GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Thermocrinis albus DSM 14484

Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate WP_012991318.1 THAL_RS01365 aspartate aminotransferase family protein

Query= curated2:Q5JFW3
         (362 letters)



>NCBI__GCF_000025605.1:WP_012991318.1
          Length = 379

 Score =  260 bits (665), Expect = 4e-74
 Identities = 148/371 (39%), Positives = 225/371 (60%), Gaps = 15/371 (4%)

Query: 5   RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64
           R  +R V+G+GVY++DEKG+RYLDL++GI VN LG+   + V  +  Q +K++    +FE
Sbjct: 9   RLPVRFVKGKGVYLYDEKGKRYLDLVSGIAVNALGYGDRDQVKAICHQAKKLIHVSNLFE 68

Query: 65  HDEREEMLEELSH--WVDYEYVYMGNSGTEAVEAAIKFARL-----ATGRSEIVAMTNAF 117
           +  +E++ + L    W     V+  NSGTEA EAAIK  R         R  I+   N+F
Sbjct: 69  NPWQEKLAKLLVERFWTKGR-VFFCNSGTEANEAAIKLVRRYFRLRGEDRYRIITFQNSF 127

Query: 118 HGRTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKEAITKETAAVIFEPIQGEGGI 177
           HGRT GS+SAT +KK + GF PL+ GF +  FN++ + ++ IT +TAAV+ E +QGEGG+
Sbjct: 128 HGRTFGSMSATAQKKIQTGFEPLLEGFDYAIFNDISSVEKLITDKTAAVMLEIVQGEGGV 187

Query: 178 VPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGF 236
             AD +F++ L+ L  + G LL+ DEVQ+G+ RTGKF A +H+ + PDI+T+ KG+G G 
Sbjct: 188 RVADRQFLEDLQKLCRERGLLLLLDEVQTGIGRTGKFYAYQHFQLEPDIITLAKGLGGGV 247

Query: 237 PVSLTLTDLEIPR----GKHGSTFGGNPLAC-RAVATTLRILRRDRLVEKAGEKFME-FS 290
           P+   L   E+ +    G HGSTFGGNPLAC  A+    ++      V + GE FME  +
Sbjct: 248 PIGALLAREEVAKAFDAGSHGSTFGGNPLACASALVVVEKVSELLDHVREVGEYFMERLA 307

Query: 291 GERVVKTRGRGLMIGIVLRRPAGNYVKALQERGILVNTAGNRVIRLLPPLIIEGDTLEEA 350
                + RG GLM+ + L       V    E+G+++N    +V+R +PPLI++   ++ A
Sbjct: 308 ALGRGEVRGMGLMLALELESNCKEVVLKALEKGLVINCTAKKVLRFVPPLILQKRHVDIA 367

Query: 351 RKEIEGVLNDI 361
            + +  VL ++
Sbjct: 368 VRILRRVLEEV 378


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: 363
Number of extensions: 18
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: 362
Length of database: 379
Length adjustment: 30
Effective length of query: 332
Effective length of database: 349
Effective search space:   115868
Effective search space used:   115868
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: 49 (23.5 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