GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Beijerinckia indica subsp. indica ATCC 9039

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012386123.1 BIND_RS16295 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= curated2:Q5JFW3
         (362 letters)



>NCBI__GCF_000019845.1:WP_012386123.1
          Length = 477

 Score =  209 bits (532), Expect = 1e-58
 Identities = 151/399 (37%), Positives = 213/399 (53%), Gaps = 57/399 (14%)

Query: 13  GEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFEHDEREE-- 70
           G+G Y++D    RYLDL++G GV  +G  HP     + R+    V+A  +    + +   
Sbjct: 59  GQGQYLFDRNDARYLDLLSGWGVFAIGRNHP-----LLRETLTSVLASDLPNLVQMDVSV 113

Query: 71  ----MLEELSHWVDY-EYVYMGNSGTEAVEAAIKFARLATGRSEIVAMTNAFHGRTLGSL 125
               + E L  +V + + V+  NSGTEAVEAAIKFAR ATGR  IV   +AFHG + GSL
Sbjct: 114 LAGLLAERLLGFVPFLDKVFFCNSGTEAVEAAIKFARRATGRPGIVYCEHAFHGLSYGSL 173

Query: 126 SATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITK-ETAAVIFEPIQGEGGIVPADEEF 184
           S    + +REGFG  +PG   +PFN++ A ++A+ K + AA I EP+QG+G  +P D+ +
Sbjct: 174 SLNGDQIFREGFGDTLPGCHAVPFNDLAALEKALAKHDIAAFIVEPVQGKGVNLP-DDGY 232

Query: 185 VKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNG-FPVSLTL 242
           +  ++ L    G L +ADE+Q+GL RTGKFLAIEH+GV PD+V + K +  G  PV   L
Sbjct: 233 LAGVQALCRKYGTLFVADEIQTGLGRTGKFLAIEHWGVEPDMVLVAKALSGGHVPVGAVL 292

Query: 243 TDLEI---------PRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA---GEKFMEF- 289
           +   I             HGSTF  N LA  A   TL ++ R++LVEKA   GE+ + F 
Sbjct: 293 SRKGIFEKVFSRMDRAVVHGSTFAKNDLAMAAGLATLEVIEREQLVEKAARNGERLLTFF 352

Query: 290 -----SGERVVKTRGRGLMIGIVLRRPAGNYVKA---------------------LQERG 323
                  E V   RG+GLMIGI    P    +KA                      +E  
Sbjct: 353 QGLADRYELVRTVRGKGLMIGIEFGAPRSLKLKASWTLLETVNTGLFCQLITIPLFKEHK 412

Query: 324 ILVNTAG--NRVIRLLPPLIIEGDTLEEARKEIEGVLND 360
           ILV  AG  +  ++LLP L+I+    +   +  E V+ D
Sbjct: 413 ILVQVAGHASHTVKLLPTLVIDDGDCDWIERAFETVIAD 451


Lambda     K      H
   0.320    0.140    0.410 

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: 427
Number of extensions: 20
Number of successful extensions: 7
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: 362
Length of database: 477
Length adjustment: 31
Effective length of query: 331
Effective length of database: 446
Effective search space:   147626
Effective search space used:   147626
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: 50 (23.9 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