GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011384430.1
          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 (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