GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-med in Rhizobium etli CFN 42

Align Glyceraldehyde dehydrogenase medium chain; Glyceraldehyde dehydrogenase subunit B; Glyceraldehyde dehydrogenase subunit beta; EC 1.2.99.8 (characterized)
to candidate WP_011426360.1 RHE_RS15975 xanthine dehydrogenase small subunit

Query= SwissProt::Q4J6M6
         (281 letters)



>NCBI__GCF_000092045.1:WP_011426360.1
          Length = 488

 Score =  114 bits (285), Expect = 4e-30
 Identities = 82/242 (33%), Positives = 114/242 (47%), Gaps = 7/242 (2%)

Query: 41  KLRVLSPDYILDINRLNELNYVKTSLNGVSIGALTRYHDILSNDIVKSKVPLMHHATRTI 100
           ++R LSP  ++ IN L+EL  V  S +G++IGA   Y    +   +  K+P +      I
Sbjct: 236 QMRRLSP--VVFINHLSELQSVTESEDGITIGAGVSYTGAFA--AISKKIPALGRLIDRI 291

Query: 101 GDMQVRNMGTIGGAISNADPASDMPVVLTALNATIILSSASGSRSVKALDFFKGPFTTDT 160
              QVRNMGTIGG I+N  P  D P  L AL AT+ L S  G R +   DFF      D 
Sbjct: 292 AGEQVRNMGTIGGNIANGSPIGDSPPPLIALGATLTLRSLEGQRKMPLEDFFIAYGKQDR 351

Query: 161 NKGELVTQIEVPVLDGYK--TVYKKVVRRAGDYALASVALAIKLKGNEI-EDIKLAYGGV 217
             GE V  + VP          YK   RR  D      A  + L   EI  DI++AYGG+
Sbjct: 352 RPGEFVESVFVPYPKATSRFAAYKITKRRDEDITAVLGAFLLTLDDAEIVTDIRIAYGGM 411

Query: 218 HDKPFRAMEVEKNVIGKKLNDDLVKDIASKVSSQINPPSDHRGSSWYRREVVKVLTMKAF 277
              P RA  VE  +IG+   +  ++       +   P +D R ++ YR+   K L  + +
Sbjct: 412 AATPKRARTVEAELIGRPWTEATIQAARPAFDADFQPLTDWRATAEYRQLTAKNLLTRFY 471

Query: 278 KE 279
            E
Sbjct: 472 LE 473


Lambda     K      H
   0.316    0.134    0.372 

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: 243
Number of extensions: 7
Number of successful extensions: 2
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: 281
Length of database: 488
Length adjustment: 30
Effective length of query: 251
Effective length of database: 458
Effective search space:   114958
Effective search space used:   114958
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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