GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Sphingomonas indica Dd16

Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_085218338.1 B9N75_RS08140 phosphoglycerate dehydrogenase

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



>NCBI__GCF_900177405.1:WP_085218338.1
          Length = 525

 Score =  195 bits (495), Expect = 5e-54
 Identities = 124/384 (32%), Positives = 197/384 (51%), Gaps = 11/384 (2%)

Query: 235 VLLLENVHPIGVEIMKQEGYNVEVVSSAMSEEELCEKIKNVSIIGIRSKTQITKKVLENA 294
           VL+ + + P   EI ++ G  V+     +S++EL   I     + IRS T++T  VLE A
Sbjct: 4   VLISDQMDPKAAEIFRERGLEVDE-RPGLSKDELKAIIGGYDGLAIRSATKVTADVLEAA 62

Query: 295 NRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTLK 354
             L  VG   IG + +D+     KG+ V N PF N+ +  E AI+ +  L R L +  + 
Sbjct: 63  PNLKVVGRAGIGVDNVDIPAASAKGVVVMNTPFGNSITTAEHAIALMFALARQLPEADVS 122

Query: 355 MHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD--IVERLALGNA 412
              G W K+     E+  K LG+IG GNIG+ ++  A  + M V  YD  +    AL   
Sbjct: 123 TQAGKWEKNRFMGVELTAKTLGLIGAGNIGSIVADRALGLRMRVIAYDPFLTPERALQLG 182

Query: 413 TKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPALRD 472
            +   LD+LL   D I+LH     + + IL+ E + K KKG  ++N +RG ++D  AL+ 
Sbjct: 183 IEKVELDDLLARADFITLHTPLTDQTRGILSAENLAKTKKGVRIINCARGGLIDEAALKA 242

Query: 473 ALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVPGK 532
           AL+SGH+AGAA+DVF  EP       +S L G P  + TPH+G ST EAQ N+A  V  +
Sbjct: 243 ALDSGHVAGAALDVFVEEPAK-----QSALFGTPGFVATPHLGASTTEAQVNVAIQVAEQ 297

Query: 533 IIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKI-NQVLASYKINIVGQY 591
           I +++ +G   N++N P++           + + +    ++ ++  Q +    I + G  
Sbjct: 298 IADFLTTGGVTNALNVPSLSAEEAPKLRPYMQLAEKLGSLVGQLEGQRMTGVAIEVEGAA 357

Query: 592 LKTNEK--IGYVITDIDKRYSNDV 613
              N+K     V+  + + YS+ V
Sbjct: 358 ASLNQKPITAAVLAGLMQVYSDTV 381



 Score = 28.5 bits (62), Expect = 8e-04
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 6/76 (7%)

Query: 558 DAHRLIHIHQNAPGVLAKINQVLASYKINI----VGQYLKTNEKIGYVITDIDKRYSNDV 613
           D   +  ++++APG + ++   L    +NI    +G++    E +  V   +D       
Sbjct: 450 DGEMIYIVNEDAPGFIGRLGTALGEAGVNIGTFNLGRHTAGGEAVALV--SVDSHIDGAT 507

Query: 614 IDALKEIEGTIRFRIL 629
           + ALK + G  R + L
Sbjct: 508 VAALKALPGVKRVKPL 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: 626
Number of extensions: 26
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: 525
Length adjustment: 36
Effective length of query: 594
Effective length of database: 489
Effective search space:   290466
Effective search space used:   290466
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