Alignments for a candidate for glyA in Pyrolobus fumarii 1A

GapMind for Amino acid biosynthesis

Alignments for a candidate for glyA in Pyrolobus fumarii 1A

Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate WP_014027034.1 PYRFU_RS07375 serine hydroxymethyltransferase

Query= BRENDA::Q9UWT5
         (433 letters)



>NCBI__GCF_000223395.1:WP_014027034.1
          Length = 441

 Score =  580 bits (1494), Expect = e-170
 Identities = 283/419 (67%), Positives = 344/419 (82%), Gaps = 6/419 (1%)

Query: 3   LPKELEKVLEITKAQNVWRRTQTLNLIASENVMSPLAESVYMSDFMSRYAEGKPYKRYYQ 62
           LP E+ +V+E T+A N WRR +T+NLIASENVMSPLAE+ Y++D M RYAEGKP KRYYQ
Sbjct: 11  LPSEVREVIETTRAHNRWRR-ETINLIASENVMSPLAEAAYLNDMMHRYAEGKPRKRYYQ 69

Query: 63  GTKYTDEIETLTMELMNEITNSKDCDLRPTSGTIANAAVFRVLA-----EPGDKALIAPV 117
           G +Y D +E L M+ M E+      + RP SGTIANA VFR LA     E   KALIAPV
Sbjct: 70  GLRYVDVVEELVMKYMGELLGGAFIEPRPVSGTIANATVFRALASCPSSEGRPKALIAPV 129

Query: 118 QAGAHVSHTKFGTLGALGIQHIEMPFDEENINVDVDKAIKMIEEVKPKFVVLGGSLYLFP 177
           QAGAHVSHTKFGTLGAL I+HIE+P+D +N+NVDVDKA+KMIE+VKP FVVLGGSLYLFP
Sbjct: 130 QAGAHVSHTKFGTLGALCIEHIELPYDPDNLNVDVDKAVKMIEDVKPVFVVLGGSLYLFP 189

Query: 178 HPTKELAQHVHAVGAKLVYDAAHVYGLIEGKVWSNPLKDGADIMTVSTHKTFPGPQGGAI 237
           HP +E+A+  H+VGAKLVYDAAHV GLI GK W NPL  GADIMT STHKTFPGPQGG I
Sbjct: 190 HPVREIAEAAHSVGAKLVYDAAHVLGLIVGKRWRNPLDHGADIMTASTHKTFPGPQGGII 249

Query: 238 FSDGSEVFKQVSKTIFPWFVSNHHLHRLPATAVTAIEMKYFGESYANQILRNSKALAEAL 297
            +   +++K VS+ +FP+FVSNHHLHRLPA A+TA+EMKY+GE+YA+Q++RN+KALAEAL
Sbjct: 250 ATRQEDLYKAVSRIVFPYFVSNHHLHRLPALAITALEMKYYGEAYADQVVRNAKALAEAL 309

Query: 298 AERGFKVIGENLGYTKSHQVAVDVRQFGGGNKIAKLLEDANIIVNKNLLPYDKPEDVSDP 357
           A  GFKV+GE+LGYT+SHQVAVDVR++GGG K A+LLE+ANIIVNKNLLPYD P+ + +P
Sbjct: 310 AAEGFKVLGEHLGYTRSHQVAVDVREYGGGAKAAQLLEEANIIVNKNLLPYDPPDAIKNP 369

Query: 358 SGLRIGVQEMTRYGMKEGEMEEIAELFKKVIIDKKDVNEVKKEVIEMRRNFLEVKYTFD 416
           SGLR+GVQEMTR+GMKE +M EIA   ++V+ID +D  +V+KEV+E RRNF +V Y FD
Sbjct: 370 SGLRLGVQEMTRWGMKEDDMREIARFMRRVVIDGEDPAKVRKEVVEFRRNFQKVHYAFD 428


Lambda     K      H
   0.316    0.134    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: 614
Number of extensions: 19
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: 433
Length of database: 441
Length adjustment: 32
Effective length of query: 401
Effective length of database: 409
Effective search space:   164009
Effective search space used:   164009
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: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis