GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Escherichia coli BW25113

Align Branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 15560 b1439 fused predicted DNA-binding transcriptional regulator/predicted amino transferase (NCBI)

Query= reanno::azobra:AZOBR_RS06555
         (404 letters)



>FitnessBrowser__Keio:15560
          Length = 468

 Score =  175 bits (444), Expect = 2e-48
 Identities = 122/386 (31%), Positives = 198/386 (51%), Gaps = 19/386 (4%)

Query: 21  IRELLKLLERPEIISFAGGIPDPDFFPTAAIARAYEKIFQSNSGAGGALQYTISEGFTPL 80
           I ++L+    P ++ FA   PDP  FP   + R+  ++  S +    ++   +  G   L
Sbjct: 93  IFDMLQASRDPSVVPFASAFPDPRLFPLQQLNRSLAQV--SKTATAMSVIENLPPGNAEL 150

Query: 81  REWICAYLGRRGIQAGLDEVLVTSGSQQALEFVGKLLIGPGEKILVTRPTYLGALQAFSP 140
           R+ I      +GI    DE+++T+G+ +AL    + +  PG+ ++V  P + GALQA   
Sbjct: 151 RQAIARRYALQGITISPDEIVITAGALEALNLSLQAVTEPGDWVIVENPCFYGALQALER 210

Query: 141 YEPQYLSVPGDA-EGPDLAAVEAALEQKP-KFFYLVPDFQNPNGTTISLARREALLDLCA 198
              + LSV  D  EG DL A+E AL++ P K  +L+ + QNP G T++  ++  L+ L  
Sbjct: 211 LRLKALSVATDVKEGIDLQALELALQEYPVKACWLMTNSQNPLGFTLTPQKKAQLVALLN 270

Query: 199 KHGVPIVEDAAYTELRYEGE-PIPSMVALDAARNGGKITNVLFCGSFSKTMVPALRVGWI 257
           ++ V ++ED  Y+EL +  E P+P       A+   +   VL C SFSK +VP  R+GW+
Sbjct: 271 QYNVTLIEDDVYSELYFGREKPLP-------AKAWDRHDGVLHCSSFSKCLVPGFRIGWV 323

Query: 258 NGP--AEVINRLVLMKQAGDLHTSTINQIVLHDVVS-QNFDSHIRRLRAGYKERRDAMLT 314
                A  I RL LM     L TS+  Q+ L D +S + +D+H+RRLR    ER+     
Sbjct: 324 AAGKHARKIQRLQLMST---LSTSSPMQLALVDYLSTRRYDAHLRRLRRQLAERKQRAWQ 380

Query: 315 ALSEFAPAGVTWTKPEGGMFVWIELPEGTDGVDLLARAIKDANVAFVPGSAFHADRSGKN 374
           AL  + PA V     + G F+W+ELPE  D  +L   A+   +++  PG  F    +   
Sbjct: 381 ALLRYLPAEVKIHHNDSGYFLWLELPEPLDAGELSLAALTH-HISIAPGKMFSTGENWSR 439

Query: 375 TLRLSFSNNNPERIREGIRRLCGLLQ 400
             R + +    ER  + +++L  L+Q
Sbjct: 440 FFRFNTAWQWGEREEQAVKQLGKLIQ 465


Lambda     K      H
   0.320    0.138    0.410 

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: 429
Number of extensions: 22
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: 404
Length of database: 468
Length adjustment: 32
Effective length of query: 372
Effective length of database: 436
Effective search space:   162192
Effective search space used:   162192
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 (21.8 bits)
S2: 51 (24.3 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