GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Acidovorax sp. GW101-3H11

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate Ac3H11_2326 Methylisocitrate lyase (EC 4.1.3.30)

Query= curated2:Q9YFM7
         (308 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2326
          Length = 289

 Score =  211 bits (536), Expect = 2e-59
 Identities = 116/246 (47%), Positives = 160/246 (65%), Gaps = 6/246 (2%)

Query: 16  LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGS-LAMPDLGLITLSELAM 74
           L+ L + R  V+ PG +N   A +   +GFEA+Y++GA +T     +PD   + L+++A 
Sbjct: 10  LKALAQARRGVIVPGAFNALSARVVADLGFEAIYVTGAGVTNMWFGLPDQAFMGLTDIAD 69

Query: 75  FTSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKA 134
            T+ I   V +P+IVDADTGFG A+N    VR LERAGA  IQ+EDQV PK+CGH  GK 
Sbjct: 70  HTARIRDAVELPLIVDADTGFGNALNTYHAVRTLERAGADCIQLEDQVSPKRCGHFNGKE 129

Query: 135 LISPEDMVKKIIAAVGARRDA--LIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEAL 192
           +I  ++M+ KI AAV ARRDA  LI+ARTDA   +GFE AVERAQ + EAGADI+F EA+
Sbjct: 130 VIGTDEMLGKIKAAVDARRDAGTLILARTDACATQGFEAAVERAQRFQEAGADILFVEAV 189

Query: 193 TSLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFR---ASLKAS 249
           T+L+E R   +R+ AP L NM   GKTP  + ++    GY +V++     +   A ++ +
Sbjct: 190 TTLDEIRALPQRLAAPQLMNMVIGGKTPITSAEELATLGYGLVLYANAALQGAVAGMQKA 249

Query: 250 ETVLRE 255
            TVLRE
Sbjct: 250 LTVLRE 255


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: 239
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 308
Length of database: 289
Length adjustment: 27
Effective length of query: 281
Effective length of database: 262
Effective search space:    73622
Effective search space used:    73622
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