GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Clostridium acetobutylicum ATCC 824

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_010964736.1 CA_RS07495 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000008765.1:WP_010964736.1
          Length = 445

 Score =  357 bits (917), Expect = e-103
 Identities = 179/423 (42%), Positives = 270/423 (63%), Gaps = 7/423 (1%)

Query: 4   NKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVV 63
           ++EL+++R + + +GV   +P+F + A+   V D++G  ++DFAGGI V N GH    VV
Sbjct: 17  SRELLKKREKYVAKGVSCSYPVFVEEAKGALVKDIDGNVFVDFAGGIGVQNIGHRDDGVV 76

Query: 64  AAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR 123
            AV+ QL K  H CF V  YEPY++L E + +  PG+FAKK +   +G+EAVENA+KIAR
Sbjct: 77  EAVKEQLDKYIHACFHVNMYEPYVDLAEKLTEITPGNFAKKAMFANSGAEAVENAIKIAR 136

Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRA----LYPCPLHGIS 179
           A TK+SG I+ +G++HGRT+ T+++T K  PY  G G      Y+A     Y CPL    
Sbjct: 137 AYTKKSGIISMNGSFHGRTNMTMSITSKYKPYKNGFGPFVCETYKADYAYCYRCPLGCKF 196

Query: 180 EDDAIASIHRI---FKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIML 236
           +D  IA   ++    K   +P+ IA +++EPVQGEGGF      + + L+ +C+E+ I+ 
Sbjct: 197 KDCGIACAEKLKTMLKTVVSPDMIACLIVEPVQGEGGFVVPPKDYFKALQQICNENNIVF 256

Query: 237 IADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGG 296
           I DEVQ+G  RTG  FA E   V  D+ T +KSIA G P++ V G+AE+MDA   GG+GG
Sbjct: 257 IVDEVQAGFARTGKFFAHEYFDVDADIITMSKSIANGLPISAVVGKAEIMDAACVGGIGG 316

Query: 297 TYAGNPIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIA 356
           TY GNP++CVAA++V+   ++ NL +K+ +LG+ + + L  + EK+  IGDVRGLGAMI 
Sbjct: 317 TYGGNPLSCVAAIKVIDKIKEANLNEKSIELGKSIMNRLNEMKEKYNVIGDVRGLGAMIG 376

Query: 357 IELFEDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEI 416
           +E  +D D  +P+ ++ + I+      G+I L+ G   NVLR L P+ + D Q++ GL+ 
Sbjct: 377 VEFVKDKDTKEPNKEIVSSILDYCFKHGVIFLNAGLLGNVLRFLPPVVMTDEQLKYGLDT 436

Query: 417 ISQ 419
           + +
Sbjct: 437 LEE 439


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: 479
Number of extensions: 14
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: 445
Length adjustment: 32
Effective length of query: 394
Effective length of database: 413
Effective search space:   162722
Effective search space used:   162722
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 25 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