GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Pseudomonas fluorescens FW300-N2E2

Align aromatic-amino-acid transaminase TyrB; EC 2.6.1.57 (characterized)
to candidate Pf6N2E2_50 Biosynthetic Aromatic amino acid aminotransferase alpha (EC 2.6.1.57) @ Aromatic-amino-acid aminotransferase (EC 2.6.1.57)

Query= CharProtDB::CH_004054
         (397 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_50
          Length = 398

 Score =  412 bits (1058), Expect = e-119
 Identities = 206/397 (51%), Positives = 271/397 (68%), Gaps = 1/397 (0%)

Query: 1   MFQKVDAYAGDPILTLMERFKEDPRSDKVNLSIGLYYNEDGIIPQLQAVAEAEARLNAQP 60
           +F  V+    DPIL L E F  D R++KVNL +G+Y NE+G IP L+AV EAE    AQ 
Sbjct: 3   LFSAVELAPRDPILGLNEAFNADTRTNKVNLGVGVYCNEEGRIPLLRAVVEAETARVAQ- 61

Query: 61  HGASLYLPMEGLNCYRHAIAPLLFGADHPVLKQQRVATIQTLGGSGALKVGADFLKRYFP 120
           H +  YLP++G+  Y  A+  LLFG D P++   RV T Q +GG+GALK+GADFLK+  P
Sbjct: 62  HVSRGYLPIDGIAAYDQAVQTLLFGKDSPLITSGRVITTQAVGGTGALKIGADFLKQLLP 121

Query: 121 ESGVWVSDPTWENHVAIFAGAGFEVSTYPWYDEATNGVRFNDLLATLKTLPARSIVLLHP 180
           ++ V +SDP+WENH A+F  AGF V  Y +YD AT+ V  + LL  L  LP RSIV+LH 
Sbjct: 122 DAVVAISDPSWENHRALFETAGFPVQNYRYYDAATHDVNRSGLLEDLNALPDRSIVVLHA 181

Query: 181 CCHNPTGADLTNDQWDAVIEILKARELIPFLDIAYQGFGAGMEEDAYAIRAIASAGLPAL 240
           CCHNPTG DL+ + W  V+ ++KA+  +PFLD+AYQGFGAG++EDA A+R  A +GL   
Sbjct: 182 CCHNPTGVDLSPEDWKNVLAVVKAKNHVPFLDMAYQGFGAGIDEDAAAVRLFAESGLTFF 241

Query: 241 VSNSFSKIFSLYGERVGGLSVMCEDAEAAGRVLGQLKATVRRNYSSPPNFGAQVVAAVLN 300
            S+SFSK FSLYGERVG LS++ E  E + RVL Q+K  +R NYS+PP  GA +VAAVLN
Sbjct: 242 ASSSFSKSFSLYGERVGALSIVSESKEESARVLSQVKRVIRTNYSNPPTHGASIVAAVLN 301

Query: 301 DEALKASWLAEVEEMRTRILAMRQELVKVLSTEMPERNFDYLLNQRGMFSYTGLSAAQVD 360
              L+A W AE+ EMR RI  MR ++V +L+   P  +F ++  Q GMFSY+GL+  QV 
Sbjct: 302 SPELRAQWEAELAEMRLRIRGMRIQMVDMLAKAAPHHDFSFVARQSGMFSYSGLTVEQVT 361

Query: 361 RLREEFGVYLIASGRMCVAGLNTANVQRVAKAFAAVM 397
           RLR EFG+Y + +GR+CVA LN  N+  V KA   V+
Sbjct: 362 RLRNEFGIYALDTGRICVAALNQNNIDAVTKAIVQVI 398


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: 404
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: 398
Length adjustment: 31
Effective length of query: 366
Effective length of database: 367
Effective search space:   134322
Effective search space used:   134322
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.

Links

Downloads

Related tools

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