GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrC in Lentibacillus jeotgali Grbi

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_010531647.1 ON01_RS13770 threonine synthase

Query= curated2:Q58860
         (405 letters)



>NCBI__GCF_000224785.1:WP_010531647.1
          Length = 403

 Score =  227 bits (578), Expect = 5e-64
 Identities = 127/374 (33%), Positives = 203/374 (54%), Gaps = 4/374 (1%)

Query: 5   CIKCGKTYDVDEIIYTCECGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKDE 64
           C  C K  +       C CGG L++ YD E +    ++E L+ R   +WRY E LPV++ 
Sbjct: 7   CKACAKATEFQLKQSKCTCGGTLQVEYDLERVGHTFTKESLKNRVTSMWRYKELLPVENP 66

Query: 65  SKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGVEV 124
             I+SL EG TPL R +  E++  +K L+VK E  NPTGSFK RG +  ++ AN  G++ 
Sbjct: 67  QNIISLGEGWTPLVRMHRAEQKYPVKRLWVKREEQNPTGSFKARGFSSALSIANAYGIKK 126

Query: 125 VGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDALD 184
           V   S GN +++LAAY++ SG    V +P+    L  + + + YGA+   V G   +A  
Sbjct: 127 VAVNSNGNAASALAAYASNSGMDSYVFVPKDCPGL-IIEECIQYGAQTYLVDGLIHNAGK 185

Query: 185 MVKQLAKEKLIYLLNSI-NPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAIWK 243
           +++    E+  Y + ++  P R EG+KT+  E+ +Q NW +PD +I P G    +  IW 
Sbjct: 186 VIEDGELEQDWYNVGTLKEPGRSEGKKTMGLELAEQFNWTLPDVIIYPTGGGSGVIGIWN 245

Query: 244 GFKEFEITGIID-ELPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGNPVN 302
              + +  G I+ +LP++  +Q +G +P+V+A           ++  +  T +R+ NP +
Sbjct: 246 ALNQLKELGFIEGDLPRIVSVQEEGCQPLVDAIENGTAFNAQTQDISSNPTGMRVPNPPD 305

Query: 303 APKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGIIDR 362
               L  +  SGG A AV++E+I EAQ  L  K+GI   P  A++ A    L++ G I +
Sbjct: 306 GELILSILRESGGTAVAVSEEDIKEAQTSLG-KQGISSSPEGAATWAAFTSLIDRGWIQQ 364

Query: 363 DERIVCITTGHGLK 376
           D+ +V   T H LK
Sbjct: 365 DDEVVLFNTSHALK 378


Lambda     K      H
   0.317    0.137    0.395 

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: 426
Number of extensions: 20
Number of successful extensions: 5
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: 405
Length of database: 403
Length adjustment: 31
Effective length of query: 374
Effective length of database: 372
Effective search space:   139128
Effective search space used:   139128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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