GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dgoD in Caulobacter crescentus NA1000

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 CCNA_01488 CCNA_01488 dihydroxyacid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01488 CCNA_01488 dihydroxyacid
           dehydratase
          Length = 600

 Score =  450 bits (1158), Expect = e-131
 Identities = 252/574 (43%), Positives = 354/574 (61%), Gaps = 19/574 (3%)

Query: 9   RKLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65
           R LRS+ W+          +Y   +L       +L  G+P+IGI  T SD++PCN H   
Sbjct: 9   RALRSRAWFDNPDNIDMTALYLERYLNFGLTLEELQSGKPIIGIAQTGSDLSPCNRHHLV 68

Query: 66  LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125
           LAE+V+ G+  AGG  LE PV    E   RPTA + RNL+ L + E + G P+DG VL +
Sbjct: 69  LAERVREGIRSAGGIALEFPVHPIQETGKRPTAGLDRNLSYLGLVELLYGYPLDGVVLTI 128

Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185
           GCDKTTP+ LM AA+ ++P+I ++ GPMLNG+ +G+R GSGT +WK  EM+ AGE+  A 
Sbjct: 129 GCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGKRTGSGTIVWKAREMLAAGEIDNAG 188

Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245
           F++  AS + S+G CNTMGTA+TM S+ EALGM+L G+AAIP     R+  A  TG RIV
Sbjct: 189 FIKLVASSAPSTGYCNTMGTATTMNSLTEALGMSLPGSAAIPAPYRDRQENAYRTGLRIV 248

Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305
           +MV +DLKPS+I+T++AF NAI  N+AIGGSTNA IHL A+A  + +DL+L+DW+  G+D
Sbjct: 249 EMVAEDLKPSDILTREAFLNAIVVNSAIGGSTNAPIHLNALARHMDVDLTLEDWETAGKD 308

Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWN 365
           VP +VNL P+G+YL E+++ AGG+P V  +L E GL+H+DA  VSG+++ ++ +  V  +
Sbjct: 309 VPLLVNLQPAGEYLGEDYYRAGGVPAVFGQLIEQGLIHQDARAVSGQSIGEQYRGAVIED 368

Query: 366 EDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVH-----------KGRAVV 414
           EDVI P  + L    G  ++RGNL    A++K S  S                 +G A+V
Sbjct: 369 EDVIRPFARPLVEHAGFAIMRGNLF-NSAIMKTSVISEEFRARYLSNPDDPDAFEGNAIV 427

Query: 415 FEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRI 474
           F+  +DY  +I+D  L I    I+ M+  GP GYPG AEV NM  P  ++K+GI  +  I
Sbjct: 428 FDGPEDYHHRIDDPALGITAYSILFMRGAGPIGYPGSAEVVNMRAPNYLIKQGIHQLPCI 487

Query: 475 SDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELA--RRL 532
            D R SGT+    +L+ SPEAA GG LA++K GD +  D+   R+ + +S  E+   RR 
Sbjct: 488 GDGRQSGTSGSPSILNASPEAAAGGGLALLKTGDRVRFDLRKSRVDVLVSASEVVERRRA 547

Query: 533 AEWQPNHDLPTSGYAFLHQQH--VEGADTGADLD 564
            E    +  P S   +   Q   V   DTGA L+
Sbjct: 548 LEAAGGYAYPESQTPWQEIQRAVVGQMDTGAVLE 581


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: 928
Number of extensions: 59
Number of successful extensions: 2
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: 600
Length adjustment: 37
Effective length of query: 542
Effective length of database: 563
Effective search space:   305146
Effective search space used:   305146
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