GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Sphingomonas koreensis DSMZ 15582

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Ga0059261_0624 Ga0059261_0624 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__Korea:Ga0059261_0624
          Length = 262

 Score =  107 bits (268), Expect = 2e-28
 Identities = 69/220 (31%), Positives = 115/220 (52%), Gaps = 8/220 (3%)

Query: 20  ILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVR 79
           ++ G++ S+ PG L+ +IGPNGAGKSTL + + GL+ P +G I   G  IT L   +I R
Sbjct: 18  VMDGMSLSLEPGRLIGIIGPNGAGKSTLIRALLGLV-PYRGNIALDGAEITSLTRARIAR 76

Query: 80  RGMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFPKLAQR------RNQR 133
             + Y+PQ   +   L+V   + +G   H  P   +     T+  +  +R      R++ 
Sbjct: 77  E-LAYLPQGQILHWPLSVERLVGLGRLPHLAPMSRISAADQTIIDRAMKRADIEHLRDRV 135

Query: 134 AGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVE 193
           A  LSGGER  + + RAL ++   L+ DEP A+L P    DV   +++  A+G  ++ V 
Sbjct: 136 ATELSGGERARVLLARALAVEARGLIADEPLASLDPGHQIDVMELLRSEAASGALVVAVL 195

Query: 194 QNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELY 233
            +   A    DR  +++ GR   +G+   +LN+  +  +Y
Sbjct: 196 HDLTMAARYCDRLLLMDRGRLVAQGAPLEVLNEANLRSVY 235


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: 108
Number of extensions: 5
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: 262
Length adjustment: 24
Effective length of query: 216
Effective length of database: 238
Effective search space:    51408
Effective search space used:    51408
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