GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dgoD in Desulfovibrio vulgaris Miyazaki F

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 8501301 DvMF_2034 dihydroxy-acid dehydratase (RefSeq)

Query= SwissProt::B5ZZ34
         (579 letters)



>lcl|FitnessBrowser__Miya:8501301 DvMF_2034 dihydroxy-acid
           dehydratase (RefSeq)
          Length = 555

 Score =  317 bits (813), Expect = 6e-91
 Identities = 193/547 (35%), Positives = 301/547 (55%), Gaps = 22/547 (4%)

Query: 27  HRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPV 86
           HR  L   G   +  + RP++G++N  +++ P + HL  +AE VKAGV  AGG P+E P 
Sbjct: 15  HRSLLHALGLTREEIE-RPLVGVVNAANEVVPGHVHLHTIAEAVKAGVRAAGGTPMEFPA 73

Query: 87  FSASENTFRPTAMMY-----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASC 141
            +  +        M+     R + A ++E      P D  V +  CDK+ P +LM     
Sbjct: 74  IAVCDGLAMNHEGMHFSLPSREIIADSIEIMATAHPFDALVFIPNCDKSVPGMLMAMLRM 133

Query: 142 DLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEM--VKAGEMTQAEFLEAEASMSRSSGT 199
           D+PSI+V+GGPML G   G   G    +  F  +  V+ G+MT AE  E   +     G+
Sbjct: 134 DIPSIMVSGGPMLAG---GTLAGRTDLISVFEAVGRVQRGDMTMAELDEMTETACPGCGS 190

Query: 200 CNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMT 259
           C  M TA+TM  MAE +G+AL GN  IP V + R  +A+  G +++++++ ++ P  I+T
Sbjct: 191 CAGMFTANTMNCMAETMGLALPGNGTIPAVTAARVRLAKHAGMKVMELLEKNITPRSIVT 250

Query: 260 KQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYL 319
            +A  NA+  + A+GGSTN V+HL A+ G  G+DL+LD +D   R  P +  L P+G + 
Sbjct: 251 PRAVANAVAVDMALGGSTNTVLHLPAVFGEAGLDLTLDIFDEVSRKTPNLCKLSPAGHHH 310

Query: 320 MEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVN--WNEDVILPAEKALT 377
           +++   AGG+P V+  L   GL+    +TV+G+T+ + + ++     N DVI  A+   +
Sbjct: 311 IQDLHAAGGIPAVMAELTRKGLVDTSVMTVTGKTLAENLAELNARVLNPDVIRSADAPYS 370

Query: 378 SSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCI 437
           + GGI +L+G+LAP+GAV+K SA +P ++V +  A VF+   +  A I      I++   
Sbjct: 371 AQGGIAILKGSLAPQGAVVKQSAVAPEMMVREAVARVFDSEGEAHAAIMGGK--INKGDA 428

Query: 438 MVMKNCGPKGYPGMAEVGNMGLPPKVLKKGI---LDMVRISDARMSGTAYGTVVLHTSPE 494
           ++++  GP+G PGM E+    L P     G+    D+  I+D R SG   G  + H SPE
Sbjct: 429 IIIRYEGPRGGPGMREM----LSPTAAIAGMGLGADVALITDGRFSGGTRGAAIGHVSPE 484

Query: 495 AAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQQHV 554
           AA GG + +V+ GD I +D+P RRL L + + ELA R   + P     TS     + + V
Sbjct: 485 AADGGNIGLVREGDHILIDIPARRLDLLVDEAELAARRETFVPLEKPVTSPLLRRYARQV 544

Query: 555 EGADTGA 561
             A TGA
Sbjct: 545 TSAATGA 551


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: 861
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: 579
Length of database: 555
Length adjustment: 36
Effective length of query: 543
Effective length of database: 519
Effective search space:   281817
Effective search space used:   281817
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 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