GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Phyllobacterium brassicacearum STM 196

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_106711690.1 CU102_RS13880 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_003010955.1:WP_106711690.1
          Length = 557

 Score =  224 bits (572), Expect = 6e-63
 Identities = 158/468 (33%), Positives = 240/468 (51%), Gaps = 28/468 (5%)

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

Query: 167 RFGHLPTIFVPGGPMPSG------ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGT 220
           R  ++P I+V GG +  G      +S     +    +  GK + E+    E  +  S G+
Sbjct: 136 RT-NVPAIYVYGGTIKPGKWKGKDLSIVSSFEAVGSFMAGKMSEEDFEGIERHACPSTGS 194

Query: 221 CTFYGTANTNQLLMEVMGLHLPGAS-FVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIG 279
           C    TANT     E +G+ L  +S   NP     D+ T E+A+ +    ++  N  P  
Sbjct: 195 CGGMYTANTMSSAFEALGMSLMSSSTMANPDAEKVDS-TAESARVLVEAVRR--NIRP-R 250

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

Query: 340 GKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLS-RYTQEPFLDNGKLVWRDGP 398
           G+         GG+  +++ LL AGLLH D  T+ GR L+      P          D P
Sbjct: 311 GQYMAVDLHKVGGIPQVLKILLNAGLLHGDCLTITGRTLADELAHIP----------DSP 360

Query: 399 IESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLA 458
               D+NI+RP+ +A   EG L +++GNL  G        L++ +++ PA VF D+Q   
Sbjct: 361 --PADQNIIRPIDKALYKEGHLAILKGNLATGGAVAKITGLKNPVIKGPARVFDDEQSAM 418

Query: 459 DAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASG 517
           DA  + ++    V V+R+ GP+   GMPE+   T  + + +  G  V L+TDGR SG + 
Sbjct: 419 DAILSDKIRPGDVLVLRYLGPKGGPGMPEMLAPTSAI-IGRGLGESVGLITDGRFSGGTW 477

Query: 518 KIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAR 565
            +    HV+PEA  GG +A VR+GD+I +D  +  L+L VD  E   R
Sbjct: 478 GMVVG-HVTPEAFEGGTIALVREGDMITIDAHQQLLQLDVDEAELEKR 524


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: 886
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 24 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