GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Herbaspirillum seropedicae SmR1

Align Aromatic-amino-acid aminotransferase 1; ARAT-I; AROAT; EC 2.6.1.57 (characterized)
to candidate HSERO_RS09050 HSERO_RS09050 2-aminoadipate aminotransferase

Query= SwissProt::H3ZPL1
         (417 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS09050 HSERO_RS09050
           2-aminoadipate aminotransferase
          Length = 398

 Score =  314 bits (805), Expect = 3e-90
 Identities = 169/410 (41%), Positives = 252/410 (61%), Gaps = 17/410 (4%)

Query: 10  KLEAPTLDYEKYFSEKALGMKASEIRELLKLVETSDVISLAGGLPAPETFPVEIIGEITK 69
           KLE P    +  FS++A  MK+S IRE+LK+    D+ S AGGLP+P TFPVE +     
Sbjct: 2   KLENPA-PLQWQFSQRADAMKSSAIREILKVTMRPDITSFAGGLPSPLTFPVEHMKTAFD 60

Query: 70  EVLEKHAAQALQYGTTKGFTPLRLALAEWMRERYDI---PISKVDIMTTSGSQQALDLIG 126
            VL +    ALQYG T G+ PLR    EW+          IS   ++  SGSQQ LDL+G
Sbjct: 61  RVLSQQGKMALQYGPTDGYLPLR----EWIAASLSTNGAQISAEQVLMVSGSQQGLDLLG 116

Query: 127 RVFINPGDIIVVEAPTYLAALQAFKYYEPEFVQIPLDDEGMNVDLLEEKLQELEKEGKKV 186
           +V I+ G  ++VE P+YL ALQAF  Y  +F  +P D+ G+  + +E             
Sbjct: 117 KVLIDEGSKVLVETPSYLGALQAFALYGAKFESVPSDEFGLQPETIEAI-------AGGA 169

Query: 187 KIVYTIPTFQNPAGVTMNEKRRKRLLELASQYDFIIVEDNPYGELRYSGEPVKPIKAWDE 246
           +++Y++P FQNP G T+  +RR +L+E  ++    ++ED+PYG L Y   P+  + + + 
Sbjct: 170 RMLYSLPNFQNPTGRTLPTERRFKLVETCARLGLPLIEDDPYGALSYQNAPLPKMLSMNP 229

Query: 247 EGRVIYLGTFSKILAPGFRIGWIAAEPHFIRKLEIAKQSVDLCTNTFSQVIAWKYVEGGY 306
            G VIY+G+FSK+L PG R+G++ A    I K+E AKQ+ DL T   +Q++ ++ ++ G+
Sbjct: 230 SG-VIYMGSFSKVLTPGIRLGYVVAPRPLILKMEQAKQATDLHTAQLTQMVVYEAIKDGF 288

Query: 307 LDKHIPKIIEFYKPRRDAMLKALEEFMPDGVKWTKPEGGMFVWATLPEGIDTKLMLEKAV 366
           LD+H+P I + Y  +  AML AL+++ P    W+KPEGGMF+W TLPE ID   +L +AV
Sbjct: 289 LDQHVPTIRKLYGDQCQAMLDALQQYFPASCSWSKPEGGMFIWVTLPEHIDAGALLNEAV 348

Query: 367 -AKGVAYVPGEAFFAHRDVKNTMRLNFTYVPEEKIREGIKRLAETIKEEM 415
             + VA+VPG  F+A+   KNT+RL+F  VP E+IR G++RL + I  ++
Sbjct: 349 EQEKVAFVPGAPFYANVAQKNTLRLSFVTVPPEQIRAGVERLGKLIASKL 398


Lambda     K      H
   0.318    0.137    0.398 

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: 444
Number of extensions: 23
Number of successful extensions: 5
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: 417
Length of database: 398
Length adjustment: 31
Effective length of query: 386
Effective length of database: 367
Effective search space:   141662
Effective search space used:   141662
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 (21.7 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 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, 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