GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Pseudomonas fluorescens GW456-L13

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate PfGW456L13_3725 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= curated2:P31961
         (608 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725
          Length = 560

 Score =  219 bits (558), Expect = 2e-61
 Identities = 156/493 (31%), Positives = 243/493 (49%), Gaps = 32/493 (6%)

Query: 113 DGVTQGEPGMELSLASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLP 172
           DG+  G  GM+ SL SR+VIA S  +      FD  + +G CDK +PG LIG  R    P
Sbjct: 86  DGIANGTEGMKYSLVSREVIADSIEVVTGCEGFDGLVTIGGCDKNMPGCLIGMARLNR-P 144

Query: 173 TVFVPAGPMPTGISNKEKAAVRQLF---AEGKATREELLASEMASYHAPGTCTFYGTANT 229
           ++FV  G +  G  + +  +V +     A G  +  ++   E  +   PG+C    TANT
Sbjct: 145 SIFVYGGTIQPGAGHTDIISVFEAVGQHARGDISEIQVKQIEEVAIPGPGSCGGMYTANT 204

Query: 230 NQLLVEVMGLHLPGASFVNPNTPLRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVN 289
               +E +G+ LPG+S  +     +   +  A +Q   L   +   +   +I+  KA  N
Sbjct: 205 MASAIEALGMSLPGSSSQDAIGADKASDSFRAGQQVMELLKLD---LKPRDIMTRKAFEN 261

Query: 290 SVVALLATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADINHFQA 349
           ++  ++A  GSTN  LHLLA+A A  ++LT  D  EL  V P +A + P+G+  ++   A
Sbjct: 262 AIRVVIALAGSTNAVLHLLAMANAVDVELTLDDFVELGKVSPVVADLRPSGKYMMSELVA 321

Query: 350 AGGMSFLIRQLLDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRP 409
            GG+  L++++LD G+LH DV TV G  L                   P+    + ++RP
Sbjct: 322 IGGIQPLMKRMLDAGMLHGDVLTVTGQTLAENLASV------------PDYPAGQDVIRP 369

Query: 410 LDKPFSAEGGLRLMEGNLGRGVMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERD 469
            D+P   +  L ++ GNL            E    E   R++H +    A    GE++  
Sbjct: 370 FDQPIKKDSHLVILRGNLSPTGAVAKITGKEGLRFEGTARVYHGEEGALAGILNGEVQPG 429

Query: 470 LVAVVRFQGPRAN-GMPELHKLTPFLGVL-QDRGFKVALVTDGRMSGASGKVPAAIHVSP 527
            V V+R++GP+   GM E+  L+P   V+ +  G +VAL+TDGR SG S       H++P
Sbjct: 430 EVIVIRYEGPKGGPGMREM--LSPTSAVMGKGLGKEVALITDGRFSGGSHGFVVG-HITP 486

Query: 528 EAIAGGPLARLRDGDRVRVDGVNGELRVLVDD---AEWQARSLEPAPQDGNLGCGRELFA 584
           EA  GGP+A + +GDR+ +D     + V V D   AE ++R + P  +       R + A
Sbjct: 487 EAFEGGPIALVENGDRIIIDAETRLITVDVSDAVLAERKSRWVRPESK-----YKRGVLA 541

Query: 585 FMRNAMSSAEEGA 597
                +SSA EGA
Sbjct: 542 KYAKTVSSASEGA 554


Lambda     K      H
   0.319    0.135    0.397 

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: 808
Number of extensions: 48
Number of successful extensions: 6
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: 608
Length of database: 560
Length adjustment: 36
Effective length of query: 572
Effective length of database: 524
Effective search space:   299728
Effective search space used:   299728
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: 53 (25.0 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