GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Putida:PP_3590
          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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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