GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Lentibacillus jeotgali Grbi

Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_010532048.1 ON01_RS16165 D-amino-acid transaminase

Query= curated2:O29329
         (290 letters)



>NCBI__GCF_000224785.1:WP_010532048.1
          Length = 284

 Score =  151 bits (382), Expect = 1e-41
 Identities = 95/273 (34%), Positives = 148/273 (54%), Gaps = 6/273 (2%)

Query: 11  VPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIPITKEEF 70
           + E +  + I D G+ +GDG++E I  Y+G    + EH++RL  SA+ + L +P +  E 
Sbjct: 10  IMERDNVIDIEDRGYQFGDGIYEVIGVYDGEPLMMDEHMERLERSARELRLTLPASTSEL 69

Query: 71  MEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYGDLYEKGL 130
              + + +  N L +  I   V+RGI          Q P++ V      +   D+ ++G 
Sbjct: 70  KSNLEKLVEANGLEEGIIYMQVSRGIASREHGFPASQTPAVTVAYTREEEREPDVEDQGA 129

Query: 131 TAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVSEGSGDNIF 190
           TA+     R     L  +IK+LN L N++AK +A      EAI L R G V+E S  N+F
Sbjct: 130 TAVLAEDIR----WLRCDIKTLNLLPNVMAKQKAVENNAVEAI-LHRGGTVTEASASNVF 184

Query: 191 VVKNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTADEVFVTGTAAE 249
           +V  G + T P  N  L GITR  +I++ + L I   E    + DL  ADEVFV+ T  +
Sbjct: 185 MVTGGELYTHPADNYILNGITRRKIIQLCDELNINVNEQTYTVDDLLNADEVFVSATKMD 244

Query: 250 IAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTE 282
           I PI+ ID + IG+GKPG+IT++++++F  L E
Sbjct: 245 IIPILKIDDQTIGNGKPGKITKQILQQFRSLYE 277


Lambda     K      H
   0.319    0.142    0.409 

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: 241
Number of extensions: 12
Number of successful extensions: 3
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: 290
Length of database: 284
Length adjustment: 26
Effective length of query: 264
Effective length of database: 258
Effective search space:    68112
Effective search space used:    68112
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 (21.7 bits)
S2: 47 (22.7 bits)

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

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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