GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Thioalkalivibrio halophilus HL17

Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_018947109.1 B1A74_RS01550 homoserine O-succinyltransferase

Query= curated2:C4Z0T6
         (310 letters)



>NCBI__GCF_001995255.1:WP_018947109.1
          Length = 356

 Score =  169 bits (429), Expect = 7e-47
 Identities = 115/344 (33%), Positives = 169/344 (49%), Gaps = 41/344 (11%)

Query: 1   MPIKIQSDLPAKAELEEENIFVMDENRAISQNIRPLEIIVLNLMP--IKQDTELQLLR-- 56
           MP+   S LP    L  E   V+  + A  Q IR L I +LN+MP      TE Q  R  
Sbjct: 1   MPLVAHSGLPTFERLRSEGESVLPNDFARQQEIRALHIGLLNMMPDAALAATERQFFRLI 60

Query: 57  GLSNTPLQIDVTFLQMSSHVSKNTSASHIKKFYQTFEEIKNNNYDGMIITGAPVEKLDFE 116
           G SN   Q  +    +           H++ +Y+ FE++K    D +IITGA V + D  
Sbjct: 61  GESNQIAQFYIHPFTLPQLKRGRKGREHVENYYEDFEQLKEEGLDALIITGANVTQPDLA 120

Query: 117 EVNYWDELITVMEWSNKHVTSTIHICWGAQAGLYYHYGIKKELLPKKLSGVYKHRVMNRK 176
              +W+ L  V++W+  +VTST+  C    A L  HYG  ++ + +KL GV+ HRV++R+
Sbjct: 121 LEPFWEPLAEVVDWAWDNVTSTLCSCLATHAVLQSHYGEHRQHMGEKLWGVFPHRVVDRR 180

Query: 177 EPLVRGFDDVFMAPHSRYTQASRQQILDNPRLKVLADSDEAGIYI-VLGDGGKEIFVMGH 235
            PLV G +  F  PHSRY + +R Q  ++  L+VL +S+EAGI++    DG + +F  GH
Sbjct: 181 HPLVTGVNTRFDVPHSRYNKVTRDQ-FEHHGLRVLVESEEAGIHLGASPDGFRMVFFQGH 239

Query: 236 PEYDRLTLDQEYKRDIDKGIE------PDLPVNYYPD-----------------DDCNRK 272
           PEYD ++L +EYKR++ + IE      P LP NY                    + C   
Sbjct: 240 PEYDSISLLKEYKREVVRYIEGDRKAYPPLPENYLMPQAAAILDEHREHVEAALEHCTEI 299

Query: 273 PLL-----------SWRSHANNLYTNWLNYYVYQITPYDLNESY 305
           P L           +W   A  +  NWL   VYQ+T  D  + +
Sbjct: 300 PALPEALLLDRLDNTWHDTALAVINNWLG-NVYQLTNLDRRKPF 342


Lambda     K      H
   0.318    0.137    0.413 

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: 322
Number of extensions: 13
Number of successful extensions: 4
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: 310
Length of database: 356
Length adjustment: 28
Effective length of query: 282
Effective length of database: 328
Effective search space:    92496
Effective search space used:    92496
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 (21.7 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