GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Lentibacillus jeotgali Grbi

Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate WP_010532043.1 ON01_RS16140 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000224785.1:WP_010532043.1
          Length = 450

 Score =  357 bits (915), Expect = e-103
 Identities = 183/427 (42%), Positives = 260/427 (60%), Gaps = 7/427 (1%)

Query: 5   KELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVA 64
           KEL++RR  A+P GV    P F + A+   + D++G  ++DFAG I V N GH H  VV 
Sbjct: 18  KELLERRHNAVPHGVSYGTPTFVESAKGALLKDIDGNHFIDFAGAIGVNNVGHSHDTVVN 77

Query: 65  AVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA 124
           A++ Q  K  HT F V+ Y+ Y+EL E +    PG F KK + + +G+EA ENAVKIAR 
Sbjct: 78  ALQDQAPKYIHTGFNVMMYDSYVELAEKLADLSPGSFDKKVMFLNSGAEANENAVKIARK 137

Query: 125 ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLH---GISE- 180
            T R   ++ +G +HGRT   +++TGKV PY    G     VY A +P       G+SE 
Sbjct: 138 YTGRQAVVSVTGGFHGRTLLAMSMTGKVKPYKYEYGPFAPEVYHAPFPYNYRRPDGMSEE 197

Query: 181 ---DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLI 237
              D+ +  +   F  +  P  +AA  +EPVQGE GF   +  F+Q +  LC +HGI+ I
Sbjct: 198 AYTDELLKRVKDFFITEVDPSQVAAFFMEPVQGESGFIIPNKKFVQGVYELCKQHGILFI 257

Query: 238 ADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGT 297
           ADE+Q+G GRTG  FAM+  GV PDL T +KS+A G P++G+ GR EVMD    G LGGT
Sbjct: 258 ADEIQTGFGRTGKYFAMDHFGVEPDLVTVSKSMAAGLPISGIIGRQEVMDFAQKGELGGT 317

Query: 298 YAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAI 357
           Y G P+ C A L VL+V E+ENL  +A  +G+K+ +    + +    IGD RGLGAM A+
Sbjct: 318 YCGTPLGCRAGLAVLEVMEKENLNDRAVKIGEKVMEKFGKMYDCFDAIGDYRGLGAMCAL 377

Query: 358 ELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417
           E  +D D  +PD  LT +++  AR++GLI L+ G + NV+R+L+PL   D Q+ +GL+I+
Sbjct: 378 EFVKDRDTKEPDKALTGQVLKEARERGLIALNAGVFDNVVRLLMPLVTTDEQLEEGLDIL 437

Query: 418 SQCFDEA 424
            +  + A
Sbjct: 438 EEAIEAA 444


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: 513
Number of extensions: 21
Number of successful extensions: 2
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: 450
Length adjustment: 32
Effective length of query: 394
Effective length of database: 418
Effective search space:   164692
Effective search space used:   164692
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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