GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmB in Pseudomonas fluorescens FW300-N1B4

Align beta-Phosphoglucomutase (EC 5.4.2.6) (characterized)
to candidate Pf1N1B4_3808 hydrolase, haloacid dehalogenase-like family

Query= BRENDA::P71447
         (221 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3808
          Length = 231

 Score = 86.3 bits (212), Expect = 4e-22
 Identities = 63/192 (32%), Positives = 96/192 (50%), Gaps = 14/192 (7%)

Query: 3   KAVLFDLDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLADK 62
           KAV+FD+DG++ DT   +      +A   G    D    + + G    D  + +++  D 
Sbjct: 12  KAVIFDMDGLLLDTEGIYTEVTSIIAGRYG-RTFDWSVKQNIIGRGAGDLARYVVEALDL 70

Query: 63  KVSAEEFKELAKRKNDNYVKMIQDVSPADVYPGILQLLKDLRSNKIKIALASASKNGPFL 122
            ++AEEF  + +        M +    A   PG  +L++ L++N I IA+ ++S    F 
Sbjct: 71  PITAEEFLVIREPL------MRERFPTALAMPGAEELVRHLKANNIPIAVGTSSSRQSFG 124

Query: 123 LEKMNLT----GYFDAI--ADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQ 176
            EK  L       FD I  AD  EV A+KPAPDIF+ AA  +GVAP + +  EDS  G+ 
Sbjct: 125 -EKTTLHREWFALFDFIVTADDPEVGAAKPAPDIFLTAARRLGVAPGDCLVFEDSPFGVT 183

Query: 177 AIKDSGALPIGV 188
           A K +G   I +
Sbjct: 184 AAKAAGMTAIAI 195


Lambda     K      H
   0.316    0.135    0.377 

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: 119
Number of extensions: 8
Number of successful extensions: 2
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: 221
Length of database: 231
Length adjustment: 22
Effective length of query: 199
Effective length of database: 209
Effective search space:    41591
Effective search space used:    41591
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 (21.6 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