GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Streptacidiphilus oryzae TH49

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_037574082.1 BS73_RS18925 aspartate aminotransferase family protein

Query= SwissProt::P22256
         (426 letters)



>NCBI__GCF_000744815.1:WP_037574082.1
          Length = 453

 Score =  222 bits (565), Expect = 2e-62
 Identities = 141/422 (33%), Positives = 214/422 (50%), Gaps = 35/422 (8%)

Query: 22  IHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVL 81
           I P+    AE    WD +G  YLDF  G+   N G+ HPKVVAA++ Q  KL  T     
Sbjct: 33  IDPLPVAGAEGSYFWDFDGNRYLDFTSGLVNANIGYQHPKVVAAIQEQAGKLV-TFAPAF 91

Query: 82  AYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSGTIAFSGAYHGR 141
           A E   E   ++ ++ PGD   K      G+EA ENA+++AR  T R   ++   +YHG 
Sbjct: 92  ALESRSEAARLIAERTPGDL-NKIFFTNGGAEANENAIRLARQYTGRHKVLSTYRSYHGA 150

Query: 142 THYTLALTGKVNPYSAGMGLMPGHVYRALYP--CPLHGISEDDAIASIHRIFKNDAA--- 196
           T   + LTG    +   +G+     +   YP   P H  SE        +  +   A   
Sbjct: 151 TANAIMLTGDPRRWQNEIGVGGVSHFWGPYPYRSPFHSTSEQQECERALQHLEETIAFEG 210

Query: 197 PEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQ 256
           P  +AA+++E + G  G     P ++  +R +CD +GI+ I DEV +G GRTG  FA + 
Sbjct: 211 PGTVAAVILETIVGTAGVLVPPPGYLAGVREICDRYGIVFILDEVMAGFGRTGEWFAADH 270

Query: 257 MGVAPDLTTFAKSIAGGF-PLAGVTGRAEVM----DAVAPGGLGGTYAGNPIACVAALEV 311
            GV PDL TFAK +  G+ PL GV     +     +   PGGL  TY+G+P+AC +A+  
Sbjct: 271 WGVTPDLLTFAKGVNSGYVPLGGVAISERIAAIFDERPFPGGL--TYSGHPLACASAVAT 328

Query: 312 LKVFEQENLLQKANDLGQK-LKDGLLAIAEKHPEIGDVRGLGAMIAIELFE--------- 361
           +    +E +++ A  LG+  L  GL  +AE+HP +G+VRGLG   A++L +         
Sbjct: 329 INAMAEEGIVEHARALGENVLGPGLRELAERHPSVGEVRGLGVFWALDLVKSKETREALV 388

Query: 362 ----DGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEII 417
                G+ NKP     AE+ A  + +GL  ++     N L ++ P T  +A+ ++GL I+
Sbjct: 389 PYNPSGEQNKP----IAELAAACKQRGLWPMT---NMNRLHVVPPCTTSEAEAKEGLAIL 441

Query: 418 SQ 419
            +
Sbjct: 442 DE 443


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: 527
Number of extensions: 29
Number of successful extensions: 6
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: 453
Length adjustment: 32
Effective length of query: 394
Effective length of database: 421
Effective search space:   165874
Effective search space used:   165874
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