GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Sphingomonas koreensis DSMZ 15582

Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate Ga0059261_0356 Ga0059261_0356 Entner-Doudoroff aldolase

Query= BRENDA::Q00384
         (208 letters)



>FitnessBrowser__Korea:Ga0059261_0356
          Length = 202

 Score =  230 bits (587), Expect = 1e-65
 Identities = 117/201 (58%), Positives = 146/201 (72%), Gaps = 1/201 (0%)

Query: 4   IDSVMRLAPVMPVLVIEDIADAKPIAEALVAGGLNVLEVTLRTPCALEAIKIMKEVPGAV 63
           I+++MR + V+PVLVIED A A+P+AEALVAGGL VLEVT+RT  AL+AI+ MK+VPGA+
Sbjct: 3   IETIMRTSAVIPVLVIEDAATARPLAEALVAGGLKVLEVTMRTAAALDAIREMKQVPGAI 62

Query: 64  VGAGTVLNAKMLDQAQEAGCEFFVSPGLTADLGKHAVAQKAALLPGVANAADVMLGLDLG 123
           VGAGTV+N     Q  +AG EF VSPGLT  LG+  V      LPGVANA D+M G DLG
Sbjct: 63  VGAGTVVNTDQFAQVMDAGAEFIVSPGLTERLGQVIVQSGVPFLPGVANAGDIMRGYDLG 122

Query: 124 LDRFKFFPAENIGGLPALKSMASVFRQVRFCPTGGITPTSAPKYLENPSILCVGGSWVVP 183
           L  FKFFPAE  GGL ALK++A  F + +FCPTGGI+P +AP +L    +LCVGGSWV P
Sbjct: 123 LRHFKFFPAETSGGLKALKALAGPFYEAKFCPTGGISPATAPDWLGFDPVLCVGGSWVTP 182

Query: 184 AGKPDVAKITALAKEASAFKR 204
            G    A++ ALA++A+   R
Sbjct: 183 KG-ASYAEVEALARDAAGLAR 202


Lambda     K      H
   0.320    0.136    0.394 

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: 176
Number of extensions: 5
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: 208
Length of database: 202
Length adjustment: 21
Effective length of query: 187
Effective length of database: 181
Effective search space:    33847
Effective search space used:    33847
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