GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_01488
          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.

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