GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Acidovorax sp. GW101-3H11

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 Ac3H11_4179 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)

Query= SwissProt::P22256
         (426 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4179
          Length = 459

 Score =  529 bits (1363), Expect = e-155
 Identities = 259/420 (61%), Positives = 320/420 (76%)

Query: 3   SNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKV 62
           +N  L+ RR  A+ RGVGQ H +F  +A N  +WDVEGR ++DFAGGIAVLNTGHLH  V
Sbjct: 33  TNAALLTRRHAAVARGVGQAHDLFIQKARNAELWDVEGRRFIDFAGGIAVLNTGHLHAGV 92

Query: 63  VAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIA 122
           +AAV+AQL   +HTCFQV+AYEPY+E+CE +N   PG FAKK+LL+TTG+EAVENA+KIA
Sbjct: 93  IAAVKAQLDLYTHTCFQVVAYEPYVEVCERLNTLAPGAFAKKSLLLTTGAEAVENAIKIA 152

Query: 123 RAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDD 182
           RA TKR G IAF+G YHGRT+ TL LTGKV PY  G G  PG  Y AL+P  LHG+S + 
Sbjct: 153 RAYTKRPGVIAFTGGYHGRTNLTLGLTGKVAPYKIGFGPFPGETYHALFPNALHGVSVEQ 212

Query: 183 AIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQ 242
           A+ S+  IFKND  PE +AA ++EPVQGEGGFY + P F+  L+ L D +GI+LIADEVQ
Sbjct: 213 ALHSVELIFKNDIEPERVAAFIVEPVQGEGGFYVAPPEFISGLKTLADRYGILLIADEVQ 272

Query: 243 SGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNP 302
           +GAGRTGT FA EQ  VAPDL T AKS+AGGFPLAGV GRA+VMDA APGGLGGTYAG+P
Sbjct: 273 TGAGRTGTWFASEQWPVAPDLITTAKSLAGGFPLAGVVGRADVMDAPAPGGLGGTYAGSP 332

Query: 303 IACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFED 362
           +AC A+L V++ F QE LL ++ D+G  L   L  +A + P IGDVRGLGAM+AIELFE+
Sbjct: 333 VACAASLAVIEAFAQEKLLARSQDMGALLVRSLKDLAARIPAIGDVRGLGAMVAIELFEN 392

Query: 363 GDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
           GD ++PDA LT ++VA A  +GLILLSCG + NV+RILVPLT  D  + +GL I++   +
Sbjct: 393 GDLSRPDAALTKQVVAEAARRGLILLSCGTHGNVIRILVPLTASDELLHEGLAILADSLE 452


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: 630
Number of extensions: 17
Number of successful extensions: 1
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: 459
Length adjustment: 32
Effective length of query: 394
Effective length of database: 427
Effective search space:   168238
Effective search space used:   168238
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