GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Marinobacter adhaerens HP15

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate GFF1457 HP15_1422 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__Marino:GFF1457
          Length = 240

 Score =  234 bits (597), Expect = 1e-66
 Identities = 118/238 (49%), Positives = 166/238 (69%)

Query: 23  IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82
           I +  ++K +G   VL+ ++L V +GE + + G SGSGKST++ CIN +E    GKI+VD
Sbjct: 2   ISVQNVHKSFGDLEVLKGVSLDVKKGEVVSVIGGSGSGKSTLLYCINAIEPINKGKILVD 61

Query: 83  GIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYL 142
            +++ +   N DK+R ++GMVFQ +N FPH+T+LEN  LAP  V+K+ K EA E A   L
Sbjct: 62  DVDVHAKETNKDKLRQKLGMVFQQWNSFPHMTVLENAALAPRIVKKMSKEEAIEIAKKEL 121

Query: 143 EKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQ 202
           E V + ++   YP ++SGGQQQR+AIAR+L MKP  ML DE TSALDPE++ EVLDT+  
Sbjct: 122 EHVGLGDKFDVYPTKMSGGQQQRLAIARALAMKPDYMLLDEVTSALDPELVGEVLDTLRL 181

Query: 203 LAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQI 260
           LAEEGMTM+CVTHEMGFA+ V++RV +  +G I E         +PQ+  T++FLS++
Sbjct: 182 LAEEGMTMICVTHEMGFARDVSDRVAYFHEGVIAEIGEARQVITDPQNPLTQKFLSKV 239


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: 177
Number of extensions: 9
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