GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Burkholderia phytofirmans PsJN

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 BPHYT_RS04815 BPHYT_RS04815 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__BFirm:BPHYT_RS04815
          Length = 557

 Score =  307 bits (787), Expect = 6e-88
 Identities = 201/539 (37%), Positives = 300/539 (55%), Gaps = 21/539 (3%)

Query: 35  GYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTF 94
           GY    FD +P+IGI N  S +TPCN  L+ LA+   A +  A   P      + S+   
Sbjct: 27  GYEKADFD-KPMIGIANGHSTITPCNAGLQRLADAAVAAIKGADANPQIFGTPTISDGMS 85

Query: 95  RPT-----AMMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVT 149
             T     +++ R + +  +E  ++GQ MDG V++ GCDK  P  ++G    ++PSI V 
Sbjct: 86  MGTEGMKYSLVSREVISDCIETCVQGQWMDGVVVIGGCDKNMPGGMIGMLRTNVPSIYVY 145

Query: 150 GGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTM 209
           GG +  G ++G  +   +      E   AG M+Q +F   E +   S+G+C  M TA+TM
Sbjct: 146 GGTIRPGNWKGTDLTIVSSFEAVGEFT-AGRMSQEDFDGIEQNACPSTGSCGGMYTANTM 204

Query: 210 ASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRT 269
           +S  EALGM+L  ++ +   D  +   A  + R +V+ VK DLKP +I+TK++ ENA+  
Sbjct: 205 SSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVESVKKDLKPRDIVTKKSIENAVAV 264

Query: 270 NAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGL 329
             A GGSTNAV+H LAIA    ++ S+DD++R  + VP I NL PSG+++  +   AGG+
Sbjct: 265 IMATGGSTNAVLHFLAIAHAAEVEWSIDDFERMRKKVPVICNLKPSGQFVATDLHKAGGI 324

Query: 330 PVVLKRLGEAGLLHKDALTVSGETVWDEVKDV---VNWNEDVILPAEKALTSSGGIVVLR 386
           P V+K L +AGLLH D +T++G T+ +E+KDV      ++ VI P ++AL   G + +L+
Sbjct: 325 PQVMKILLDAGLLHGDCITITGRTIAEELKDVPGKPRADQQVIFPIDQALYKEGHLAILK 384

Query: 387 GNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPK 446
           GNLA  GAV K +     ++   G A VF+D       I  D +   +  ++V++  GPK
Sbjct: 385 GNLAVDGAVAKITGLKNPVIT--GPARVFDDEQSALEAILADKIVAGD--VVVLRYLGPK 440

Query: 447 GYPGMAEVGNMGLPPKVLKKGILDMV-RISDARMSGTAYGTVVLHTSPEAAVGGPLAVVK 505
           G PGM E+  +     ++ KG+ + V  I+D R SG  +G VV H +PEA VGG +A V+
Sbjct: 441 GGPGMPEM--LAPTSAIIGKGLGESVGLITDGRFSGGTWGMVVGHVAPEAFVGGTIAFVQ 498

Query: 506 NGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSG----YAFLHQQHVEGADTG 560
            GD I +D     L L+I + EL RR A WQ      T G    Y  L Q   +GA TG
Sbjct: 499 EGDSITIDAHKLLLQLNIDNAELERRRAAWQQPKPRYTRGVMAKYFALAQPANKGAITG 557


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: 913
Number of extensions: 58
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 579
Length of database: 557
Length adjustment: 36
Effective length of query: 543
Effective length of database: 521
Effective search space:   282903
Effective search space used:   282903
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