GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Acidovorax sp. GW101-3H11

Align phosphogluconate dehydratase (characterized)
to candidate Ac3H11_3523 Xylonate dehydratase (EC 4.2.1.82)

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3523
          Length = 593

 Score =  182 bits (462), Expect = 3e-50
 Identities = 148/477 (31%), Positives = 221/477 (46%), Gaps = 45/477 (9%)

Query: 146 DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYA 198
           D  +    CDK  P   MAA S   +PA+ +  GPM  G  + + V       R R+  A
Sbjct: 120 DAVVLTTGCDKTTPAGVMAA-STVDIPAIVLSGGPMLDGWHDGQLVGSGTVIWRSRRQLA 178

Query: 199 EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALT 258
            G++D    L+    S  + G C   GTA+T   V E +G+ LPG + +      R  + 
Sbjct: 179 AGEIDEEEFLQRACNSAPSAGHCNTMGTASTMNAVAEALGLSLPGCAAIPAPYRERGQMA 238

Query: 259 AAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQI 318
               R++  M     E +   +++  +  +N +  +   GGS+N  +H++AMAR AG+Q+
Sbjct: 239 YETGRRIVEMA---YEDLRPSRILTRESFLNALSVVSVAGGSSNAQVHIMAMARHAGVQL 295

Query: 319 NWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGL 378
              D++D +  +PL+  + P G      F  AGGVP L+ EL +AG LH D  +V G  +
Sbjct: 296 TAQDWTDHAYDLPLLLNMQPAGQFLGERFFRAGGVPALMWELQQAGKLHADCASVTGKTV 355

Query: 379 SRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKVLSGNL-GRAVMKTSAV 437
                        L  RE    + D  VI  F  P  H  G  VLSGNL    +MKTS +
Sbjct: 356 GE----------NLQGRE----THDREVIRPFSNPLMHKAGFMVLSGNLFDFGIMKTSVI 401

Query: 438 -----------PVENQVIEAPAVVFESQHDVMPAFE--AGLLDRDCVVVVRHQGPKA-NG 483
                      P +  + EA AVVFE   D        A  +D  C++V+R  GP    G
Sbjct: 402 SEAFRQRYLSRPGQEGIFEARAVVFEGADDYHARINDPALNIDEGCILVMRGAGPIGWPG 461

Query: 484 MPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDI 543
             E+  + PP  ++      +  + DGR SG +   PS ++ +PE+  GG L+ ++ GD 
Sbjct: 462 SAEVVNMQPPDALIKRGINTLPTLGDGRQSGTADS-PSILNASPESAVGGGLSWLQSGDT 520

Query: 544 IRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSAL-REKLSGAEQGAT 599
           +R++  TG    LV   E+A R+    DL A  V   +  + AL REK      GAT
Sbjct: 521 VRIDLNTGRCDALVTPEEIARRK---RDLPAPPVPASQSPWEALYREKTGQLADGAT 574


Lambda     K      H
   0.318    0.134    0.392 

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: 893
Number of extensions: 46
Number of successful extensions: 5
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: 603
Length of database: 593
Length adjustment: 37
Effective length of query: 566
Effective length of database: 556
Effective search space:   314696
Effective search space used:   314696
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