GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Paraburkholderia bryophila 376MFSha3.1

Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate H281DRAFT_02907 H281DRAFT_02907 arginine:pyruvate transaminase

Query= curated2:Q30ZX9
         (388 letters)



>FitnessBrowser__Burk376:H281DRAFT_02907
          Length = 395

 Score =  188 bits (478), Expect = 2e-52
 Identities = 112/370 (30%), Positives = 189/370 (51%), Gaps = 6/370 (1%)

Query: 20  QIDKVKAEVAARGVDIISLGIGDPDMPTPDFVIEALKKAAEKPANHQYPSYTGMLAFRQE 79
           +I +V  + AA G D+I L +GDPD  TP  ++E    A      H Y + +G    R  
Sbjct: 19  EIHRVAQQAAANGNDVIVLSVGDPDFATPAPIVERAIDALRGGDTH-YSAVSGRDPLRAA 77

Query: 80  VANWYKRRYAVELDPKTEVLTLIGSKEGIAHFPTAFVNPGDLVLVCPPCYPVYAIASRFM 139
           +A    R     +     +LT  G++ G+       +  GD V+V  P Y  Y    R  
Sbjct: 78  IAEEQARMTGCTVSAANVILTA-GAQNGVFATSLCLLEAGDEVIVPEPMYLTYEACVRAA 136

Query: 140 GGVVQELPLLEENDFLPDLDAVDEATWEKARCIFVNYPNNPTAAMAPRSFFEKLIGIARK 199
           G  +  +P+     F  D DA++ A   + + IF   P NPT  + PR+  E++  +A +
Sbjct: 137 GATLVPVPVDPARAFHLDCDALERAVTPRTKAIFFATPCNPTGVVMPRADLERIARLACE 196

Query: 200 HNVIVVHDAAYTEMYYNENNRPLSIMEIPGAMDVAIEFNSLSKPYNMTGWRIAMAVGNAS 259
           H++ V+ D  Y ++ +   +  +SIM +PG  +  +   SLSK + M GWR+  A+G   
Sbjct: 197 HDLWVLSDEVYADLTFEREH--VSIMSLPGMAERTVTLGSLSKSHAMAGWRVGWAIGPTQ 254

Query: 260 LVAGLGKVKENMDSGAFQAVQEAAIVALRDGDAFLAEIRDIYRKRRDTVIAALNKI-GIT 318
           L+  +G++   M  G    +Q+AA+ AL++  + +A++RDIYR+RRD V   L+++  + 
Sbjct: 255 LIEHMGRLALAMLYGLPGFIQQAALTALQEKSSIVAQMRDIYRRRRDVVFERLSRVPRLR 314

Query: 319 CRVPEASLYVWARVP-EGYTSSDFVTRVLQETGVVMTPGNGFGAAGEGYFRISLTVNDER 377
           C +PEA +++   V   G  + DF  ++ +  GV +   + FG    G+ R+   V++ R
Sbjct: 315 CLLPEAGMFMMVDVSGTGLDTVDFTWQLFRAQGVSVLDASAFGETANGFVRLGFVVDEAR 374

Query: 378 LEEAVSRIAS 387
           L EA  RIA+
Sbjct: 375 LAEACERIAA 384


Lambda     K      H
   0.320    0.136    0.403 

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: 339
Number of extensions: 18
Number of successful extensions: 4
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: 388
Length of database: 395
Length adjustment: 31
Effective length of query: 357
Effective length of database: 364
Effective search space:   129948
Effective search space used:   129948
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