GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|NCBI__GCF_000009985.1:WP_043744393.1 AMB_RS12355 ABC
           transporter ATP-binding protein
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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