GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8501301
          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.

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:

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