GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Echinicola vietnamensis KMM 6221, DSM 17526

Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase

Query= reanno::Marino:GFF3099
         (404 letters)



>FitnessBrowser__Cola:Echvi_3848
          Length = 381

 Score =  214 bits (544), Expect = 4e-60
 Identities = 143/380 (37%), Positives = 200/380 (52%), Gaps = 20/380 (5%)

Query: 24  IIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPGLVGALHDQAEKIWHLSNVMTNEP 83
           + PV+  GS IWD +G E++DL GG AV  +GHSHP     + +Q + I   SN +    
Sbjct: 12  VTPVKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAFYSNSVQIPI 71

Query: 84  ALRLAKTLCDLTFAER--VFFANSGAEANEAAFKLARRYAWEHHGKEKNEIISFKNSFHG 141
              LA  L  L+      +F  NSGAEANE A KLA           K   I+F   FHG
Sbjct: 72  QKELATKLGQLSGYPDYDLFLCNSGAEANENALKLAS------FETGKKGFIAFTKGFHG 125

Query: 142 RTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKLISKEKTCAIVVEPIQGEGGVM 201
           RT   V++   PK +  F  A  G+H   FNDLE+V+K ++      ++VE IQG GG+ 
Sbjct: 126 RTSGAVALTDNPKIIAPFN-AHEGVHILPFNDLEAVEKQLATGTIAGVIVEGIQGVGGIQ 184

Query: 202 PGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAYQ-MYGVVPDILSSAKGLGGGF 260
             D AFL GL  L  +  A L+ DEVQSG  RSG F+A+Q + G+ PD+++ AKG+G GF
Sbjct: 185 VPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMGNGF 244

Query: 261 PVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDTVSQPEILKGVKARSDKLRKG 320
           P+  +L + +  AS G+   G+T+GGN LACA A  V++ + +  ++           K 
Sbjct: 245 PIGGVLISPEFKASHGL--LGTTFGGNHLACAAALAVLEVIDEENLITAAAENG----KA 298

Query: 321 MMDIGERYGVFTEVRGAGLLLGCVL-TEKWQGKAKDFLNAGLEEGVMVLVAGANVIRLAP 379
           +M   E+    TEVRG GL++G  L TE    +A       +  G      G + IRL P
Sbjct: 299 IMAALEKVAGVTEVRGKGLMIGFDLATEAGPVRAALIHEHKIFTG---SAGGKHTIRLLP 355

Query: 380 SLIIPEPDIELALERFEAAV 399
            L I    + L LE+ E  +
Sbjct: 356 PLNIEPKALTLFLEKLETVL 375


Lambda     K      H
   0.318    0.137    0.406 

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: 406
Number of extensions: 37
Number of successful extensions: 8
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: 381
Length adjustment: 31
Effective length of query: 373
Effective length of database: 350
Effective search space:   130550
Effective search space used:   130550
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 (21.7 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