GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Thermophagus xiamenensis HS1

Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_010527895.1 GQW_RS0110425 serine hydroxymethyltransferase

Query= BRENDA::Q5SI56
         (407 letters)



>NCBI__GCF_000220155.1:WP_010527895.1
          Length = 426

 Score =  476 bits (1225), Expect = e-139
 Identities = 237/412 (57%), Positives = 300/412 (72%), Gaps = 17/412 (4%)

Query: 5   LKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAEGYPGARYYGGC 64
           +KRDE +F LI  E++RQ  G+ELIASENFVS QV  A+GS +TNKYAEG PG RYYGGC
Sbjct: 1   MKRDEKIFALIEKEKQRQLNGIELIASENFVSDQVMAAMGSCMTNKYAEGLPGKRYYGGC 60

Query: 65  EVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLT 124
           +V+D  E+LAIER K LF A WANVQPHSG+QANMAV M ++ PGD  +G+DLA GGHL+
Sbjct: 61  QVVDESETLAIERLKELFDAEWANVQPHSGAQANMAVLMTVLNPGDKFLGLDLAHGGHLS 120

Query: 125 HGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFR 184
           HGS VN SGKLY+ ++YGV+ DT L+D + + +LALEH+PK+I+ GASAY R WD++  R
Sbjct: 121 HGSPVNSSGKLYQPIAYGVKEDTGLVDYDMMEQLALEHKPKLIIGGASAYSRDWDYERMR 180

Query: 185 EIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDP--- 241
            IAD+VGA L++DMAH AGL+AAGL  NP+ YAH+VTSTTHKTLRGPRGG+IL       
Sbjct: 181 AIADKVGAILMIDMAHPAGLIAAGLLKNPVKYAHIVTSTTHKTLRGPRGGIILMGKDFDN 240

Query: 242 ------------ELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVEN 289
                       ++   +D  +FPGIQGGPLEH+IA KAVAF+EALQPE+KEY + V +N
Sbjct: 241 PMGIKTKKGEIRKMSSLLDSAVFPGIQGGPLEHIIAAKAVAFYEALQPEYKEYQKQVQKN 300

Query: 290 AKRLAEELARRGYRIVTGGTDNHLFLVDLRPK--GLTGKEAEERLDAVGITVNKNAIPFD 347
           A+++AE    +GY++++GGTDNH  L+DLR K   LTGK+AE  L    IT+NKN +PFD
Sbjct: 301 ARKMAECFMAKGYKVISGGTDNHSMLIDLRTKFPELTGKKAENTLVLADITINKNMVPFD 360

Query: 348 PKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRR 399
            + P  TSGIR+GT A+TTRG   E M  V + ID  L    SE     V++
Sbjct: 361 DRSPFQTSGIRVGTAALTTRGLKEEHMISVVDFIDEVLSNPDSEETITSVQK 412


Lambda     K      H
   0.319    0.137    0.398 

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: 532
Number of extensions: 19
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: 407
Length of database: 426
Length adjustment: 31
Effective length of query: 376
Effective length of database: 395
Effective search space:   148520
Effective search space used:   148520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 26 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