GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Phyllobacterium brassicacearum STM 196

Align fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) (characterized)
to candidate WP_106711063.1 CU102_RS09940 phosphoglycerate dehydrogenase

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



>NCBI__GCF_003010955.1:WP_106711063.1
          Length = 531

 Score =  188 bits (478), Expect = 5e-52
 Identities = 115/339 (33%), Positives = 180/339 (53%), Gaps = 15/339 (4%)

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

Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353
           A  L  +G   IG + +D+     +GI V N PF N+ +  E A++ +  + R L +   
Sbjct: 65  AKNLKVIGRAGIGVDNVDIPAASRRGIIVMNTPFGNSITTAEHAVALMFAVARELPEADS 124

Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDIVERLALGNAT 413
               G W K+     E+ GK LG+IG GNIG+ ++     + M+V  +D    L+ G A 
Sbjct: 125 STRAGKWEKNRFMGVEITGKTLGVIGCGNIGSIVATRGIGLKMHVVAFD--PFLSEGRAE 182

Query: 414 KID----SLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPA 469
           ++      LDELL   D ISLH     + + I+N + I KMK G  ++N +RG ++    
Sbjct: 183 ELGVEKVELDELLTRADFISLHTPMTDKTRGIINADAIAKMKDGVRIINCARGGLIVEKD 242

Query: 470 LRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFV 529
           L   L+SG +AGA +DVF  EP       E+EL   PN + TPH+G ST EAQEN+A  V
Sbjct: 243 LIAGLKSGKVAGAGIDVFEVEPAT-----ENELFHLPNVVCTPHLGASTSEAQENVALQV 297

Query: 530 PGKIIEYINSGNTFNSVNFPNI---QLPFLKDAHRLIHI 565
             ++ +Y+  G   N++N P+I   + P LK   +L  +
Sbjct: 298 AEQMSDYLIKGAVSNAINMPSITAEEAPRLKPFVKLAEV 336


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: 714
Number of extensions: 38
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: 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