GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Cupriavidus basilensis 4G11

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 RR42_RS27380 RR42_RS27380 4-aminobutyrate aminotransferase

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__Cup4G11:RR42_RS27380
          Length = 435

 Score =  180 bits (457), Expect = 7e-50
 Identities = 123/391 (31%), Positives = 193/391 (49%), Gaps = 15/391 (3%)

Query: 24  PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLS-HTCFQVLA 82
           P+   R +   ++D  G  YLD    +A  + GH HP+VV A+  Q  +L+ HT +    
Sbjct: 32  PLHIVRGDGVWLYDANGERYLDAYNNVA--SVGHCHPQVVQAIARQAAQLNTHTRY---L 86

Query: 83  YEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGRT 142
           +E  L+  + +   +P D     +L  TGSEA + A++IARA T   G I    AYHG T
Sbjct: 87  HEGILDYAQRLLATMP-DALGHAMLTCTGSEANDLAMRIARAHTGAQGLIITRFAYHGVT 145

Query: 143 HYTLALTGKVNPY---SAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRIFKNDAAPED 199
                 +  +  Y      +  +P      + P  L  +  +    +I  +  +   P  
Sbjct: 146 ASIAEASPSLGRYVKLGDNVRTVPAPDSYRVVPAQLGAVFAEGVRHAIEDLRAHGIRP-- 203

Query: 200 IAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLF-AMEQMG 258
            AA++++ V    G +   P F++   A     G + IADEVQ G GRTG  F   ++ G
Sbjct: 204 -AALLVDTVFSSDGIFTDPPGFLKDAVAAIRAAGGVFIADEVQPGLGRTGEAFWGFQRHG 262

Query: 259 VAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPG-GLGGTYAGNPIACVAALEVLKVFEQ 317
           V PD+ T  K +  G PLAG+  R EV++A         T+ GNP++  A + VL V EQ
Sbjct: 263 VVPDIVTMGKPMGNGHPLAGLAVRPEVLEAFGRECRYFNTFGGNPVSVAAGMAVLDVIEQ 322

Query: 318 ENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPDAKLTAEIV 377
             L+ +   +G+ L++ L  +A + P IGD+RG G  +A+E  EDGD  +P    TA IV
Sbjct: 323 TQLMAQVRRVGKYLRERLAGVAARRPLIGDIRGAGLFVAVEFVEDGDAARPATARTARIV 382

Query: 378 ARARDKGLILLSCGPYYNVLRILVPLTIEDA 408
              R + +++ + G   N+L+I  P+   +A
Sbjct: 383 NGLRRRHVLVGATGEAANILKIRPPMVFTEA 413


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: 462
Number of extensions: 35
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 426
Length of database: 435
Length adjustment: 32
Effective length of query: 394
Effective length of database: 403
Effective search space:   158782
Effective search space used:   158782
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