GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Phaeobacter inhibens BS107

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 GFF723 PGA1_c07380 dihydroxy-acid dehydratase IlvD

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Phaeo:GFF723
          Length = 571

 Score =  659 bits (1699), Expect = 0.0
 Identities = 327/568 (57%), Positives = 422/568 (74%), Gaps = 2/568 (0%)

Query: 12  RSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVK 71
           R++ WYG   +D   HR W+KNQG+P   FDGRP+IGI NTWS++TPCN  LR+LAE VK
Sbjct: 6   RNRAWYGKLDKDGFIHRSWMKNQGFPDHAFDGRPIIGICNTWSELTPCNSGLRDLAEGVK 65

Query: 72  AGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTT 131
            GVWEAGGFP+E PV S  E   +PTAM++RNL A+ VEE+IR   +DG VLL GCDKTT
Sbjct: 66  RGVWEAGGFPVEFPVMSLGETQMKPTAMLFRNLLAMDVEESIRAYGIDGVVLLGGCDKTT 125

Query: 132 PSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEA 191
           P  LMGAAS DLP+IVV+ GPMLNG ++G+ +GSGT +WKFSE V+AGEMT  +F+ AE+
Sbjct: 126 PGQLMGAASVDLPAIVVSSGPMLNGKWQGKDIGSGTDVWKFSEAVRAGEMTLQDFMAAES 185

Query: 192 SMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD 251
            MSRS G C TMGTASTMAS+ EA+GM+L  NAA+P VD+RR  +A LTG+RIV+MV++D
Sbjct: 186 GMSRSKGVCMTMGTASTMASLVEAMGMSLPTNAALPAVDARRMALAHLTGKRIVEMVEED 245

Query: 252 LKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVN 311
           +KPS+++T++AF NAI  NAA+GGSTNAV+HLLA+AGRVG +LSLDD+D  G D+P +VN
Sbjct: 246 IKPSDVLTREAFVNAIMANAAVGGSTNAVVHLLALAGRVGAELSLDDFD-LGSDIPLLVN 304

Query: 312 LMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNEDVILP 371
            MPSGKYLME+F YAGG+PVVLK+L + G L  +  TV G  +    +    +N+DVI  
Sbjct: 305 CMPSGKYLMEDFCYAGGMPVVLKQLADNGHLRSNT-TVLGGDILAYAEGAECFNDDVIKS 363

Query: 372 AEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLD 431
            ++ +  + G+ VLRGNLAP GA++KPSAA+ HLL H+G A VFE I+D KA I+ D+L 
Sbjct: 364 FDEPVKPAAGLRVLRGNLAPNGAIVKPSAATDHLLEHEGVAHVFETIEDMKANIDRDDLP 423

Query: 432 IDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVVLHT 491
           + ++ I+V+K  GPKGYPGM EVGNM +P K++++G+ DM+RISD RMSGTA+GTV+LH 
Sbjct: 424 VTKDSILVLKGVGPKGYPGMPEVGNMPIPRKLVREGVRDMIRISDGRMSGTAFGTVILHV 483

Query: 492 SPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQ 551
           SPE+  GGPL +V+ GD I +   N  L L +S+EEL  R   WQP     T GYA L+ 
Sbjct: 484 SPESQAGGPLGLVQTGDRIRVSAKNGTLDLLVSEEELTARREAWQPEPLHYTRGYAKLYV 543

Query: 552 QHVEGADTGADLDFLKGCRGNAVGKDSH 579
             V  A+ GADLDFL G     V ++SH
Sbjct: 544 DSVLQAEKGADLDFLVGKDTRPVTRESH 571


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: 1062
Number of extensions: 50
Number of successful extensions: 3
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: 571
Length adjustment: 36
Effective length of query: 543
Effective length of database: 535
Effective search space:   290505
Effective search space used:   290505
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