GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Dyella japonica UNC79MFTsu3.2

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3950
          Length = 239

 Score =  129 bits (323), Expect = 7e-35
 Identities = 76/227 (33%), Positives = 124/227 (54%), Gaps = 13/227 (5%)

Query: 20  ILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVR 79
           +++   FSI  GE+V ++GPNGAGK+T    + GL+    G I     +ITGL      +
Sbjct: 16  VVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKLDKYDITGLPMHARAK 75

Query: 80  RGMCYVPQVCNVFGSLTVAENL--------DMGAFLHQGPTQTLKDRIYTMFPKLAQRRN 131
            G+ Y+PQ  +VF  LTVA+N+        ++ A    G  ++L D +     K+A   +
Sbjct: 76  LGIGYLPQEPSVFRRLTVADNIMAVLELRENLSAKQRAGELESLLDEL-----KIAHIAD 130

Query: 132 QRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIIL 191
           QR  +LSGGER+ + + RAL  +P  +LLDEP A + PI V ++   ++ +   G  +++
Sbjct: 131 QRGISLSGGERRRVEIARALAAEPRYMLLDEPFAGVDPISVGEIQRIVRHLKERGIGVLI 190

Query: 192 VEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLGAAY 238
            + N ++ L + DR Y+L +G     G+   +L D  V E+YLG  +
Sbjct: 191 TDHNVRETLGICDRAYILNDGEVLSRGTPAHILADEKVREVYLGREF 237


Lambda     K      H
   0.320    0.139    0.393 

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: 147
Number of extensions: 7
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: 240
Length of database: 239
Length adjustment: 23
Effective length of query: 217
Effective length of database: 216
Effective search space:    46872
Effective search space used:    46872
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