GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Pseudomonas fluorescens FW300-N2E3

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 AO353_03420 AO353_03420 phosphogluconate dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03420
          Length = 608

 Score =  197 bits (500), Expect = 1e-54
 Identities = 156/516 (30%), Positives = 250/516 (48%), Gaps = 49/516 (9%)

Query: 47  IGILNTWSDMTPCNGHLRELAEKVKAGVWEAGG---FPLEVPVFSASENTFRP---TAMM 100
           + I+++++DM   +       E++K  + E G    F   VP          P     + 
Sbjct: 68  VAIVSSYNDMLSAHQPYEHYPEQIKHALREIGSVGQFAGGVPAMCDGVTQGEPGMELGIA 127

Query: 101 YRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYFR 159
            R + A++   A+     D  ++L  CDK  P L+MGA     LP+I V GGPM++G   
Sbjct: 128 SREVIAMSTAVALSHNMFDAAMMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISN 187

Query: 160 GERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMA 219
            E+           +    G+ ++ E LE+E     S GTC   GTA+T   + E +G+ 
Sbjct: 188 KEKAD-------VRQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 220 LSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD---LKPSEIMTKQAFENAIRTNAAIGGS 276
           L G + +      R  + +    +I ++ K     +   EI+ +++  N+I    A GGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQITRLTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300

Query: 277 TNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRL 336
           TN  +H+ AIA   GI L+  D       VPT+ ++ P+GK  +  F  AGG+  +++ L
Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360

Query: 337 GEAGLLHKDALTV---------------SGETVWDEVKDVVNWNEDVILPAEKALTSSGG 381
            EAGLLH+D  TV               +GE VW E   + + +E+++ P  +A +  GG
Sbjct: 361 LEAGLLHEDVNTVAGHGLSRYTQEPFLENGELVWRE-GPIESLDENILRPVARAFSPEGG 419

Query: 382 IVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFED----IDDYKAKINDDNLDIDENCI 437
           + V+ GNL     V+K SA +P   V +  A+VF+D     D +KA +      ++++ +
Sbjct: 420 LRVMEGNLG--RGVMKVSAVAPEHQVVEAPAMVFQDQQDLADAFKAGL------LEKDFV 471

Query: 438 MVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSPEA 495
            VM+  GP+   GM E+  M     VL+     +  ++D RMSG A G +   +H SPEA
Sbjct: 472 AVMRFQGPRS-NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVSPEA 529

Query: 496 AVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARR 531
            VGG LA V+ GD+I +D     L L +  +E A R
Sbjct: 530 FVGGALARVQEGDIIRVDGVKGTLQLLVDADEFAAR 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: 773
Number of extensions: 40
Number of successful extensions: 8
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