GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Burkholderia phytofirmans PsJN

Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate BPHYT_RS26755 BPHYT_RS26755 aromatic amino acid aminotransferase

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



>FitnessBrowser__BFirm:BPHYT_RS26755
          Length = 399

 Score =  559 bits (1441), Expect = e-164
 Identities = 272/399 (68%), Positives = 319/399 (79%)

Query: 1   MFEHIDAYPGDPILSLNESFQLDPRTDKVNLSIGIYFDDEGRLPVMQAVREAEAALMADM 60
           MF+HI AYPGDPILSLNE FQLDPR++KVNLSIGIYFDD G+LPVM AVR AE AL+  +
Sbjct: 1   MFDHIPAYPGDPILSLNEDFQLDPRSNKVNLSIGIYFDDAGKLPVMDAVRRAETALLDSI 60

Query: 61  GPRPYLPMAGFAAYRDAVQALVFGQPCQARAEGRIATVQTLGGSGALRVGADFLKRYFPD 120
           GPR YLPMAG   YRDA QALVFG   +AR  GRIAT+QT+GGSGAL+VGADFLKRYFP 
Sbjct: 61  GPRSYLPMAGLPLYRDAAQALVFGADSEARKAGRIATLQTIGGSGALKVGADFLKRYFPG 120

Query: 121 AQVWISDPSWENHRVIFERTGFTVNTYPYYDDATGGLKFDAMLDALRLIPKRSIVLLHAC 180
           +Q+WISDPSWENHRV+FE  G TVNTYPYYD+ TGGL+F  M++ +  +P++S+VLLHAC
Sbjct: 121 SQIWISDPSWENHRVVFEGAGLTVNTYPYYDEHTGGLRFADMIETIDSLPEQSVVLLHAC 180

Query: 181 CHNPTGVDLNHDQWRQLITLLKQHELLPFVDMAYQGFGAGLDDDAFAVRELVAQGVPCLV 240
           CHNPTGVDL+  QW +L+ +L++ +L+ FVDMAYQGFGAGL++DA  VR L   G+P + 
Sbjct: 181 CHNPTGVDLSPAQWAELVPVLQRRKLIAFVDMAYQGFGAGLEEDAACVRLLADAGIPLIA 240

Query: 241 ANSFSKNFSLYGERCGGLSVVCDSAEETGRVLGQLTGAVRANYSNPPTHGARVVARVLTT 300
           ANSFSKNFSLYGER G LSVVC SAEE GRVLGQL   VRANYSNPPTHGAR+VA VL  
Sbjct: 241 ANSFSKNFSLYGERVGALSVVCKSAEEAGRVLGQLMSTVRANYSNPPTHGARLVANVLAD 300

Query: 301 PALRTIWERELAGKCERIAKMRAAIHKGLAAHVSGEALSRYLTQRGMFTYTGLTADQVDR 360
            +LR  WE ELA   ERI  MR  IH GLA  V     +RY+ QRGMFTYTGL+  QV+R
Sbjct: 301 ASLRASWEAELATMRERILAMRGTIHAGLAGRVDEVMRARYVAQRGMFTYTGLSESQVER 360

Query: 361 LRTEHGVYLLRSGRMCVAGLNERNVTQVAQAIASVLAPA 399
           LR+E+ VY+LRSGRMCVAGLNERN   VA +IA+V++ A
Sbjct: 361 LRSEYAVYVLRSGRMCVAGLNERNAEYVAASIAAVVSGA 399


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: 534
Number of extensions: 16
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: 400
Length of database: 399
Length adjustment: 31
Effective length of query: 369
Effective length of database: 368
Effective search space:   135792
Effective search space used:   135792
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