GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Cereibacter sphaeroides ATCC 17029

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_011840643.1 RSPH17029_RS04315 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000015985.1:WP_011840643.1
          Length = 425

 Score =  457 bits (1175), Expect = e-133
 Identities = 227/423 (53%), Positives = 288/423 (68%), Gaps = 1/423 (0%)

Query: 4   NKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVV 63
           N ++ +RR++A+ RGVG    I+ADRA N  +WD+EGR Y+DFA GIAV+NTGH HPKV+
Sbjct: 3   NADVSRRRTEAVSRGVGMQTQIYADRALNAEIWDIEGRRYIDFAAGIAVVNTGHCHPKVM 62

Query: 64  AAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR 123
           AAV  Q+ + +HTC QVL YE Y+ L E +N   PGDFAKKT+ VTTG+E+VENA+KIAR
Sbjct: 63  AAVAEQMGRFTHTCHQVLPYENYIRLAERLNAAAPGDFAKKTVFVTTGAESVENAIKIAR 122

Query: 124 AATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDA 183
             T RS  +AF G +HGRT  T++LTGKV PY  G G M   VY   +P  LHGIS ++A
Sbjct: 123 IHTGRSAVVAFGGGFHGRTFMTMSLTGKVEPYKKGFGTMMPEVYHVPFPQALHGISTEEA 182

Query: 184 IASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQS 243
           +A++ R+FK D  P  +AAI+ EPVQGEGGFY + P  ++ +R LCD HGI++IADEVQ+
Sbjct: 183 MAALARLFKADLDPGRVAAIIFEPVQGEGGFYPAPPDLVRAIRQLCDAHGIVMIADEVQT 242

Query: 244 GAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPI 303
           G  RTGTLFAM    VAPDL T AK + GG P+A VTGRAE+MDA  PGGLGGTY GNP+
Sbjct: 243 GFARTGTLFAMHGYDVAPDLVTMAKGLGGGLPIAAVTGRAEIMDAAHPGGLGGTYGGNPL 302

Query: 304 ACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDG 363
              AA  VL V E+ENL  +A +LG +LK  L  I    PEI D+RG G M+  E F D 
Sbjct: 303 GIAAAHAVLDVIEEENLCARATELGSRLKQKLAEIRATAPEIADIRGPGFMVGAE-FADP 361

Query: 364 DHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDE 423
               PDA  T  +   A  +GLILL+CG + NV+R L P+TI +    + LEI+      
Sbjct: 362 GSKAPDAGFTNRVREEALKRGLILLTCGVHGNVIRFLAPITIPEPHFAEALEILEASVAA 421

Query: 424 AKQ 426
           A+Q
Sbjct: 422 ARQ 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: 602
Number of extensions: 20
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: 425
Length adjustment: 32
Effective length of query: 394
Effective length of database: 393
Effective search space:   154842
Effective search space used:   154842
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 Apr 16 2024. The underlying query database was built on Apr 09 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