GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Pseudomonas fluorescens FW300-N2C3

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 AO356_24585 AO356_24585 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_24585
          Length = 578

 Score =  741 bits (1912), Expect = 0.0
 Identities = 369/571 (64%), Positives = 446/571 (78%), Gaps = 2/571 (0%)

Query: 11  LRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKV 70
           LRS +W+G   ++   +R W+KNQG     F G+P+IGI NTWS++TPCN H R++AE V
Sbjct: 8   LRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAEHV 67

Query: 71  KAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKT 130
           K GV EAGGFP+E PVFS  E+  RPTAM+ RNLA++ VEEAIRG P+DG VLL GCDKT
Sbjct: 68  KRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVLLTGCDKT 127

Query: 131 TPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAE 190
           TP+LLMGAASCD+P+IVVTGGPMLNG  +G+ +GSGT +W+ SE VKAG +T  +FL AE
Sbjct: 128 TPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSGTVVWQLSEQVKAGTITIDDFLAAE 187

Query: 191 ASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKD 250
             MSRS+GTCNTMGTASTMA MAEALG +L  NAAIP VD+RR V+A ++G R V+MV++
Sbjct: 188 GGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRAVEMVRE 247

Query: 251 DLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIV 310
           DLK S+I+TK+AFENAIR NAAIGGSTNAVIHL AIAGR+G+ L LDDW R GR +PTIV
Sbjct: 248 DLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVQLDLDDWTRIGRGMPTIV 307

Query: 311 NLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLL-HKDALTVSGETVWDEVKDVVNWNED-V 368
           +L PSG++LMEEF+YAGGLP VL+RLGEA L+ + +ALTV+G+++ +  KD   + +D V
Sbjct: 308 DLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSLGENTKDAPIYGQDEV 367

Query: 369 ILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDD 428
           I   +  + + GGI VLRGNLAP GAVLKPSAA+  L+ H+GRAVVFE+ D+YKA+IND 
Sbjct: 368 IRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATAELMQHRGRAVVFENFDEYKARINDP 427

Query: 429 NLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTVV 488
            LD+D N I+VMKNCGPKGYPGMAEVGNMGLP K+L +G+ DMVRISDARMSGTAYGTVV
Sbjct: 428 ELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAYGTVV 487

Query: 489 LHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYAF 548
           LH +PEAA GGPLA VK GD IELD  + RLHLDI D ELA RLA+  P   L   GY  
Sbjct: 488 LHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIPDAELAARLADLAPPQQLLVGGYRQ 547

Query: 549 LHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579
           L+  HV  AD G D DFL GCRG  V + SH
Sbjct: 548 LYIDHVLQADQGCDFDFLVGCRGAEVPRHSH 578


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: 1136
Number of extensions: 63
Number of successful extensions: 4
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: 578
Length adjustment: 36
Effective length of query: 543
Effective length of database: 542
Effective search space:   294306
Effective search space used:   294306
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