GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__PS:Dsui_2433 Dsui_2433
           aspartate/tyrosine/aromatic aminotransferase
          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 Sep 17 2021. The underlying query database was built on Sep 17 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.

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