GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Leptospirillum ferrooxidans C2-3

Align Serine hydroxymethyltransferase; SHMT; Serine methylase; L-threonine/L-allo-threonine aldolase; EC 2.1.2.1; EC 4.1.2.48 (characterized)
to candidate WP_014450291.1 LFE_RS10975 serine hydroxymethyltransferase

Query= SwissProt::D3DKC4
         (427 letters)



>NCBI__GCF_000284315.1:WP_014450291.1
          Length = 413

 Score =  491 bits (1264), Expect = e-143
 Identities = 235/410 (57%), Positives = 313/410 (76%)

Query: 4   LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63
           L  TD E++EAI +E +R+   L LIASEN+ S +++EA GSVMTNKYAEG P +RYY G
Sbjct: 4   LNQTDPEVHEAIAQELKREQEKLVLIASENYVSRSILEAVGSVMTNKYAEGYPGRRYYAG 63

Query: 64  CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123
           CE VD  E LAIERA+ LF AEH NVQPHSG+QANMAVY++ ++PGDTI+GMDLSHGGHL
Sbjct: 64  CEAVDQVETLAIERARLLFGAEHVNVQPHSGSQANMAVYLSSIRPGDTILGMDLSHGGHL 123

Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183
           THG+ V+FSG  YNAV+YGVH +T LID  Q+  LAK+H+P +I+ GASAYPR+ID+A  
Sbjct: 124 THGSPVSFSGHYYNAVFYGVHRDTGLIDEQQVEALAKQHRPAIIIAGASAYPRIIDFAFF 183

Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243
           R +A+ VGA L+VDMAH++GL+A G +P+P P+A FVT++THKTLRGPR G    K  +A
Sbjct: 184 RRVANEVGAILLVDMAHFSGLVATGHHPSPFPHADFVTTSTHKTLRGPRGGMAFSKSNWA 243

Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKV 303
           K +DK+VFP +QGGPLMHVIA KAV  KEA+S +FK+Y+   + NA++LA E  + G+++
Sbjct: 244 KALDKAVFPMMQGGPLMHVIAGKAVMLKEALSPDFKQYSENTLKNAKLLASELSEAGYRI 303

Query: 304 VSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAM 363
            +GGTD+H++LLDLR+  LTG+E E  L +A I  NKN VP+D  PP  TSGIRLGTPA+
Sbjct: 304 STGGTDNHLMLLDLRNKNLTGKEAESYLAQAGIICNKNGVPYDDKPPTVTSGIRLGTPAI 363

Query: 364 TTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLYPEL 413
           TTRG+ E ++  IA +I +++ + G   VI+ V+ E++ + + FP+Y  L
Sbjct: 364 TTRGLGEKEVVKIASMIHRILDSKGQGSVIDSVKSELVSLLKDFPIYAGL 413


Lambda     K      H
   0.319    0.136    0.395 

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: 570
Number of extensions: 24
Number of successful extensions: 1
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: 427
Length of database: 413
Length adjustment: 32
Effective length of query: 395
Effective length of database: 381
Effective search space:   150495
Effective search space used:   150495
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 (21.8 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