GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Pseudomonas stutzeri RCH2

Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate GFF1955 Psest_1998 Entner-Doudoroff aldolase

Query= metacyc::MONOMER-15645
         (213 letters)



>FitnessBrowser__psRCH2:GFF1955
          Length = 214

 Score =  195 bits (496), Expect = 5e-55
 Identities = 96/201 (47%), Positives = 133/201 (66%)

Query: 9   EQILTAGPVVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAIRLIAQEVPDAI 68
           E+I     ++PVI I   E  +P+A AL AGG+R LE+TLR+   + AIR + +E PD  
Sbjct: 11  ERICVDARILPVITIGSEEQILPLADALAAGGLRTLEITLRSSHGLTAIRRLREERPDLC 70

Query: 69  VGAGTVTNPQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLGMDYG 128
           VGAGTV + + + EV A GAQF ++PG T  +L+A    ++PL+PGIS+ S+LM G   G
Sbjct: 71  VGAGTVLDRRMMDEVEATGAQFIVTPGSTREILEAGVSCSVPLLPGISSASDLMEGYALG 130

Query: 129 LREFKFFPAEANGGVKALQAIAGPFGKIRFCPTGGISLKNYRDYLALKSVLCVGGSWLVP 188
            R FK FPAE  GGV AL+A+ GPF  +RFCPTGG++  N   YLAL +V+CVGG+W++ 
Sbjct: 131 YRRFKLFPAEVCGGVAALKALGGPFADVRFCPTGGVTAANAASYLALPNVMCVGGTWMID 190

Query: 189 ADALESGDYDRITALAREAVA 209
           + +L  GD+  I     EA+A
Sbjct: 191 STSLGEGDWPSIQQRTAEALA 211


Lambda     K      H
   0.318    0.135    0.390 

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: 170
Number of extensions: 7
Number of successful extensions: 1
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: 213
Length of database: 214
Length adjustment: 22
Effective length of query: 191
Effective length of database: 192
Effective search space:    36672
Effective search space used:    36672
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: 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