GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Rhizorhabdus wittichii RW1

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_012050345.1 SWIT_RS21085 4-aminobutyrate--2-oxoglutarate transaminase

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000016765.1:WP_012050345.1
          Length = 434

 Score =  431 bits (1107), Expect = e-125
 Identities = 216/419 (51%), Positives = 284/419 (67%), Gaps = 1/419 (0%)

Query: 2   NSNKELMQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPK 61
           +SN  L  RR  A+P+GV    PIFA RAEN  +WDVEGR Y+DFA GIAVLN GH HP+
Sbjct: 7   SSNDALWGRRLAAVPQGVATAAPIFAARAENAEIWDVEGRRYIDFASGIAVLNVGHRHPR 66

Query: 62  VVAAVEAQLKKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKI 121
           ++AAVE QL + +HT FQV+ YEPY+ L E +N   P     KT+  TTG+EA ENAVKI
Sbjct: 67  IIAAVEEQLGRFTHTAFQVVGYEPYVRLAERLNALAPVVGPAKTIFFTTGAEATENAVKI 126

Query: 122 ARAATKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISED 181
           AR A+ RS  IAF   +HGRT    A+TGKV PY  G G +PG +Y   +P   HGI+ +
Sbjct: 127 ARYASGRSAVIAFVNGFHGRTLLASAMTGKVLPYKKGFGPLPGDIYHIPFPSEAHGITVE 186

Query: 182 DAIASIHRIFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEV 241
            ++A++  +  +D    ++AAI++EPVQGEGGF+ +   F++ LR+LCDEHGI LIADEV
Sbjct: 187 HSLAALANVLSSDVEAANVAAIILEPVQGEGGFHVAPFEFLRALRSLCDEHGIALIADEV 246

Query: 242 QSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGN 301
           Q+G GRTG LFA+E  GV PDL T AKS+ GGFPL+ V G A ++D V PGGLGGTYAG+
Sbjct: 247 QTGIGRTGKLFAVEHAGVRPDLITVAKSLGGGFPLSAVVGNAALIDRVPPGGLGGTYAGS 306

Query: 302 PIACVAALEVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHP-EIGDVRGLGAMIAIELF 360
           PIAC A L VL V EQ+ L  +A  +G+++ + L A+A +    IG  RGLGAMIA ++ 
Sbjct: 307 PIACAAGLAVLDVIEQDRLCDRAERMGRRITERLSAVAARRELPIGLPRGLGAMIAFDIR 366

Query: 361 EDGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQ 419
              D  +PD      +  RA + GLILL+CG +   +R+L PLT  DA + +GL+I++Q
Sbjct: 367 AGLDDLRPDGAAAKRVCVRALELGLILLTCGQHGEAIRLLAPLTASDAVLDEGLDILAQ 425


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: 543
Number of extensions: 22
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: 434
Length adjustment: 32
Effective length of query: 394
Effective length of database: 402
Effective search space:   158388
Effective search space used:   158388
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