GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Dechlorosoma suillum PS

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate Dsui_2433 Dsui_2433 aspartate/tyrosine/aromatic aminotransferase

Query= CharProtDB::CH_004054
         (397 letters)



>FitnessBrowser__PS:Dsui_2433
          Length = 402

 Score =  407 bits (1045), Expect = e-118
 Identities = 208/398 (52%), Positives = 272/398 (68%), Gaps = 3/398 (0%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAE-ARLNAQ 59
           +F  V+    DPIL L E F  D R+ KVNL +G+YY+++G IP L AV  AE ARL   
Sbjct: 5   IFASVEMAPRDPILGLTEAFNADTRATKVNLGVGVYYDDNGKIPLLAAVKAAEKARLETM 64

Query: 60  PHGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYF 119
           P     Y P+EGLN Y  A+  LLFGA   +L   RV T + LGG+GALK+GADFLKR  
Sbjct: 65  PPRG--YQPIEGLNAYNQAVQNLLFGAGSELLAAGRVITAEALGGTGALKIGADFLKRIS 122

Query: 120 PESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLH 179
           P + V++SDP+WENH A+F  AGF V  YP+YD AT GV F  + + L+ L A SI++LH
Sbjct: 123 PNAKVYISDPSWENHRALFESAGFVVENYPYYDAATRGVNFAGMKSFLEGLAAGSIIILH 182

Query: 180 PCCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPA 239
            CCHNPTGADL++ QW  V+++ KA+ L+PFLD+AYQGF  G++ DA A+RA +++GL  
Sbjct: 183 ACCHNPTGADLSDAQWQEVVDVCKAKGLVPFLDMAYQGFADGIDADAVAVRAFSASGLQF 242

Query: 240 LVSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVL 299
            VS+SFSK FSLYGERVG LSV+    E + RVL Q+K  +R NYS+PP  G  VVAAVL
Sbjct: 243 FVSSSFSKSFSLYGERVGALSVVTASKEESARVLSQVKRVIRTNYSNPPTHGGAVVAAVL 302

Query: 300 NDEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQV 359
           +   L+  W  E+  MR RI AMR  LV  L  +   ++F +++ QRGMFSYTGL++AQV
Sbjct: 303 STPELRQMWEDELAGMRDRIRAMRVALVDKLKAKGVAQDFSFVVKQRGMFSYTGLTSAQV 362

Query: 360 DRLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           D LR EFG+Y + +GR+C+A LN+ N+  V  A AAV+
Sbjct: 363 DVLRNEFGIYAVGTGRICLAALNSKNIDAVVDAIAAVL 400


Lambda     K      H
   0.320    0.135    0.401 

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: 441
Number of extensions: 13
Number of successful extensions: 2
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: 397
Length of database: 402
Length adjustment: 31
Effective length of query: 366
Effective length of database: 371
Effective search space:   135786
Effective search space used:   135786
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: 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