GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_026185995.1 THITHI_RS0102480 alanine--glyoxylate aminotransferase family protein

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



>NCBI__GCF_000378965.1:WP_026185995.1
          Length = 393

 Score =  220 bits (561), Expect = 5e-62
 Identities = 134/376 (35%), Positives = 205/376 (54%), Gaps = 5/376 (1%)

Query: 8   KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66
           + LM PGP+ V P VL AMA P IGH    + +++++    L+  F TEN  T  ++  G
Sbjct: 11  RTLMGPGPSDVNPRVLAAMARPTIGHLDPVFVDMMDEMKGLLQYAFQTENQLTLPVSAPG 70

Query: 67  TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126
           +A M+M   N+++ GD V+  + G FG R    V+     A+ ++ EWG   +P  ++E 
Sbjct: 71  SAGMEMCFVNLVEPGDTVVVCINGVFGGRMKENVERCGATAVVVEDEWGKPVDPGKLEEA 130

Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186
           L  + +   V  VH ETSTGA +  K + E+   +D L IVD+V+ LGG  + VD + ID
Sbjct: 131 LKAHPEAGVVAFVHAETSTGACSDAKALTEIAHRHDCLVIVDSVTGLGGVELRVDDWGID 190

Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLDLLAYKKYYEE--KKQTPY 243
              +GSQKCL+  PGL+ ++ SE+A   IK    KV  ++LDL     Y+    K+   +
Sbjct: 191 AIYSGSQKCLSCTPGLSPVSFSERAVARIKGRSHKVQSWFLDLNLVMGYWGSGTKRAYHH 250

Query: 244 TPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTS 303
           T  +N  YAL+ +L ++ EEG+EN   RH    +A +AGLE+MG+ L     +R   + +
Sbjct: 251 TAPINALYALHESLVILQEEGLENAWARHRAHHEALKAGLESMGLNLIVPRDSRLPQLNA 310

Query: 304 AKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGI-CGEKEVLATLACVELA 362
              P G++++  R  L + Y + +  G   LAGK++RIG MG     K VL  L  +E  
Sbjct: 311 VSVPAGVDEAAVRKALLDDYGLEIGAGLGPLAGKVWRIGLMGFGANRKNVLLCLGALENT 370

Query: 363 LKELGFEVKESGVEVA 378
           L   G +V+  G   A
Sbjct: 371 LAGQGTDVRAGGAVAA 386


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: 376
Number of extensions: 14
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: 393
Length adjustment: 30
Effective length of query: 355
Effective length of database: 363
Effective search space:   128865
Effective search space used:   128865
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.

Links

Downloads

Related tools

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