GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ARO8 in Dyella japonica UNC79MFTsu3.2

Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate N515DRAFT_3488 N515DRAFT_3488 aromatic-amino-acid transaminase

Query= reanno::Cup4G11:RR42_RS33490
         (400 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3488 N515DRAFT_3488
           aromatic-amino-acid transaminase
          Length = 400

 Score =  388 bits (997), Expect = e-112
 Identities = 199/395 (50%), Positives = 262/395 (66%), Gaps = 2/395 (0%)

Query: 2   FEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADMG 61
           F  ++  PGDPIL L E++  D R  KVNL +GIY+D++GR+P+++AV E E  L  +  
Sbjct: 4   FASVEMTPGDPILGLTEAYLADARPGKVNLGVGIYYDEQGRIPLLRAVHEVEQRLAQEAK 63

Query: 62  PRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPDA 121
           PR YLP+ G  AY    Q LVFG      A GR+AT QT+GGSGALRVGAD LK+  P A
Sbjct: 64  PRGYLPIDGLPAYTQGTQKLVFGAESPLLAAGRVATSQTIGGSGALRVGADVLKKALPKA 123

Query: 122 QVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHACC 181
           ++ IS+PSWENHRV+F   GF V  Y YYD  T GL F  ML  L  +   ++VLLHACC
Sbjct: 124 KIAISNPSWENHRVVFIAAGFEVVEYTYYDPQTHGLDFAGMLADLGKLEPGTVVLLHACC 183

Query: 182 HNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPC-LV 240
           HNPTGVDLN  QW+Q++ ++K+ +LLPF+DMAYQGF  G+D DA AVR   A G+   +V
Sbjct: 184 HNPTGVDLNAAQWQQVVEVVKERQLLPFIDMAYQGFDQGIDADATAVRLFAASGIESFVV 243

Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300
            +S++K+FSLYGER G L+ V    +E  RV   +   +R+ YS+P THG  +VA VL +
Sbjct: 244 TSSYAKSFSLYGERAGALTFVAADRDEALRVQSLVKRTIRSIYSSPSTHGGALVAGVLNS 303

Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360
           P LR +WE+EL    ERI  MRA + + LAAH      +    Q GMF+Y+GL+  QVDR
Sbjct: 304 PELRAMWEQELGEMRERIHAMRAGMVEKLAAH-GAPQFAFIQQQAGMFSYSGLSKAQVDR 362

Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASV 395
           LR E+ +Y + +GR+CVA LN  N+  VA A+A+V
Sbjct: 363 LRDEYAIYAIGTGRICVAALNRSNLDTVAAAVAAV 397


Lambda     K      H
   0.323    0.137    0.417 

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: 422
Number of extensions: 20
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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