GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azorhizobium caulinodans ORS 571

Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_012170490.1 AZC_RS10175 D-amino-acid transaminase

Query= CharProtDB::CH_012531
         (298 letters)



>NCBI__GCF_000010525.1:WP_012170490.1
          Length = 284

 Score =  153 bits (386), Expect = 5e-42
 Identities = 91/275 (33%), Positives = 144/275 (52%), Gaps = 10/275 (3%)

Query: 7   FLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEIP 66
           ++NG+FVP  EA++S  D G+L+ DG++E   V  G +     HL RL  S   I L++P
Sbjct: 6   YVNGDFVPLAEARISPLDRGFLFADGIYEVSAVLDGKLVDNDSHLARLKRSVGEIALDLP 65

Query: 67  YSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSLFPQE 126
            +L+E+  +  E +R+N L+ G + + V+RG  +         KP + +  ++ ++   +
Sbjct: 66  VTLEELVELERELVRRNSLTEGVVYMQVTRGVADRDFTFPKDAKPTLFMFTQEKNILASK 125

Query: 127 YYEKGIPVVTVATRRNRPDV--LSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVA 184
             E GI V +V      PD+      +KS+  L  +L +  A  AG QEA M+ D G++ 
Sbjct: 126 AAETGIRVKSV------PDLRWARRDIKSVALLAQVLAKQAAAEAGCQEAWMVQD-GFIT 178

Query: 185 EGSGDNVFIVKGNK-LITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVADE 243
           EG   + FI+  N  ++T P+S   L G TR A+L +  +    V E LFT  +   A E
Sbjct: 179 EGGSSSAFIITANDVVVTRPNSTAVLPGCTRRALLALAAEGTITVEERLFTLDEALAAKE 238

Query: 244 VFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLE 278
            F+   ++ V AV  +D + IG G  GP T RL E
Sbjct: 239 AFIASASSFVQAVVAIDDKPIGTGTPGPLTKRLRE 273


Lambda     K      H
   0.317    0.138    0.390 

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: 182
Number of extensions: 8
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: 298
Length of database: 284
Length adjustment: 26
Effective length of query: 272
Effective length of database: 258
Effective search space:    70176
Effective search space used:    70176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Jul 25 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