GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF4432 PS417_22690 phosphogluconate
           dehydratase
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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