GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Herbaspirillum seropedicae SmR1

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate HSERO_RS00320 HSERO_RS00320 peptide ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__HerbieS:HSERO_RS00320
          Length = 240

 Score =  264 bits (674), Expect = 1e-75
 Identities = 127/239 (53%), Positives = 177/239 (74%)

Query: 23  IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82
           I+++Q+ K +GQ H+LR I+  +   E + + GPSGSGKST +RC+N LEE   G I ++
Sbjct: 2   IKVNQLQKRFGQAHILRGIDCEIRAREVVCVIGPSGSGKSTFLRCLNGLEEVSDGDIFIE 61

Query: 83  GIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYL 142
           G++L     N++ +R+E+GMVFQ FNLFPH+T+LENL +AP+ V+K+ +REA   A   L
Sbjct: 62  GVKLNDPKVNLNALRAELGMVFQRFNLFPHMTVLENLIMAPMQVKKLSRREAVLVAEKLL 121

Query: 143 EKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQ 202
           +KV + ++   +P QLSGGQQQRVAIAR+L M+PK+MLFDEPTSALDPE++ EVL  M Q
Sbjct: 122 QKVGLLDKIDAFPNQLSGGQQQRVAIARALAMEPKVMLFDEPTSALDPELVGEVLTVMKQ 181

Query: 203 LAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQIL 261
           LAEEGMTM+ VTHEMGFA+ V++RV+F+  G I+E+  P     +P  ERT+ FL ++L
Sbjct: 182 LAEEGMTMVVVTHEMGFAREVSDRVLFIDQGVIMEEGPPQQVLGDPHHERTRDFLRKVL 240


Lambda     K      H
   0.320    0.134    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: 204
Number of extensions: 6
Number of successful extensions: 1
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: 263
Length of database: 240
Length adjustment: 24
Effective length of query: 239
Effective length of database: 216
Effective search space:    51624
Effective search space used:    51624
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