GapMind for catabolism of small carbon sources

 

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

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011385946.1 AMB_RS18160 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385946.1 AMB_RS18160 ABC
           transporter ATP-binding protein
          Length = 265

 Score =  193 bits (490), Expect = 4e-54
 Identities = 101/269 (37%), Positives = 170/269 (63%), Gaps = 8/269 (2%)

Query: 8   TMSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPT 67
           +++D+ +L+V  +S+ FGG+ A+ + SF+  +G++ ++IGPNGAGKT++ NC++G YKPT
Sbjct: 2   SVTDNPVLEVRDVSLAFGGVRALTEVSFQVNKGELFSIIGPNGAGKTSMLNCVSGRYKPT 61

Query: 68  MGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKA 127
            G +  + +     +    P+ R T    + RTFQN+ LF  ++VL+N++V +H+ L   
Sbjct: 62  SGRVFMDGRD----VTGLSPNVRAT--LGLGRTFQNLALFGHMSVLDNIMVGRHHLLGNN 115

Query: 128 SGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMC 187
           +    L  +  G  K E A   ++    ++  ++       AG LPYG ++R+E+ARAM 
Sbjct: 116 AATGALYWLS-GARKEELAHRRKVEDI-IDFLEIAHIRKAVAGTLPYGLRKRVELARAMA 173

Query: 188 TGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEY 247
             P+++ LDEP AG+N  E   +   +  +  E G ++++IEHDM VVM+IS  V+VLE+
Sbjct: 174 VEPKVILLDEPMAGMNLEEKEDMARYIVDLNEEWGMTVIMIEHDMGVVMDISHRVMVLEF 233

Query: 248 GQKISDGTPDHVKNDPRVIAAYLGVEDEE 276
           G+KI++G PD V N+ RV  AYLG++++E
Sbjct: 234 GRKIAEGLPDEVMNNERVKVAYLGIDEDE 262


Lambda     K      H
   0.318    0.136    0.386 

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: 186
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: 292
Length of database: 265
Length adjustment: 25
Effective length of query: 267
Effective length of database: 240
Effective search space:    64080
Effective search space used:    64080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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, 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