GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Herbaspirillum seropedicae SmR1

Align 2-dehydro-3-deoxy-D-gluconate-6-phosphate aldolase (EC 4.1.2.55) (characterized)
to candidate HSERO_RS05525 HSERO_RS05525 ketohydroxyglutarate aldolase

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



>FitnessBrowser__HerbieS:HSERO_RS05525
          Length = 209

 Score =  225 bits (574), Expect = 4e-64
 Identities = 112/205 (54%), Positives = 147/205 (71%), Gaps = 1/205 (0%)

Query: 5   KTSAEQILTAGPVVPVIVINKLEHAVPMAKALVAGGVRVLELTLRTECAVEAIRLIAQEV 64
           KT+ E I+ A PV+PVI I+K EHAVP+A+ALVAGG+RVLE+TLRTE  + AIR IA+ V
Sbjct: 2   KTTLE-IMRASPVIPVIAIDKFEHAVPLARALVAGGIRVLEITLRTEHGLPAIRAIAESV 60

Query: 65  PDAIVGAGTVTNPQQLAEVTAAGAQFAISPGLTEPLLKAATEGTIPLIPGISTVSELMLG 124
           PDAIVG GT+T+P++      AGA F +SPGLT  L++AA    +PL+PG+ T SE+M  
Sbjct: 61  PDAIVGVGTLTSPEEFTASRDAGAVFGVSPGLTPALIEAAKRSGLPLLPGVMTPSEVMAA 120

Query: 125 MDYGLREFKFFPAEANGGVKALQAIAGPFGKIRFCPTGGISLKNYRDYLALKSVLCVGGS 184
            + G R+ K FPA   GGV  L  IAGP   + FCPTGGI+ +    +LA K+V+CVGGS
Sbjct: 121 REAGFRQLKLFPAVPAGGVGMLNGIAGPLADVSFCPTGGITQETAPQFLACKNVVCVGGS 180

Query: 185 WLVPADALESGDYDRITALAREAVA 209
           WL P  A+E+GD+D+IT +A+ A A
Sbjct: 181 WLTPKAAIEAGDWDKITEIAKAASA 205


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: 193
Number of extensions: 3
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: 209
Length adjustment: 21
Effective length of query: 192
Effective length of database: 188
Effective search space:    36096
Effective search space used:    36096
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