GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Marivita geojedonensis DPG-138

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_085640649.1 MGEO_RS17175 ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_002115805.1:WP_085640649.1
          Length = 251

 Score =  161 bits (407), Expect = 1e-44
 Identities = 100/257 (38%), Positives = 149/257 (57%), Gaps = 16/257 (6%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           LL  + ++K FGGL+A+ + ++ V E +   +IGPNGAGK+TL N L   + PD G V+F
Sbjct: 3   LLEVKDVNKRFGGLQALGNVNLSVAENTCHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62

Query: 78  NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137
           +G S+    P +I   G  R FQ  ++   LTV+ENML+    +    F   L   R V 
Sbjct: 63  DGQSVLGRTPFEINQMGISRVFQTPEIFGDLTVMENMLIPCFAKRDGSF--ALHGIRSVL 120

Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197
            E    R++A  ML+ V +  K   ++ ++S G ++ LEMA  L+ NPKL+LLDEP AG+
Sbjct: 121 SEGEL-RDQAEQMLDDVNMLDKRNMHSASMSRGDKRRLEMAMCLVQNPKLLLLDEPTAGM 179

Query: 198 -----NPT--LIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTP 250
                N T  L+ +I E      ++ IT  +IEH+M V+ +L   + VLA+G  L + TP
Sbjct: 180 ARADTNNTIDLLKEIKE------KRDITIAIIEHDMHVVFSLAERITVLAQGTPLVEDTP 233

Query: 251 EQIQSDPRVLEAYLGDS 267
           E I+  P+V EAYLG++
Sbjct: 234 ENIKGHPKVKEAYLGEA 250


Lambda     K      H
   0.319    0.136    0.389 

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: 183
Number of extensions: 5
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: 267
Length of database: 251
Length adjustment: 24
Effective length of query: 243
Effective length of database: 227
Effective search space:    55161
Effective search space used:    55161
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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