GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ilvE 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS26755 BPHYT_RS26755 aromatic
           amino acid aminotransferase
          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 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