GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Cupriavidus basilensis 4G11

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate RR42_RS22765 RR42_RS22765 carboxyvinyl-carboxyphosphonate phosphorylmutase

Query= curated2:Q9YFM7
         (308 letters)



>FitnessBrowser__Cup4G11:RR42_RS22765
          Length = 281

 Score =  210 bits (534), Expect = 4e-59
 Identities = 108/244 (44%), Positives = 155/244 (63%), Gaps = 2/244 (0%)

Query: 15  VLRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGSLAMPDLGLITLSELAM 74
           +LR+ ++   +++APG Y+   A L E+ GF A Y++GA  + +   PD GL+T+SE+  
Sbjct: 6   ILRQRLQAPGMIIAPGAYDAIGARLIEQAGFSACYMTGAGTSAARGFPDFGLLTMSEMVE 65

Query: 75  FTSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKA 134
             + + R V +P+I DADTG+G  +NV RTVRE E  G AAI IEDQV PK+CGHL GK 
Sbjct: 66  NAAVMARSVSIPLIADADTGYGNQLNVTRTVREYEARGVAAIHIEDQVAPKRCGHLDGKE 125

Query: 135 LISPEDMVKKIIAAVGARR--DALIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEAL 192
           ++S E+ V KI AAV ARR  D +I+ARTDAR + G E+A+ RA   +EAGAD+ F EA 
Sbjct: 126 VVSREEFVSKIRAAVQARRTPDFVIIARTDARAMLGLEEAIWRANAALEAGADLAFVEAT 185

Query: 193 TSLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETV 252
            ++EE     R V+ P L N+   G+TP   + +    GYK+ I P    +A+++A +  
Sbjct: 186 QTIEEVAAVPRLVRGPCLLNVVPGGRTPIFDLREAEVMGYKLAILPGLMLKAAIQAGDEA 245

Query: 253 LREI 256
           L E+
Sbjct: 246 LAEL 249


Lambda     K      H
   0.321    0.137    0.378 

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: 251
Number of extensions: 5
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: 308
Length of database: 281
Length adjustment: 26
Effective length of query: 282
Effective length of database: 255
Effective search space:    71910
Effective search space used:    71910
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: 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