GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Phyllobacterium endophyticum PEPV15

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_106717846.1 CU100_RS17540 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_003010935.1:WP_106717846.1
          Length = 427

 Score =  410 bits (1054), Expect = e-119
 Identities = 197/418 (47%), Positives = 276/418 (66%), Gaps = 2/418 (0%)

Query: 5   KELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVA 64
           ++L++RR + I RG+   HPI A +A+   +WDVEGR YLDF GGI VLN GH HP+VV 
Sbjct: 9   QDLLERRDRNIARGIATAHPILASKAKGTELWDVEGRRYLDFVGGIGVLNVGHNHPRVVD 68

Query: 65  AVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARA 124
           AV+ Q++ LSH CFQVL YEPY+ L E +N  +  D+  K+   T+G+EAVEN+VKIAR 
Sbjct: 69  AVKRQIETLSHACFQVLGYEPYVALAEKLNTLIGKDY--KSAFFTSGAEAVENSVKIARG 126

Query: 125 ATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAI 184
            T R   IAF G +HGRT   ++LTG   PY    G     ++   YP    G++  DA+
Sbjct: 127 YTNRPAVIAFRGGFHGRTLLGVSLTGMSQPYKQNFGPFAPEIFHIPYPNAYRGVTTADAL 186

Query: 185 ASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSG 244
           A++  +F  D APE +AAI+IEPVQG+GGF+ +   F+  LR + ++HGI+LI DE+Q+G
Sbjct: 187 AALAEVFATDVAPERVAAIIIEPVQGDGGFHPAPVNFVAALREITNKHGIVLILDEIQTG 246

Query: 245 AGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIA 304
            GRTG +F  +  G+ PDL T AKS+AGG PL+ V G+AE+MDA  PGGLGGTY GN +A
Sbjct: 247 FGRTGEMFGFQHSGIEPDLVTIAKSLAGGLPLSAVVGKAEIMDAPTPGGLGGTYGGNALA 306

Query: 305 CVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGD 364
           C AAL V++ FE++++L+       +L+ GL+A+ ++H  IGDVRGLG M+AIE+  D  
Sbjct: 307 CAAALAVIETFERDDILRNGRQRAAQLRKGLIALQQRHAFIGDVRGLGFMLAIEIVSDRA 366

Query: 365 HNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFD 422
              PDA  T  ++  AR  GL+L+ CG + N +R L PL   +A+I + L  + +  +
Sbjct: 367 TKAPDADRTQHVLDEARKGGLLLIKCGIHRNTVRFLAPLVATEAEIDEALAALGEALE 424


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: 533
Number of extensions: 25
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: 427
Length adjustment: 32
Effective length of query: 394
Effective length of database: 395
Effective search space:   155630
Effective search space used:   155630
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