GapMind for Amino acid biosynthesis

 

Aligments for a candidate for glyA in Bacteroides thetaiotaomicron VPI-5482

Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate 350266 BT0738 serine hydroxymethyltransferase (NCBI ptt file)

Query= BRENDA::Q5HE87
         (412 letters)



>lcl|FitnessBrowser__Btheta:350266 BT0738 serine
           hydroxymethyltransferase (NCBI ptt file)
          Length = 426

 Score =  471 bits (1212), Expect = e-137
 Identities = 239/423 (56%), Positives = 304/423 (71%), Gaps = 17/423 (4%)

Query: 6   KQDKVIAEAIEREFQRQNSNIELIASENFVSEAVMEAQGSVLTNKYAEGYPGRRYYGGCE 65
           K+D +I + IE+E QRQ   IELIASENFVS+ VM+A GS LTNKYAEGYPG+RYYGGCE
Sbjct: 2   KRDDLIFDIIEKEHQRQLKGIELIASENFVSDQVMQAMGSCLTNKYAEGYPGKRYYGGCE 61

Query: 66  FVDVTESIAIDRAKALFGAEHVNVQPHSGSQANMAVYLVALEMGDTVLGMNLSHGGHLTH 125
            VD +E IAIDR K +FGAE  NVQPHSG+QAN AV+L  L  GD  +G+NL+HGGHL+H
Sbjct: 62  VVDQSEQIAIDRLKEIFGAEWANVQPHSGAQANAAVFLAVLNPGDKFMGLNLAHGGHLSH 121

Query: 126 GAPVNFSGKFYNFVEYGVDKDTERINYDEVRKLALEHKPKLIVAGASAYSRTIDFKKFKE 185
           G+ VN SG  Y   EY ++++T R++YD++ ++AL  KPK+I+ G SAYSR  D+K+ +E
Sbjct: 122 GSLVNTSGIIYTPCEYNLNQETGRVDYDQMEEVALREKPKMIIGGGSAYSREWDYKRMRE 181

Query: 186 IADEVNAKLMVDMAHIAGLVAAGLHPNPVEYADFVTTTTHKTLRGPRGGMILCKEEYKKD 245
           IAD+V A LM+DMAH AGL+AAGL  NPV+YA  VT+TTHKTLRGPRGG+I+  +++   
Sbjct: 182 IADKVGAILMIDMAHPAGLIAAGLLENPVKYAHIVTSTTHKTLRGPRGGVIMMGKDFPNP 241

Query: 246 ----------------IDKTIFPGIQGGPLEHVIAAKAVAFGEALENNFKTYQQQVVKNA 289
                           +D  +FPG+QGGPLEHVIAAKAVAFGE L+  +K Y +QV KNA
Sbjct: 242 WGKKTPKGEIKMMSQLLDSAVFPGVQGGPLEHVIAAKAVAFGEILQPEYKEYAKQVQKNA 301

Query: 290 KVLAEALINEGFRIVSGGTDNHLVAVDVKGSI-GLTGKEAEETLDSVGITCNKNTIPFDQ 348
            +LA+ALI+ GF IVSGGTDNH + VD++     LTGK AE+ L S  IT NKN +PFD 
Sbjct: 302 AILAQALIDRGFTIVSGGTDNHSMLVDLRSKYPDLTGKVAEKALVSADITVNKNMVPFDS 361

Query: 349 EKPFVTSGIRLGTPAATTRGFDEKAFEEVAKIISLALKNSKDEEKLQQAKERVAKLTAEY 408
              F TSGIRLGTPA TTRG  E    E+A++I   L N ++EE + Q + RV +   +Y
Sbjct: 362 RSAFQTSGIRLGTPAITTRGAKEDLMIEIAEMIETVLSNVENEEVIAQVRARVNETMKKY 421

Query: 409 PLY 411
           PL+
Sbjct: 422 PLF 424


Lambda     K      H
   0.315    0.133    0.372 

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: 523
Number of extensions: 23
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: 412
Length of database: 426
Length adjustment: 32
Effective length of query: 380
Effective length of database: 394
Effective search space:   149720
Effective search space used:   149720
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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