GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Kyrpidia tusciae DSM 2912

Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_013075073.1 BTUS_RS05245 alanine--glyoxylate aminotransferase family protein

Query= metacyc::MONOMER-15919
         (385 letters)



>NCBI__GCF_000092905.1:WP_013075073.1
          Length = 394

 Score =  269 bits (687), Expect = 1e-76
 Identities = 145/372 (38%), Positives = 232/372 (62%), Gaps = 4/372 (1%)

Query: 7   KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGS 65
           +++L+ PGP+   PEVL AMA P++GH    +   + +T+++L++VF T    T  ++G+
Sbjct: 8   QRILLGPGPSDCHPEVLKAMATPLVGHLDPVFLEQMNETMQRLREVFQTRYPLTLAMSGT 67

Query: 66  GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125
           G+A M+    N ++ GD+V+  + G FGER  ++      E I++   WG   +P  ++E
Sbjct: 68  GSAGMETVFVNALEPGDRVVIGICGAFGERMVDVASRTGAEVIQVRAPWGRTVDPGQIQE 127

Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185
            L  +  +KAV VVH ETSTG   P++EIG + +D+ AL++VD V+SLGG  V V++  I
Sbjct: 128 ALKNHPGVKAVAVVHAETSTGVLQPLEEIGRLARDHGALFLVDAVTSLGGVPVPVEEAAI 187

Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEEKKQTPYT 244
           D C +G+QKCL+APPGL+  T S K  E +++   KV  +YLDL   ++Y+  ++   +T
Sbjct: 188 DACYSGTQKCLSAPPGLSPATFSPKFEEALERRKRKVQSWYLDLTMVRQYWGSERFYHHT 247

Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304
             + + YAL+ AL L+LEEG+E+  +RH    +A +AGLEAMG++L+A    R   +TS 
Sbjct: 248 APITMMYALHEALGLLLEEGLESVFRRHWVNGRALQAGLEAMGLQLYADAGHRLPQLTSV 307

Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICG-EKEVLATLACVELAL 363
             PEG+ED+  R  L N+Y I + GG   + G+++RIG +G     + VL  L+ +E  L
Sbjct: 308 WIPEGVEDTLVRNRLLNEYGIEIGGGLGEVKGRVWRIGLLGHSSRRRNVLLLLSALEQIL 367

Query: 364 KELGFEVKESGV 375
           + +G+ V ESG+
Sbjct: 368 RSVGYSV-ESGI 378


Lambda     K      H
   0.316    0.135    0.379 

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: 340
Number of extensions: 8
Number of successful extensions: 3
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: 385
Length of database: 394
Length adjustment: 30
Effective length of query: 355
Effective length of database: 364
Effective search space:   129220
Effective search space used:   129220
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 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