GapMind for catabolism of small carbon sources

 

Aligments for a candidate for edd in Paraburkholderia bryophila 376MFSha3.1

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate H281DRAFT_00127 H281DRAFT_00127 dihydroxyacid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00127 H281DRAFT_00127
           dihydroxyacid dehydratase
          Length = 557

 Score =  215 bits (547), Expect = 5e-60
 Identities = 150/471 (31%), Positives = 239/471 (50%), Gaps = 28/471 (5%)

Query: 107 GTPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGAL 166
           GTP + DG++ G  GM+ SL SREVIA      +     D  +++G CDK +PG M+G  
Sbjct: 76  GTPTISDGMSMGTEGMKYSLVSREVIADCIETCVQGQWMDGVVVIGGCDKNMPGGMIGLA 135

Query: 167 RFGHLPTIFVPGGPMPSG------ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGT 220
           R  ++P I+V GG +  G      ++     +    +  G+ ++E+    E  +  S G+
Sbjct: 136 RM-NVPGIYVYGGTIRPGNWKGTDLTIVSSFEAVGEFTAGRMSQEDFEGVERNACPSTGS 194

Query: 221 CTFYGTANTNQLLMEVMGLHLPGAS-FVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIG 279
           C    TANT     E +G+ L  +S   NP     D+    A   V  + K   +  P  
Sbjct: 195 CGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVEAVKK---DLKP-R 250

Query: 280 EIVDERSLVNSIVALHATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN 339
           +I+ ++S+ N++  + ATGGSTN  LH  AIA AA ++ T +D   + + VP + ++ P+
Sbjct: 251 DIITKKSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWTIEDFERMRKKVPVICNLKPS 310

Query: 340 GKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPI 399
           G+        AGG+  +++ LL+AGLLH D  T+ G+ L+               +D P 
Sbjct: 311 GQYVATDLHKAGGIPQVMKILLDAGLLHGDCITITGKTLAEEL------------KDVPS 358

Query: 400 E-SLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLA 458
               D+ ++ P+ +A   EG L +++GNL           L++ ++  PA VF D+Q   
Sbjct: 359 RPRADQKVIFPIDQALYKEGHLAILKGNLAEDGAVAKITGLKNPVITGPARVFDDEQSAL 418

Query: 459 DAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASG 517
           +A  A ++    V V+R+ GP+   GMPE+   T  + + +  G  V L+TDGR SG + 
Sbjct: 419 EAILADKIVAGDVVVLRYLGPKGGPGMPEMLAPTSAI-IGKGLGESVGLITDGRFSGGTW 477

Query: 518 KIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPA 568
            +    HV+PEA VGG +  V++GD I +D  K  L+L VD  E   R  A
Sbjct: 478 GMVVG-HVAPEAFVGGTIGLVQEGDSITIDAHKLLLQLNVDDAELQRRRAA 527


Lambda     K      H
   0.318    0.134    0.386 

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: 817
Number of extensions: 56
Number of successful extensions: 6
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: 608
Length of database: 557
Length adjustment: 36
Effective length of query: 572
Effective length of database: 521
Effective search space:   298012
Effective search space used:   298012
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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