GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Magnetospirillum magneticum AMB-1

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_011384430.1 AMB_RS10235 ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384430.1 AMB_RS10235 ABC
           transporter ATP-binding protein
          Length = 245

 Score =  185 bits (469), Expect = 9e-52
 Identities = 104/251 (41%), Positives = 150/251 (59%), Gaps = 14/251 (5%)

Query: 4   PILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIR 63
           P+L V  L   F GL AVN V  +V    +V++IGPNGAGKTT FN + G   P+ G + 
Sbjct: 6   PMLSVENLGKSFRGLRAVNQVAFEVPRGDIVALIGPNGAGKTTTFNLIAGALPPSDGKVV 65

Query: 64  LDGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAF 123
           LDG +I GL    I R GV RTFQ V+ F  ++  EN++V   RH N +    + K  A 
Sbjct: 66  LDGHDITGLGQAAICRAGVGRTFQIVKPFAGLSVEENVMVGALRHDNGD----VDKARAA 121

Query: 124 RRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183
            R+  + +E          L + A   A TL    ++RLE+A+ + TRP++L+LDE  AG
Sbjct: 122 SRATLDLLE----------LGDKARDPAQTLTLPDRKRLEVAKALATRPKLLLLDEVMAG 171

Query: 184 LNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRD 243
           L P E D + A++  L  E  +T+LLIEH M+ VM++SDH+VV++ G  +A+GTP ++  
Sbjct: 172 LRPVECDRMVAILTGLNKETGLTILLIEHVMRAVMALSDHVVVLHHGEKIAEGTPAEVTS 231

Query: 244 NPDVIKAYLGE 254
           +P V++ YLGE
Sbjct: 232 HPKVLECYLGE 242


Lambda     K      H
   0.320    0.137    0.391 

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: 163
Number of extensions: 6
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: 255
Length of database: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
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 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