GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sinorhizobium fredii NGR234

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19); 4-aminobutyrate-pyruvate transaminase (EC 2.6.1.96) (characterized)
to candidate WP_015886801.1 NGR_RS03310 aspartate aminotransferase family protein

Query= BRENDA::Q94CE5
         (504 letters)



>NCBI__GCF_000018545.1:WP_015886801.1
          Length = 466

 Score =  385 bits (988), Expect = e-111
 Identities = 198/451 (43%), Positives = 281/451 (62%), Gaps = 8/451 (1%)

Query: 55  MLAPFT--AGWQSADLDPLVIAKSEGSYVYDDTGKKYLDSLAGLWCTALGGNEPRLVSAA 112
           +L PFT    +      P ++   +G  + D +G++Y+D  AGL+C  +G     +  A 
Sbjct: 15  VLHPFTYLKDYAEGATAPTIVETGKGVRIKDASGREYIDGFAGLYCVNVGYGRTEVAEAI 74

Query: 113 VEQLNTLPFYHSFWNRTTKPSLDLAKVLLEMFTANKMAKAFFTSGGSDANDTQVKLVWYY 172
             Q   L +YHS+   TT+    L+  L++M   + M+K FF   GSDAN+TQ K+VWYY
Sbjct: 75  ARQAYKLAYYHSYAAHTTEELARLSDRLVKMAPGH-MSKVFFGLSGSDANETQAKIVWYY 133

Query: 173 NNALGRPEKKKFIARKKSYHGSTLISASLSGLPPLHQNFDLPAPFVLHTDCPHYWRFHLP 232
           NN  G+P KKK IAR++ YHG +++S S++GL   H + DLP   +L T  PH++R  LP
Sbjct: 134 NNLRGKPAKKKIIARERGYHGCSVVSGSMTGLSFYHDHMDLPVAGILRTGVPHHYRGALP 193

Query: 233 GETEEEFSTRLAKNLEDLIIKEGPETIGAFIAEPVMGAGGVIPPPATYFEKVQAVVKKYD 292
           GETEE FS R A+ LE LI+ EGPET+ A IAEPV+G GG+IPPP+ Y+ ++QAV+KKYD
Sbjct: 194 GETEETFSERRARELEALILAEGPETVAALIAEPVLGTGGIIPPPSGYWPRIQAVLKKYD 253

Query: 293 ILFIADEVICAFGRLGTMFGCDKYNIKPDLVTLAKALSSAYMPIGAILMSQEVADVINSH 352
           +L IADEVIC FGR G MFG D Y + PDLVT+AK L+SAY+P+ A ++S++V +V+   
Sbjct: 254 VLLIADEVICGFGRTGAMFGSDLYGMVPDLVTVAKGLTSAYVPLSASIVSEQVYEVMQEA 313

Query: 353 SSKLGVFSHGFTYSGHPVSCAVAIEALKIYKERNIPEYVAKVAPRFQDGVKAFASGSPII 412
           + ++G FSHG+TYSGHP+  A A   L I +  ++P   AK        +KA    +PI+
Sbjct: 314 TPQVGAFSHGYTYSGHPLGAAAANAVLDIVERDDLPGQAAKKGAYLMGRLKAEFEQNPIV 373

Query: 413 GETRGTGLILGTEFVDNKSPNEPFPPEWGVGAFFGAECQKHGMLVRVA--GDGILMSPPL 470
           GE RG G++   EFV ++  N PF P   VGA      +   ++ R    GD +  +PPL
Sbjct: 374 GEVRGVGMMAAVEFVPDRGANVPFSPALKVGARISQAARNRNLIARAMPHGDILGFAPPL 433

Query: 471 IISPEEIDELISIYGKALKATEEKVKELKAQ 501
            +S  EIDE++ I   A  A +E ++EL AQ
Sbjct: 434 TMSEAEIDEMVFI---AKAAVDEVLRELYAQ 461


Lambda     K      H
   0.318    0.135    0.404 

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: 607
Number of extensions: 23
Number of successful extensions: 3
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: 504
Length of database: 466
Length adjustment: 34
Effective length of query: 470
Effective length of database: 432
Effective search space:   203040
Effective search space used:   203040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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