
Sbjct: 121 QFDRFPRLRERQ---------NQPAGTLSGGEQQMLAIARALMSRPRLLLLDEPSLGLAP 171

Query: 182 RQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDI 235
           +    + + I  +R+QG+ ++ +  N   AL   DR  VL  G+ L +    D+
Sbjct: 172 QIVQEIFSVIRSLREQGMTILLVEQNATLALQTADRGYVLEAGQLLFSGPAADL 225


Lambda     K      H
   0.321    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: 149
Number of extensions: 6
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: 261
Length of database: 237
Length adjustment: 24
Effective length of query: 237
Effective length of database: 213
Effective search space:    50481
Effective search space used:    50481
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: 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