GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11885 in Cronobacter condimenti 1330

Align Rhizopine-binding protein (characterized, see rationale)
to candidate WP_007675902.1 BN137_RS06865 galactose/glucose ABC transporter substrate-binding protein MglB

Query= uniprot:A0A0N9WNI6
         (308 letters)



>NCBI__GCF_000319285.1:WP_007675902.1
          Length = 331

 Score =  130 bits (328), Expect = 3e-35
 Identities = 98/300 (32%), Positives = 155/300 (51%), Gaps = 22/300 (7%)

Query: 1   MKTKIRFASLALSLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQ 60
           M  K+   S  +S ML   AA A  RIGV++ ++DD +++ +R++++K+A +  D V+L 
Sbjct: 1   MNKKVLTLSAVMSCMLFGTAAQAADRIGVTIYKYDDNFMSVVRKAIEKEASASSD-VQLL 59

Query: 61  FEDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDL 120
             D+++D  KQ  Q++  +++ V ++ +N VD AA   + E A    IP+V+ N+ P   
Sbjct: 60  MNDSQNDQSKQNDQIDVLLAKGVKSLAINLVDPAAAGTVIEKARGQNIPIVFFNKEPSRK 119

Query: 121 KLPK--GVITVASNDLEAGQMQMQYLAEKMK----------GKGDIVILLGDLANNSTTN 168
            L        V ++  E+G +Q   +A+  K          G+   V+L G+  +     
Sbjct: 120 ALDSYDKAYYVGTDSKESGIIQGDLIAKHWKANANWDLNKDGQIQYVLLKGEPGHPDAEA 179

Query: 169 RTKGV-KEVLAKYPGIKIDQEQ--TGTWSRDKGMTLVNDWLT--QGRKFDAIVSNNDEMA 223
           RT  V KE+  K  GIK  Q Q  T  W   +    ++ WL+     K + +++NND MA
Sbjct: 180 RTTYVIKELNDK--GIKTQQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMA 237

Query: 224 IGAAMALKQAGVEKGSVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMA 283
           +GA  ALK     K SV + GVD  P+ L  VK G LA +V  DAN QA  + D A  +A
Sbjct: 238 MGAVEALKAHN--KSSVPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLA 295


Lambda     K      H
   0.315    0.130    0.360 

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: 253
Number of extensions: 14
Number of successful extensions: 3
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: 308
Length of database: 331
Length adjustment: 28
Effective length of query: 280
Effective length of database: 303
Effective search space:    84840
Effective search space used:    84840
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 (21.5 bits)
S2: 48 (23.1 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