GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Desulforamulus ruminis DSM 2154

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_013840109.1 DESRU_RS00105 alanine--glyoxylate aminotransferase family protein

Query= BRENDA::P74281
         (384 letters)



>NCBI__GCF_000215085.1:WP_013840109.1
          Length = 385

 Score =  316 bits (809), Expect = 8e-91
 Identities = 169/385 (43%), Positives = 246/385 (63%), Gaps = 5/385 (1%)

Query: 1   MDNKQMLMIPGPTPVPEKVLLAMAKHPIGHRSGDFSKIIAELTANLKWLHQTENDVLMLT 60
           M +K+ L+IPGPTPVP +V+ AM++  IGHRS  F  ++  +T  LK + QTEN V +L 
Sbjct: 2   MKDKKYLLIPGPTPVPPRVVEAMSRPIIGHRSAGFQAVMERVTGKLKKVFQTENHVFILG 61

Query: 61  TSGTGAMEASIINFLSPGDRVLVGNNGKFGDRWVKVAKTFGLAVEEIKAEWGKALDPNDF 120
           +SGTGA+EA++ N + PGD+VL  + GKFG+R+ ++A+ +G  V+ +   WG  +D N  
Sbjct: 62  SSGTGALEAAVANLVHPGDKVLALSCGKFGERFAELARIYGGNVDFVDFGWGYDIDLNVV 121

Query: 121 KTLLEADSDKTIKALIITHSETSTGVLNDLAAINAAAKAHGGALMIVDAVTSLGATPVAI 180
           K  L  D D  IK ++ T +ETST V ND+  +     A   A++ VDAV+ L A  +  
Sbjct: 122 KRKL--DEDSAIKVVLATQNETSTAVQNDIEGLGKLV-AQYDAVLAVDAVSGLAAIDLKT 178

Query: 181 DDLGLDVVASGSQKGYMIPPGLGFVSVSAKAWQAYETATIPRFYLDLKKYKKSTDEDSSP 240
           D+  +D+V SGSQK +M+PPGL F+SVS KAW   E  T P +Y DLKK KKS  + ++ 
Sbjct: 179 DEWNVDMVVSGSQKAFMLPPGLAFISVSDKAWAKIEKNTSPVYYFDLKKAKKSIAKWNTA 238

Query: 241 FTPPINLMYGLQASLQMMKAEGLDAIFTRHQRHTNATRGAMKALNLPLFAPDNAASNAIT 300
           +T P++++YGL+A+L M+  EGL  +F RH     ATR A++ L L L APD  AS A+T
Sbjct: 239 YTTPVSMVYGLEAALDMILEEGLPQVFARHALLAKATRAAVQGLGLELLAPDECASKAVT 298

Query: 301 AV-APLGVEAEKIRSTMRKKFDIAMAGGQDHLKGKIFRIGHLGFVCDRDILSCIGALEAT 359
           AV +P+ V+A+ +R  + K++ +  AGGQ+ +KGKIFRI H+G+    D++  I ALE  
Sbjct: 299 AVQSPMVVDADTLRKVLLKEYGVTFAGGQEMMKGKIFRIAHMGYAGKMDVIIAIAALEMA 358

Query: 360 LIELGYEGVTPGSGVAAAAGVLAKG 384
           L + GY+    G+GV  A  V   G
Sbjct: 359 LGKCGYKAEL-GAGVREAQMVFVGG 382


Lambda     K      H
   0.317    0.134    0.386 

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: 353
Number of extensions: 16
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: 384
Length of database: 385
Length adjustment: 30
Effective length of query: 354
Effective length of database: 355
Effective search space:   125670
Effective search space used:   125670
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: 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