GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Streptacidiphilus oryzae TH49

Align 2-methylisocitrate lyase; 2-MIC; MICL; EC 4.1.3.30; (2R,3S)-2-methylisocitrate lyase (uncharacterized)
to candidate WP_037571386.1 BS73_RS10660 isocitrate lyase/PEP mutase family protein

Query= curated2:Q9YFM7
         (308 letters)



>NCBI__GCF_000744815.1:WP_037571386.1
          Length = 288

 Score =  209 bits (532), Expect = 6e-59
 Identities = 111/243 (45%), Positives = 152/243 (62%), Gaps = 2/243 (0%)

Query: 16  LRELIEKRDIVVAPGVYNPAVALLAERMGFEALYLSGAAITGSLAMPDLGLITLSELAMF 75
           LR L+ +R  V+APGV++   A L  R GF A Y++GA +     +PD+GL T SE+   
Sbjct: 9   LRALLAERSAVLAPGVFDGLSASLTARAGFRAAYMTGAGVAAVTGLPDVGLATQSEMVRQ 68

Query: 76  TSYITRVVRVPVIVDADTGFGEAINVERTVRELERAGAAAIQIEDQVMPKKCGHLQGKAL 135
              +  ++ +PVI DADTGFG+A +V RTVR  E+AGAAAIQ+EDQ  PK+CGHL  K +
Sbjct: 69  LGLVAGLLDIPVIADADTGFGDATHVFRTVRLYEQAGAAAIQLEDQEFPKRCGHLDRKRV 128

Query: 136 ISPEDMVKKIIAAVGARR--DALIVARTDARGVEGFEKAVERAQLYVEAGADIIFPEALT 193
           I  +   ++I AAV ARR  D +IVARTDAR   GF++AV R  LY EAGAD++F EA  
Sbjct: 129 IGADAFARRIEAAVEARRDPDTVIVARTDARATHGFDEAVRRVNLYAEAGADLVFLEAPQ 188

Query: 194 SLEEFREFARRVKAPLLANMTEFGKTPYITVDQFREAGYKIVIFPVTTFRASLKASETVL 253
           + +E R   R VKAP L N+   G+TP     +  +A Y +VI PV +  +++ A    L
Sbjct: 189 TADEVRRIPRAVKAPALFNLVPGGRTPQADAAELAQAKYALVILPVVSLGSAVAAMSAAL 248

Query: 254 REI 256
             +
Sbjct: 249 DRV 251


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: 253
Number of extensions: 16
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: 288
Length adjustment: 26
Effective length of query: 282
Effective length of database: 262
Effective search space:    73884
Effective search space used:    73884
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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