GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Pseudomonas simiae WCS417

Align D-galactose-binding periplasmic protein DGAL aka MglB aka B2150, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF2331 PS417_11885 rhizopine-binding protein

Query= TCDB::P0AEE5
         (332 letters)



>FitnessBrowser__WCS417:GFF2331
          Length = 309

 Score =  133 bits (334), Expect = 7e-36
 Identities = 101/333 (30%), Positives = 168/333 (50%), Gaps = 32/333 (9%)

Query: 3   KKVLTLSAVMASMLFGAA-AHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPD---VQ 58
           K  +  +A+  SML  +  A AAD +IGV++  +DD F++ +R+ +++ AK+ P    VQ
Sbjct: 2   KTPIRFTALALSMLLASGVASAADLKIGVSMSAFDDTFLTYLREDMDKQAKSYPKGDGVQ 61

Query: 59  LLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPS 118
           L   D++ D  KQ  Q++  +++ V A+ +N VD A+   +I+ A    +P+VF N+ P 
Sbjct: 62  LQFEDARADVVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPD 121

Query: 119 RKALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDA 178
            + L     A  V +D  E+G +Q   IA+             G+   V+L G+  +   
Sbjct: 122 SQTLAPGVAA--VTSDDVEAGKLQMQYIAEKLG----------GKGNIVILLGDLANNST 169

Query: 179 EARTTYVIKELNDK--GIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDA 236
             RT  V KE+  K  GIK EQ Q  T +W   +    ++ WL+       + V++NND 
Sbjct: 170 TNRTKGV-KEVLTKYPGIKIEQEQ--TGIWLRDRGMTLVNDWLT--QGRDFQAVLSNNDE 224

Query: 237 MAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLA 296
           MA+GA  ALK+  K  + + GVD  P+ L  +  G +  +   DA  QA  + + A+ +A
Sbjct: 225 MAIGAAMALKSAGKKGVLIAGVDGTPDGLNAITKGDMTVSAFQDAKGQADKSVETARKMA 284

Query: 297 DGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEF 329
                    N  I+  VV +P+  +  DN+ +F
Sbjct: 285 --------KNEPIEQNVV-IPFQLITPDNVKDF 308


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: 230
Number of extensions: 8
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 332
Length of database: 309
Length adjustment: 28
Effective length of query: 304
Effective length of database: 281
Effective search space:    85424
Effective search space used:    85424
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