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_010531860.1 ON01_RS14825 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000224785.1:WP_010531860.1
          Length = 433

 Score =  377 bits (967), Expect = e-109
 Identities = 184/424 (43%), Positives = 268/424 (63%), Gaps = 7/424 (1%)

Query: 5   KELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVA 64
           K L ++R   IP+GV   +      A    V D++  E++DFAG I  LN GH HPKV  
Sbjct: 9   KALQEKRENYIPKGVSNGNSNIVKDAIGATVTDIDNNEWIDFAGAIGTLNVGHTHPKVTT 68

Query: 65  AVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA 124
           AV+ Q  K  H  F V+ YE Y+ L E + Q  PG F K+ LL+ +G+EA+ENA+K++R 
Sbjct: 69  AVKEQADKFLHPGFNVMMYEGYINLAEKLCQITPGHFNKQALLLNSGAEAIENAIKVSRK 128

Query: 125 ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISE---- 180
            T +   ++F   +HGRT+ T+ +T KV PY  G G     +Y+A YP   H  S+    
Sbjct: 129 YTGKQAVVSFERGFHGRTNLTMGMTSKVKPYKFGFGPFAPDIYQAPYPYLYHKPSQLTDD 188

Query: 181 ---DDAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLI 237
              D  I      F +  APE++A +V+EPVQGEGGF      F+Q ++  C++HGI+ +
Sbjct: 189 EYVDQVIRDFEDFFVSSVAPENVACVVMEPVQGEGGFIIPPKRFVQYVKEFCEKHGIVFV 248

Query: 238 ADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGT 297
           ADE+Q+G GRTG LFA++   V PDL T +KS+A G PL+GV G+ E+++A  PG LGGT
Sbjct: 249 ADEIQTGFGRTGKLFAVDHFDVEPDLMTVSKSMAAGLPLSGVVGKKEILNAANPGELGGT 308

Query: 298 YAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAI 357
           YAGNP+AC AAL V+ V E+ENL +KA+ +G+K++  L  + +K+  +G++R LGAM+A+
Sbjct: 309 YAGNPVACSAALAVIDVMEEENLPEKADVIGRKIEGKLQELQKKYEFVGEIRRLGAMVAV 368

Query: 358 ELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417
           E+ ED +  +PD + T++I A A   GL+LLS G   N++R L PL I D ++ +GL+I+
Sbjct: 369 EIVEDRESKRPDKQKTSDITANANQNGLLLLSAGINSNIVRFLAPLVITDEELEKGLDIL 428

Query: 418 SQCF 421
            Q F
Sbjct: 429 EQTF 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: 454
Number of extensions: 23
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: 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 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