GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztA in Pantoea rwandensis LMG 26275

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_084938021.1 HA51_RS24860 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q52663
         (338 letters)



>NCBI__GCF_002095475.1:WP_084938021.1
          Length = 341

 Score =  353 bits (906), Expect = e-102
 Identities = 176/341 (51%), Positives = 230/341 (67%), Gaps = 3/341 (0%)

Query: 1   MKKSVFFGSVALAALVAGAASA---STLDDVKARGQLICGSNPGLTGFAAPDANGVYQGF 57
           MKK +    VA A+L+A A  A   +TLD +K +G + CG + GL GF+  DA+G + G 
Sbjct: 1   MKKMMLSTLVAAASLLAVAQQAHAGTTLDAIKKKGFVQCGISDGLPGFSYADASGKFTGI 60

Query: 58  DVAVCKAVAAAVLGDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFV 117
           DV VC+A AAAV GD  KVKY PLT + RFTAL SGEVD+L RN+TWT SRD  +   F 
Sbjct: 61  DVDVCRAAAAAVFGDASKVKYTPLTAKERFTALQSGEVDILSRNTTWTSSRDGGMGFLFA 120

Query: 118 AVNYYDGQGFMVNKSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADD 177
            VNYYDG GF+ +K  G+ SAKELDGAT+C+Q GT TE+N+AD+FKAN M YTPV     
Sbjct: 121 GVNYYDGIGFLTHKKAGLKSAKELDGATVCIQAGTDTELNVADYFKANKMQYTPVTFDRS 180

Query: 178 AEGQQKFAAGACDSYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGD 237
            E  +   +G CD+ ++D S L + R  L    D ++LPE+ISKEPLGPVVR GD++W  
Sbjct: 181 DESAKALDSGRCDTLSSDQSQLYALRVKLGKPDDFIVLPEVISKEPLGPVVRRGDDDWFT 240

Query: 238 IVRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAIL 297
           IV+WS +A++ AEE GI   N++++AA    P++  LLG EGD GK + LDN +A   I 
Sbjct: 241 IVKWSLFAMLNAEEMGINSKNVDQMAAKPTTPDMAHLLGAEGDFGKDLKLDNKWAYNIIK 300

Query: 298 ASGNYGEVFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338
             GNY EVF+ N+G  +++ +ARG NA W QGG+ YAPP R
Sbjct: 301 QVGNYQEVFDRNVGKDSALKIARGQNALWNQGGIQYAPPVR 341


Lambda     K      H
   0.316    0.132    0.384 

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: 340
Number of extensions: 9
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: 338
Length of database: 341
Length adjustment: 28
Effective length of query: 310
Effective length of database: 313
Effective search space:    97030
Effective search space used:    97030
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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