GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Burkholderia phytofirmans PsJN

Align 4-aminobutyrate aminotransferase GabT; (S)-3-amino-2-methylpropionate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.22 (characterized)
to candidate BPHYT_RS10155 BPHYT_RS10155 2,2-dialkylglycine decarboxylase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__BFirm:BPHYT_RS10155
          Length = 433

 Score =  208 bits (530), Expect = 2e-58
 Identities = 134/438 (30%), Positives = 224/438 (51%), Gaps = 24/438 (5%)

Query: 2   NSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPK 61
           N++    +   Q + R  G   P+  +RA+   V+D +GR  LDF  G      GH HP+
Sbjct: 4   NNDAVFWRNAKQHLIRYGGTFEPMIIERAQGSFVYDADGRAILDFTSGQMSAVLGHSHPE 63

Query: 62  VVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKI 121
           +V+ +     KL H  F  +   P ++L   + +  P D   + LL++TG+E+ E A+++
Sbjct: 64  IVSVINEYAGKLDHL-FSGMLSRPVVDLATRLAEITP-DGLDRALLLSTGAESNEAAIRM 121

Query: 122 ARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGM-GLMPGHVYRALYPCPL----- 175
           A+  T +   + F+ ++HG T    + T     YSAG  G+ P  V     P P      
Sbjct: 122 AKLVTGKYEIVGFAQSWHGMTAAAASAT-----YSAGRKGVGPAAVGSFAIPAPFLYRPR 176

Query: 176 ---HGISEDDAIASIHRIFK--NDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCD 230
              HG  + D +A +   F   +  +  ++AA + EP+   GG       +M  L+  C+
Sbjct: 177 FERHG--DYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPEGYMTALKRKCE 234

Query: 231 EHGIMLIADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVA 290
           E G++LI DE Q+G GRTGT+FA ++ GV PD+ T +K++  G PLA V   A++ +   
Sbjct: 235 ERGMLLILDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAVVTSAQIEERAH 294

Query: 291 PGG--LGGTYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDV 348
             G     T+  +P+     L VL+V E++ L+ +AN +G +LK GLL + E+   IGD+
Sbjct: 295 ELGYLFYTTHVSDPLPAAVGLRVLEVVERDGLVARANLMGARLKRGLLDLMERFDCIGDI 354

Query: 349 RGLGAMIAIELFEDGDHNKPDAKLTAEIVARARDKGLI--LLSCGPYYNVLRILVPLTIE 406
           RG G ++ +E+ +D    +P   L A+I     + GL   ++       V RI  PLT+ 
Sbjct: 355 RGRGLLLGMEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVH 414

Query: 407 DAQIRQGLEIISQCFDEA 424
           + +I  GL+++ Q  + +
Sbjct: 415 EDEIDLGLDLLGQAIERS 432


Lambda     K      H
   0.320    0.137    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: 471
Number of extensions: 23
Number of successful extensions: 5
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: 426
Length of database: 433
Length adjustment: 32
Effective length of query: 394
Effective length of database: 401
Effective search space:   157994
Effective search space used:   157994
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: 51 (24.3 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