GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Pseudomonas fluorescens FW300-N2E3

Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate AO353_21380 AO353_21380 rhizopine-binding protein

Query= TCDB::P0AEE5
         (332 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_21380
          Length = 308

 Score =  135 bits (339), Expect = 2e-36
 Identities = 99/332 (29%), Positives = 169/332 (50%), Gaps = 31/332 (9%)

Query: 3   KKVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPD-VQLLM 61
           K  +  +++  S++  + A  AD RIGV++ ++DD +++ +R+++++ AK+ PD V+L  
Sbjct: 2   KTKIRFASLALSLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQF 61

Query: 62  NDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKA 121
            D+++D  KQ  Q++  +++ V A+ +N VD AA   + E A    +P+V+ N+ P    
Sbjct: 62  EDARSDVVKQLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLK 121

Query: 122 LDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEAR 181
           L        V ++  E+G +Q   +A+             G+   V+L G+  +     R
Sbjct: 122 LPK--GVITVASNDLEAGQMQMQYLAE----------KMKGKGDIVILLGDLANNSTTNR 169

Query: 182 TTYVIKELNDK--GIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAM 239
           T  V KE+  K  GIK +Q Q  T  W   +    ++ WL+     K + +++NND MA+
Sbjct: 170 TKGV-KEVLAKYPGIKIDQEQ--TGTWSRDKGMTLVNDWLT--QGRKFDAIVSNNDEMAI 224

Query: 240 GAVEALK--AHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLAD 297
           GA  ALK     K S+ + GVD  P+ L  VK G LA +V  DAN QA  + D A  +A 
Sbjct: 225 GAAMALKQAGVEKGSVLIAGVDGTPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAK 284

Query: 298 GKGAADGTNWKIDNKVVRVPYVGVDKDNLAEF 329
            +            + V VPY  +  +N+ +F
Sbjct: 285 NEPV---------EQAVWVPYRLITPENVDQF 307


Lambda     K      H
   0.313    0.129    0.363 

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: 255
Number of extensions: 13
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: 332
Length of database: 308
Length adjustment: 28
Effective length of query: 304
Effective length of database: 280
Effective search space:    85120
Effective search space used:    85120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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