Aligments for a candidate for tyrB in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Aligments for a candidate for tyrB in Pseudomonas putida KT2440

Align Tyrosine aminotransferase; TyrAT; Aromatic-amino-acid transaminase; Aspartate aminotransferase; EC 2.6.1.5; EC 2.6.1.57; EC 2.6.1.1 (characterized)
to candidate PP_3590 PP_3590 D-lysine aminotransferase

Query= SwissProt::O85746
         (397 letters)



>lcl|FitnessBrowser__Putida:PP_3590 PP_3590 D-lysine
           aminotransferase
          Length = 398

 Score =  569 bits (1466), Expect = e-167
 Identities = 283/396 (71%), Positives = 325/396 (82%)

Query: 1   MFQKVDAYAGDPILSLMERFKEDPRSDKVNLSIGLYYNDDGIIPQLQAVAEAEARLNAEP 60
           MF+ VDAYAGDPILSLME FK DPR+DKVNLSIGLYY++ G++PQL AV   E R+  + 
Sbjct: 1   MFKHVDAYAGDPILSLMETFKADPRADKVNLSIGLYYDEAGVVPQLAAVDAVEKRIAGQD 60

Query: 61  HGASLYLPMEGFSGYRQAIAPLLFGAEHTALKQNRIASIQTVGGSGALKVGADFLKRYFP 120
           H ASLYLPMEG + YRQAI  LLFGA+H A+   R+A++QTVGGSGALKVGADFLKRYFP
Sbjct: 61  HEASLYLPMEGLASYRQAIQALLFGADHPAVTGGRVATVQTVGGSGALKVGADFLKRYFP 120

Query: 121 ESHVWVSDPTWENHIAIFEGAGFEVSTYPWFDKATNGVRFENLLAMLQTLPARDIVLLHP 180
           +S VWVS+PTW+NH AIFEGAGF+V TYP+FD+AT GV F+ +LA LQ+LPA  +VLLHP
Sbjct: 121 QSEVWVSNPTWDNHRAIFEGAGFKVHTYPYFDQATRGVDFDGMLATLQSLPANSVVLLHP 180

Query: 181 CCHNPTGADLTPAQWDRVVEVLKARQLIPFLDIAYQGFGGGLEEDAYAIRAIASAGMPML 240
           CCHNPTGADL   QW +VVEV+KARQLIPFLDIAYQGF  GL EDAYAIR +A AG+P L
Sbjct: 181 CCHNPTGADLQQHQWQQVVEVVKARQLIPFLDIAYQGFAEGLVEDAYAIREMARAGVPCL 240

Query: 241 VSNSFSKIFSLYGERVGGLSVVCEDSETAGRVLGQLKATVRRNYSSPPSFGAQVVATVLN 300
           VSNSFSKIFSLYGERVGGLSVVC+D  TA  VLGQLKATVRRNYSSPP+FGAQ+VA VL+
Sbjct: 241 VSNSFSKIFSLYGERVGGLSVVCDDEATAQSVLGQLKATVRRNYSSPPNFGAQLVAGVLS 300

Query: 301 DAALKATWQAEVDAMRAHILTMRQALVDALQQVAPGSKVDYLLKQRGMFSYTGFSAAQVD 360
           DA L A W  EV+ MR  IL MRQALVDAL  + PG    + L+QRGMFSYTGFS  QV 
Sbjct: 301 DAGLNAQWAEEVEVMRKRILDMRQALVDALAVLLPGQDFQFFLRQRGMFSYTGFSVEQVR 360

Query: 361 RLRDEFGVYLIASGRMRVAGLNSRNVQQVAKAFVAV 396
           RLRDEFGVYLI SGR+ ++GL   N+Q+VA+AF AV
Sbjct: 361 RLRDEFGVYLIDSGRVCMSGLRPANLQRVAEAFAAV 396


Lambda     K      H
   0.321    0.135    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: 528
Number of extensions: 13
Number of successful extensions: 1
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: 397
Length of database: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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Candidates (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis