GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Hippea jasoniae Mar08-272r

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_035587918.1 EK17_RS04610 phosphate ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_000744435.1:WP_035587918.1
          Length = 252

 Score =  141 bits (355), Expect = 2e-38
 Identities = 86/255 (33%), Positives = 144/255 (56%), Gaps = 12/255 (4%)

Query: 17  VSDEIAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEE--- 73
           +S+ I I +  +N +YG   VL+DINL++++ +   + GPSG GK+T +RC NR+ +   
Sbjct: 1   MSENILISVEHLNFYYGNNQVLKDINLSIYKNKITALIGPSGCGKTTFLRCFNRMHDLYK 60

Query: 74  --HQSGKIIVDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131
                GKII  G  + +  K I ++R ++GMVFQ    FP ++I +N+           K
Sbjct: 61  NNRYEGKIIYQGENILT-TKRIIELRGKIGMVFQKPTPFP-MSIFDNVAYGLKLKGVKNK 118

Query: 132 REAEETAMYYLEKV----KIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSA 187
            E  E     L++     ++ ++  +    LSGGQQQR+ IAR L ++P I+LFDEPTSA
Sbjct: 119 EEIRERVEKALKQAALWDEVKDKLFESGLSLSGGQQQRLVIARVLAVEPDIILFDEPTSA 178

Query: 188 LDPEMIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHN 247
           LDP    ++ + + +L +   T+L VTH M  A  +++   F+  G+++E +     F N
Sbjct: 179 LDPIATAKIEELVSEL-KNITTILIVTHNMQQAARISDFTAFLFKGELIEFSETEKLFTN 237

Query: 248 PQSERTKQFLSQILG 262
           P+ E T+++++   G
Sbjct: 238 PEKELTERYITGRFG 252


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: 160
Number of extensions: 6
Number of successful extensions: 4
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: 252
Length adjustment: 24
Effective length of query: 239
Effective length of database: 228
Effective search space:    54492
Effective search space used:    54492
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: 47 (22.7 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