GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Phyllobacterium endophyticum PEPV15

Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_106719584.1 CU100_RS26240 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme

Query= SwissProt::P96847
         (388 letters)



>NCBI__GCF_003010935.1:WP_106719584.1
          Length = 400

 Score =  158 bits (399), Expect = 3e-43
 Identities = 114/366 (31%), Positives = 181/366 (49%), Gaps = 14/366 (3%)

Query: 24  AERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQR 83
           A+R R   D+V L  G+     P  +  AA AAL      Y+ +LG+P LR A+ +DY  
Sbjct: 35  ADRGRDDPDVVKLWIGEGDLPTPPYIVEAAEAALRAGHTRYTYSLGLPRLRQAL-SDYHF 93

Query: 84  RH-GITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEI 142
           RH  + +  +   +T G     + +  A  D GD + + +P +P     +   G   V +
Sbjct: 94  RHWNVRLPVERFTVTVGGMNALMQSAQAVLDPGDEIIVPTPAWPNLIESMRLAGGTPVLV 153

Query: 143 PCGPQTRFQPTA---QMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRL 199
           P G Q+  +       +LA I P  + +++ SP+NPTG V+P E++         +++ +
Sbjct: 154 PYGIQSDGRLALNIDDVLAAITPKTKAILINSPSNPTGWVMPREDMEKFVDLSRQTNIWI 213

Query: 200 ISDEVYHGLVYQGAPQTSCAWQTSRN--AVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVD 257
           I+DEVY    Y G+   S    T  N   +V N+FSK +AMTGWR+GW +VP  L +   
Sbjct: 214 IADEVYAQFKYDGSVAPSFLQITDENDKVIVTNTFSKNWAMTGWRIGWAVVPRGLDKFYA 273

Query: 258 CLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTD 317
            L+   T   P   Q AA++A   +        ++  A  R + +DGL +I    + P D
Sbjct: 274 KLSEYNTTGVPTFVQHAAIAAL-DQGDEFIRQMVSRCAETRKIFVDGLSQIEGVTVLPPD 332

Query: 318 GAFYVYADVSDFTSD--SLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIE 375
           GAFY+   +  F  D  SL    ++LA+  V +APG  F +A G  ++R+ FA       
Sbjct: 333 GAFYL---MVGFPGDETSLDVAIRMLAEAKVGVAPGTAFGSA-GQGYLRLCFAISPKLAR 388

Query: 376 EALRRI 381
           EA++R+
Sbjct: 389 EAVKRL 394


Lambda     K      H
   0.321    0.136    0.416 

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: 428
Number of extensions: 20
Number of successful extensions: 4
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: 388
Length of database: 400
Length adjustment: 31
Effective length of query: 357
Effective length of database: 369
Effective search space:   131733
Effective search space used:   131733
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 (21.9 bits)
S2: 50 (23.9 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