GapMind for catabolism of small carbon sources

 

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

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011385946.1 AMB_RS18160 ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



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

 Score =  116 bits (290), Expect = 5e-31
 Identities = 76/246 (30%), Positives = 136/246 (55%), Gaps = 13/246 (5%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           +LE+RDV  +FG V+AL  VS ++NKGE+ +++G NGAGK++++  +SG +KP  G +  
Sbjct: 8   VLEVRDVSLAFGGVRALTEVSFQVNKGELFSIIGPNGAGKTSMLNCVSGRYKPTSGRVFM 67

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLARE-------VTNKIFL---N 113
           +G+ V   SPN   +LG+   +Q+LAL   + +  NI + R         T  ++     
Sbjct: 68  DGRDVTGLSPNVRATLGLGRTFQNLALFGHMSVLDNIMVGRHHLLGNNAATGALYWLSGA 127

Query: 114 KKKMMEESKKLLDSLQ-IRIPDINMKVE-NLSGGQRQAVAVARAVYFSAKMILMDEPTAA 171
           +K+ +   +K+ D +  + I  I   V   L  G R+ V +ARA+    K+IL+DEP A 
Sbjct: 128 RKEELAHRRKVEDIIDFLEIAHIRKAVAGTLPYGLRKRVELARAMAVEPKVILLDEPMAG 187

Query: 172 LSVVEARKVLELARNLKKK-GLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNV 230
           +++ E   +     +L ++ G+ V++I H++    +++ R+ VL+ G+ I     +E   
Sbjct: 188 MNLEEKEDMARYIVDLNEEWGMTVIMIEHDMGVVMDISHRVMVLEFGRKIAEGLPDEVMN 247

Query: 231 EEITEV 236
            E  +V
Sbjct: 248 NERVKV 253


Lambda     K      H
   0.318    0.137    0.371 

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: 153
Number of extensions: 7
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: 251
Length of database: 265
Length adjustment: 24
Effective length of query: 227
Effective length of database: 241
Effective search space:    54707
Effective search space used:    54707
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, 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