GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Paraburkholderia bryophila 376MFSha3.1

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate H281DRAFT_02542 H281DRAFT_02542 2-Methylisocitrate lyase, PEP mutase family

Query= curated2:Q9YFM7
         (308 letters)



>FitnessBrowser__Burk376:H281DRAFT_02542
          Length = 290

 Score =  216 bits (550), Expect = 5e-61
 Identities = 117/262 (44%), Positives = 159/262 (60%), Gaps = 2/262 (0%)

Query: 16  LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGSLAMPDLGLITLSELAMF 75
           LR+ +E ++++VAPG ++   A L E+ GF   Y++GA +  +   PD GL+TL+E+   
Sbjct: 7   LRKQLESKELIVAPGAWDGISARLIEQAGFPVAYMTGAGVAAANGYPDFGLVTLTEMTAA 66

Query: 76  TSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKAL 135
              +TR V +PVI DADTGFG A+NV RTV+E E +G AAIQIEDQ+ PK+CGHL+GK L
Sbjct: 67  ARTLTRSVSIPVIADADTGFGNALNVRRTVQEYEISGVAAIQIEDQLFPKRCGHLEGKEL 126

Query: 136 ISPEDMVKKIIAAVGARRDA--LIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEALT 193
           +   + V+KI AA  AR +   LIVARTDAR V G + A+ER    ++AGADI F EA  
Sbjct: 127 VQTTEFVEKIAAAAAARGEGGMLIVARTDARAVTGLDDAIERVNRALDAGADIAFVEAPQ 186

Query: 194 SLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETVL 253
           S EE    ARRV  P L N+   GKTP I +    E G++I I P     + + A++  L
Sbjct: 187 SAEEAAAIARRVNGPCLLNLVPGGKTPNIPLKDVAELGFRIAILPGLLLTSMMGAADLAL 246

Query: 254 REIMEKGTQKDILDKLYTRTEF 275
             +   G  +   D L  R  F
Sbjct: 247 ATVRNTGRVEVRPDALPIRDLF 268


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: 237
Number of extensions: 10
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: 290
Length adjustment: 27
Effective length of query: 281
Effective length of database: 263
Effective search space:    73903
Effective search space used:    73903
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