GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Marivita geojedonensis DPG-138

Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_085635038.1 MGEO_RS02170 phosphoglycerate dehydrogenase

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



>NCBI__GCF_002115805.1:WP_085635038.1
          Length = 531

 Score =  206 bits (523), Expect = 3e-57
 Identities = 119/320 (37%), Positives = 176/320 (55%), Gaps = 8/320 (2%)

Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSS-AMSEEELCEKIKNVSIIGIRSKTQITKKVLEN 293
           VL+ + +    V+I K  G  V+   +    +++L E I     + IRS T++T  +LEN
Sbjct: 5   VLISDKLSDAAVQIFKDRGIEVDFQPNLGKDKDKLAEVIGQYDGLAIRSATKVTPTILEN 64

Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353
           A  L  +G   IGT+ ID +   +KG+ V N PF N  +  E AI+ +    R + + + 
Sbjct: 65  ATNLKVIGRAGIGTDNIDKDAASKKGVIVMNTPFGNMITTAEHAIAMMFACARQIPEASA 124

Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGN 411
             H G W KS     E+ GK LG+IG GNIG  +   A  + M V  YD  + E  A   
Sbjct: 125 STHAGKWEKSKFMGVELTGKTLGVIGAGNIGGIVCDRARGLKMKVIAYDPFLGEDKAKQM 184

Query: 412 ATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALR 471
             +   LD+LL+  D I+LHV    + +NIL++E + K KKG  ++N +RG +VD  AL 
Sbjct: 185 QVEKVELDDLLKRADFITLHVPLTDQTRNILSRENLEKTKKGVRIINCARGGLVDEEALA 244

Query: 472 DALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPG 531
           D L+SGH+AGAA DVF  EP       E+ L   PN + TPH+G +T EAQEN+A  V  
Sbjct: 245 DLLKSGHVAGAAFDVFSEEPAT-----ENPLFNLPNVVCTPHLGAATTEAQENVALQVAE 299

Query: 532 KIIEYINSGNTFNSVNFPNI 551
           ++  Y+ +G   N++N P++
Sbjct: 300 QMANYLLTGAVENALNMPSV 319



 Score = 25.0 bits (53), Expect = 0.009
 Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 2/62 (3%)

Query: 559 AHRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIGYVIT--DIDKRYSNDVIDA 616
           AH +   +++ PG++  +   +    +NI    L  +   G  I    +D+    +V+D 
Sbjct: 454 AHMVYTTNEDVPGIIGTLGTTMGENNVNIANFTLGRSAAKGEAIALLYVDEPVPANVVDK 513

Query: 617 LK 618
           LK
Sbjct: 514 LK 515


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: 677
Number of extensions: 35
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: 531
Length adjustment: 36
Effective length of query: 594
Effective length of database: 495
Effective search space:   294030
Effective search space used:   294030
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 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