GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Echinicola vietnamensis KMM 6221, DSM 17526

Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate Echvi_3630 Echvi_3630 Entner-Doudoroff aldolase

Query= BRENDA::A0A0B6VQ18
         (222 letters)



>FitnessBrowser__Cola:Echvi_3630
          Length = 222

 Score =  196 bits (499), Expect = 2e-55
 Identities = 90/219 (41%), Positives = 142/219 (64%), Gaps = 1/219 (0%)

Query: 3   QFSRIEVAQVMKETGLVPLFYHKDVEVSKKVLKACYDGGARLLEFTSRGDFAHEIFAALV 62
           +FS  E+ + M++TG++P+F H D+EV+K V+ A Y+GG R+ EFT+RG+ A E+F  L 
Sbjct: 2   KFSNSEIIEAMEKTGMIPVFNHSDLEVAKNVMDASYNGGVRVFEFTNRGENALEVFRELK 61

Query: 63  KYAVAELPGMILGVGSVTDAAAASLYMQLGANFIVTPVFREDIAIVCNRRKVMWSPGCGS 122
            Y+ +   G++LG+G++        +++ GA+FIV+P    ++A+   R   +W PGCG+
Sbjct: 62  AYS-SRHKGLMLGIGTIFTPKEVEDFIEAGADFIVSPALIPNVAVTATRNDTLWIPGCGT 120

Query: 123 LTEIARAEEMGCEVVKLFPGELYGPAFINGIKGPQPWTTIMPTGGVSPTKESLTEWIKAG 182
           +TEI  A EMG +V+K FPG + GP+FI+ +K   P   IMPTGGV PT+E+L +W KAG
Sbjct: 121 VTEIFNAREMGAQVIKAFPGNVLGPSFISAVKAVLPSLKIMPTGGVEPTEENLGQWFKAG 180

Query: 183 AVCVGMGSKLIKPESDGNFDLNKIQSLTKECIDIIKELK 221
             CVGMGS+L K +       + ++    E +D I+ ++
Sbjct: 181 VTCVGMGSQLFKKDWIKQKKFDALEKQISEALDTIQRIR 219


Lambda     K      H
   0.320    0.137    0.411 

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: 178
Number of extensions: 9
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: 222
Length of database: 222
Length adjustment: 22
Effective length of query: 200
Effective length of database: 200
Effective search space:    40000
Effective search space used:    40000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 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