GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Enterococcus termitis LMG 8895

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate WP_069661914.1 BCR25_RS01940 NADP-dependent isocitrate dehydrogenase

Query= curated2:O29627
         (326 letters)



>NCBI__GCF_001730305.1:WP_069661914.1
          Length = 425

 Score =  137 bits (345), Expect = 5e-37
 Identities = 114/402 (28%), Positives = 179/402 (44%), Gaps = 79/402 (19%)

Query: 4   IVVIPGDGIGKEVMEAAMLILE-------KLDLPFEYSYYDAGDEALEKYGKALPDETLE 56
           I  I GDGIG E+ +AA L+ +       K +    +    AG++A +  G  LP+ETL 
Sbjct: 22  IPFIEGDGIGPEIWQAAKLVFDAAVNKAYKNERKVVWQEVLAGEKAFKMTGDWLPEETLT 81

Query: 57  ACRKSDAVLFGAA----GETAADVIVRLRRELGTFANVRPAKAIEGIEC--LYPGL-DIV 109
             +     + G      G     + V LR+EL  +   RP +  EG+     +P L D++
Sbjct: 82  VIKDHLVAIKGPLTTPIGGGFRSLNVTLRQELDLYVCYRPVRYFEGVPSPLKHPELTDMM 141

Query: 110 VVRENTECLYMGFEFG----------------FG------DVTEAIRV--ITREASERIA 145
           + RENTE +Y G EF                 FG        T AI +  +++E +ER+ 
Sbjct: 142 IFRENTEDIYAGIEFPAESLEAEKLITYLKTEFGIDKIRFPKTSAIGIKPVSKEGTERLV 201

Query: 146 RYAFELAKREGRKKVTALHKANVMKKTCGLFRDVCREVAK-----------DY------- 187
           R A E A +  RK VT +HK N+MK T G F+     +AK           DY       
Sbjct: 202 RGAIEHALKHKRKSVTLVHKGNIMKFTEGGFKQWGYALAKTEFSDAVFTWEDYLKSKEEL 261

Query: 188 ---------------PEIQYNDYYIDAACMYLVMDPFRFDVIVTTNMFGDIVSDLAAGLV 232
                           ++   D   D     +++ P  +DV+ T N+ GD +SD  A  V
Sbjct: 262 GKTAADQQLAAAETAGKLIIKDRIADIFLQDILLHPTNYDVVATLNLNGDYISDALAAQV 321

Query: 233 GGLGLAPSANVGERT--AIFEPVHGAAFDIAGKGIANPTAMILTACMMLRHFGYVEEAKK 290
           GG+G+AP AN+   T   IFE  HG A + AG    NP++++L+  ++  + G+ E ++ 
Sbjct: 322 GGIGIAPGANLNLETGHGIFEATHGTAPEFAGLNQLNPSSLLLSGALLFEYLGWFEVSRL 381

Query: 291 VEEAVEKTIKEGKKTPDLGGN------LKTMEFANEVASLLD 326
           + E++E  +     T D          L   +F  E+  L++
Sbjct: 382 IIESIEAALINRTVTKDFADQMEQATLLSCSDFGEELVRLIE 423


Lambda     K      H
   0.321    0.139    0.399 

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: 275
Number of extensions: 17
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 326
Length of database: 425
Length adjustment: 30
Effective length of query: 296
Effective length of database: 395
Effective search space:   116920
Effective search space used:   116920
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: 49 (23.5 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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