GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Kyrpidia tusciae DSM 2912

Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_013075791.1 BTUS_RS09020 phosphoglycerate dehydrogenase

Query= reanno::Cola:Echvi_2777
         (630 letters)



>NCBI__GCF_000092905.1:WP_013075791.1
          Length = 527

 Score =  168 bits (425), Expect = 6e-46
 Identities = 100/320 (31%), Positives = 167/320 (52%), Gaps = 7/320 (2%)

Query: 259 VSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENANRLMAVGAFCIGTNQIDLETCQEK 318
           +   +  EEL   I     + +RS+T++T  +L  A  L AVG   +G + ID+E    +
Sbjct: 28  IRPGLPPEELKALIGEYDALLVRSQTKVTADLLAGARNLKAVGRAGVGVDNIDIEAATRR 87

Query: 319 GIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGII 378
           GI V NAP  NT S  E   + ++ L RN+      +  G W++ +    E+RGK LGI+
Sbjct: 88  GIIVVNAPDGNTISTAEHTFAMLMALARNIPQAYASIQSGKWDRKSFVGVELRGKTLGIV 147

Query: 379 GYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNATKIDSLDELLETCDIISLHVDGRT 436
           G G IG +++  A   GM V  YD  +    A     +  S+D++    D I++H     
Sbjct: 148 GLGRIGTEVAKRAMAFGMTVLAYDPFLTRERADQLGVESVSVDDICRRADFITVHTPLTK 207

Query: 437 ENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRDALESGHLAGAAVDVFPTEPKNNDE 496
           E +++++  +   MKKG  ++N +RG ++D  AL  ALE G + GAA+DVF  EP     
Sbjct: 208 ETRHMISGPQFALMKKGVRILNCARGGIIDEKALLAALEDGTVGGAALDVFEEEP----- 262

Query: 497 PFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFL 556
           P ++ L+     I TPH+G ST+EAQ N+A  V  +I+  ++     N+VN P++    +
Sbjct: 263 PKDNPLLASNRVIATPHLGASTVEAQINVAIDVGEEILNILHDRPFKNAVNLPSLPAEVM 322

Query: 557 KDAHRLIHIHQNAPGVLAKI 576
           +     + + +    ++++I
Sbjct: 323 RAVQPYLALGEKLGQLISQI 342



 Score = 26.6 bits (57), Expect = 0.003
 Identities = 14/68 (20%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 562 LIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIG--YVITDIDKRYSNDVIDALKE 619
           LI  H + PG++ ++  +L +  +NI    +   E  G   ++  +DK    + +  + +
Sbjct: 456 LITRHIDQPGIIGQVGSLLGAAGVNIAAMQVGRKELGGQAVMVLAVDKPVDAETLANIGQ 515

Query: 620 IEGTIRFR 627
           + G +  R
Sbjct: 516 VPGILAVR 523


Lambda     K      H
   0.317    0.136    0.377 

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: 616
Number of extensions: 27
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 630
Length of database: 527
Length adjustment: 36
Effective length of query: 594
Effective length of database: 491
Effective search space:   291654
Effective search space used:   291654
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: 53 (25.0 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