GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Cupriavidus basilensis 4G11

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 RR42_RS33305 RR42_RS33305 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Cup4G11:RR42_RS33305
          Length = 579

 Score =  550 bits (1416), Expect = e-161
 Identities = 268/579 (46%), Positives = 380/579 (65%), Gaps = 3/579 (0%)

Query: 1   MKKKAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCN 60
           M  + + P  LRS  W+         HR  +   GY  D +  RP+I I+NTWSD+ PC+
Sbjct: 1   MTSRKKTPETLRSARWFAPDDLRSSGHRSRIMQMGYSPDEWLDRPIIAIINTWSDINPCH 60

Query: 61  GHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDG 120
            H ++  + VK G+ +AGGFP+E+P  S SE+  +PT M+YRN+ A+  EE IR  P+DG
Sbjct: 61  SHFKQRVDDVKRGILQAGGFPIELPAISLSESAVKPTTMLYRNMLAMEAEELIRSHPVDG 120

Query: 121 CVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGE 180
            VL+ GCDKTTP LLMGA+S  +P+I V  GPML G ++G  +GSG+  WKF +  +AG 
Sbjct: 121 AVLMGGCDKTTPGLLMGASSAGVPAIYVPAGPMLRGNWKGNVLGSGSDAWKFWDERRAGN 180

Query: 181 MTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLT 240
           +++ E++  E  ++RS GTC TMGTASTM ++AEA+GM L G ++IP  D+    M    
Sbjct: 181 ISKTEWIGIEGGIARSHGTCMTMGTASTMTAIAEAIGMTLPGASSIPAADANHIRMCSEA 240

Query: 241 GRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWD 300
           GRRIV MV +DL P  I T+ +FENAI    A+G STNA+IH++A+A R G D+ L+D+D
Sbjct: 241 GRRIVDMVWEDLTPQRIQTRASFENAIAVAMAMGCSTNAIIHVIAMARRAGHDIGLEDFD 300

Query: 301 RCGRDVPTIVNLMPSG-KYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVK 359
           +  R VP I N+ PSG KYLME+FFYAGGLP ++ R+ +   L+ DALTV+G T+ + + 
Sbjct: 301 KTSRHVPVIANIRPSGDKYLMEDFFYAGGLPALMNRISDK--LNLDALTVTGRTLGENIA 358

Query: 360 DVVNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDID 419
               +N+DVI   E AL   G + VL+GN+AP G V+KPSA       H G A+VF+D  
Sbjct: 359 GAEVYNDDVIRTKENALYQEGALAVLKGNIAPDGCVIKPSACEKRFFKHTGPALVFDDYP 418

Query: 420 DYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARM 479
             K  +  D+LD+  + I++++N GP+G PGM E G + +P K++++G+ DM+R+SDARM
Sbjct: 419 SMKEAVERDDLDVTADHILILRNAGPQGGPGMPEWGMLPIPKKLVQQGVRDMLRMSDARM 478

Query: 480 SGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNH 539
           SGT+YG  +LH SPE+ +GGP A+V+ GDMI +D+  R +HL++SDEELARR A W P  
Sbjct: 479 SGTSYGACILHVSPESYIGGPFALVRTGDMISVDIDRRSIHLEVSDEELARRKAAWTPPP 538

Query: 540 DLPTSGYAFLHQQHVEGADTGADLDFLKGCRGNAVGKDS 578
                GY ++  +H+  A+ G D DFL+   G   G+ S
Sbjct: 539 PRFGRGYGWMFSKHIRQANDGCDFDFLQTDFGAPTGEPS 577


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: 41
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: 579
Length adjustment: 36
Effective length of query: 543
Effective length of database: 543
Effective search space:   294849
Effective search space used:   294849
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:

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