GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Pseudomonas simiae WCS417

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate GFF4432 PS417_22690 phosphogluconate dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__WCS417:GFF4432
          Length = 608

 Score =  201 bits (512), Expect = 5e-56
 Identities = 155/513 (30%), Positives = 248/513 (48%), Gaps = 43/513 (8%)

Query: 47  IGILNTWSDMTPCNGHLRELAEKVKAGVWE-------AGGFPLEVPVFSASENTFRPTAM 99
           + I+++++DM   +       E++K  + E       AGG P      +  E      ++
Sbjct: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREVGSVGQFAGGTPAMCDGVTQGEPGME-LSL 126

Query: 100 MYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYF 158
           + R + A++   A+     D  ++L  CDK  P L+MGA     LP I V GGPM +G  
Sbjct: 127 LSREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRYGHLPMIFVPGGPMPSGIS 186

Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218
             ++           +    G+ T+ E LE+E     S GTC   GTA+T   + E +G+
Sbjct: 187 NKQKAD-------VRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239

Query: 219 ALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD---LKPSEIMTKQAFENAIRTNAAIGG 275
            L G + +      R  + +    ++ ++ K +   +   EI+ +++  N+I    A GG
Sbjct: 240 HLPGASFVNPYTPLRDALTREAAHQVTRLTKANGSFMPIGEIVDEKSIVNSIIALNATGG 299

Query: 276 STNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKR 335
           STN  +H+ AIA   GI L+ DD       VPT+ ++ P+GK  +  F  AGG+  +++ 
Sbjct: 300 STNHTLHMPAIAMSAGIILTWDDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRE 359

Query: 336 LGEAGLLHKDALTVS---------------GETVWDEVKDVVNWNEDVILPAEKALTSSG 380
           L EAGLLH+D  TV+               GE +W E   + + +E ++ P  +A +  G
Sbjct: 360 LLEAGLLHEDVNTVAGKGLSRYTQEPFLVDGELIWRE-GPIESLDETILRPVARAFSPEG 418

Query: 381 GIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVM 440
           G+ V+ GNL     V+K SA +P   + +  AVVF+D  D         L+ D   + VM
Sbjct: 419 GLRVMEGNLG--RGVMKVSAVAPEHQIVEAPAVVFQDQQDLADAFKAGQLEKD--FVAVM 474

Query: 441 KNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSPEAAVG 498
           +  GP+   GM E+  M     VL+     +  ++D RMSG A G +   +H +PEA  G
Sbjct: 475 RFQGPRS-NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVNPEAQSG 532

Query: 499 GPLAVVKNGDMIELDVPNRRLHLDISDEELARR 531
           GPLA V++GD+I +D     L L +  EE A R
Sbjct: 533 GPLARVRDGDIIRVDGVKGTLELKVDAEEFAAR 565


Lambda     K      H
   0.318    0.135    0.408 

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: 766
Number of extensions: 46
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: 579
Length of database: 608
Length adjustment: 37
Effective length of query: 542
Effective length of database: 571
Effective search space:   309482
Effective search space used:   309482
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 (21.7 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