GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Magnetospirillum magneticum AMB-1

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_043744393.1 AMB_RS12355 ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_000009985.1:WP_043744393.1
          Length = 243

 Score =  173 bits (438), Expect = 4e-48
 Identities = 102/249 (40%), Positives = 141/249 (56%), Gaps = 16/249 (6%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           LLL +GL K+F GLRAVD     V  G +  LIGPNGAGKTT+FN+++    PD+G +  
Sbjct: 6   LLLVEGLVKNFRGLRAVDGVSFSVAAGEVVALIGPNGAGKTTVFNMIAGVFEPDEGRIEM 65

Query: 78  NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137
            G S+  L P Q+   G  RTFQ+ K    ++V EN+L+     T +           V 
Sbjct: 66  EGASLVGLRPDQVCRTGIGRTFQLVKPFGNISVEENVLIGALRWTHD-----------VD 114

Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197
           +  R  RE    +LE +GL  K +  A  L+   RK LE+ARAL + PKL+LLDE  AG+
Sbjct: 115 QARRRARE----VLELLGLADKRRQMARGLTLPDRKCLEVARALATGPKLLLLDEVMAGL 170

Query: 198 NPTLIGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSD 256
            P    ++ E     NR+ G+T ++IEH M  +M L   V V+  G+ + +G PE++  D
Sbjct: 171 RPAETDRMVETFRRLNRETGLTIVLIEHVMRAVMALSQRVVVINTGKPVCEGAPEEVVRD 230

Query: 257 PRVLEAYLG 265
           PRVLE YLG
Sbjct: 231 PRVLECYLG 239


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: 202
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: 267
Length of database: 243
Length adjustment: 24
Effective length of query: 243
Effective length of database: 219
Effective search space:    53217
Effective search space used:    53217
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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