GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztA in Sinorhizobium meliloti 1021

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate SMc00676 SMc00676 amino acid-binding periplasmic signal peptide protein

Query= TCDB::Q52663
         (338 letters)



>FitnessBrowser__Smeli:SMc00676
          Length = 331

 Score =  348 bits (892), Expect = e-100
 Identities = 170/328 (51%), Positives = 223/328 (67%), Gaps = 1/328 (0%)

Query: 11  ALAALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKAVAAAVL 70
           A A L    A A+TLD VK RG+L CG + G+ GF+APD  G + GFD+  C+AVAAA L
Sbjct: 5   ATAFLAGTTAQAATLDVVKQRGELRCGVSQGVLGFSAPDDKGEWSGFDIDFCRAVAAATL 64

Query: 71  GDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYDGQGFMVN 130
           G P KVKYVPL+ + RFTAL SGEVD+L R +TWT SRDT+L + FV VNYYDGQ FMV 
Sbjct: 65  GSPDKVKYVPLSTKERFTALQSGEVDLLSRQTTWTLSRDTDLGMSFVGVNYYDGQAFMVR 124

Query: 131 KSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQKFAAGACD 190
             +GV S KEL GA++C +TGTTTE N+AD+F AN + Y  +      +  Q F +G CD
Sbjct: 125 GDIGVKSVKELSGASVCTETGTTTEQNMADYFSANKIEYQVIAFEKADQTIQAFNSGRCD 184

Query: 191 SYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSFYALVAAE 250
            Y+TDAS L S R TL +    V+LPE+ISKEPLGP VR GD+ W  +VRW+ +A++ AE
Sbjct: 185 VYSTDASALYSQRLTLNDPDRFVVLPEVISKEPLGPAVRQGDDQWFKVVRWTLFAMIEAE 244

Query: 251 EYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYGEVFEANI 310
           E GIT+ N   +  S    + +R LG++ + GK +GLD  +A + + A GNYGE+FE ++
Sbjct: 245 ELGITRENAASLLESGTAAQ-KRFLGIDNEAGKALGLDPKWAYQTVAAVGNYGEIFERHL 303

Query: 311 GASTSIGLARGLNAQWTQGGLMYAPPFR 338
           G  +++ + RGLN  W  GGL+YAPP R
Sbjct: 304 GKESALRIDRGLNKLWNNGGLIYAPPVR 331


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: 310
Number of extensions: 11
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: 331
Length adjustment: 28
Effective length of query: 310
Effective length of database: 303
Effective search space:    93930
Effective search space used:    93930
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 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