GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacE in Pseudomonas simiae WCS417

Align L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (characterized)
to candidate GFF1354 PS417_06885 dihydrodipicolinate synthase

Query= reanno::acidovorax_3H11:Ac3H11_603
         (294 letters)



>FitnessBrowser__WCS417:GFF1354
          Length = 290

 Score =  101 bits (252), Expect = 2e-26
 Identities = 85/270 (31%), Positives = 137/270 (50%), Gaps = 12/270 (4%)

Query: 3   TTFHEDGT-LDLDSQKRCLDFMIDAGVDGVCILANFSEQFSLSDAEREVLTRTSLEHVAG 61
           T F  DG  +DL++  R +D +I+ GV  +  L +  E   LSDAE + ++  SL  +A 
Sbjct: 15  TPFSTDGQRIDLNTLGRSIDRLIEGGVHAIAPLGSTGEGAYLSDAEWDEVSAYSLAKIAR 74

Query: 62  RVPVIVTTTHYGTRVCAERSRAAQDMGAAMVMVMPPYHGATFRVPEAQIYEFYARVSDAI 121
           RVP IV+ +   T     R+R A+  GA +VMV+P  +   +++ EA+I   YA + D+I
Sbjct: 75  RVPTIVSVSDLTTAKAVRRARYAEANGADVVMVLPTSY---WKLSEAEILAHYAAIGDSI 131

Query: 122 RIPIMVQDAPA-SGTVLSAPFLARMAQEIENLAYFKIEVPGAASKLRELIRLGGDAIEGP 180
            +PIM+ + PA SGT +S   + R+ +++ N+   K E  G   ++  L R         
Sbjct: 132 GVPIMLYNNPATSGTDMSVDLILRIIKQVPNVTMVK-ESTGDIQRMHHLHRQSDVPF--- 187

Query: 181 WDGEEAITLLADLDAGATGAMTG--GAFPDGIRPIIEAHRQGDMDQAFALYQRWLPLINH 238
           ++G   + L A   AGA G  T      P+    + EA    D+ QA  ++ R LPL++ 
Sbjct: 188 YNGCNPLALEA-FAAGAKGWCTAAPNLIPELNLALYEAVLANDLTQAREVFYRQLPLLDF 246

Query: 239 ENRQGGILTAKALMKEGGVIACEAGRHPFP 268
             + G   T KA ++  G+ A +     FP
Sbjct: 247 ILKGGLPATIKAGLRLTGLEAGDPRLPVFP 276


Lambda     K      H
   0.322    0.138    0.415 

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: 204
Number of extensions: 9
Number of successful extensions: 3
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: 294
Length of database: 290
Length adjustment: 26
Effective length of query: 268
Effective length of database: 264
Effective search space:    70752
Effective search space used:    70752
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 (21.9 bits)
S2: 48 (23.1 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