GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Dinoroseobacter shibae DFL-12

Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate 3609936 Dshi_3318 D-3-phosphoglycerate dehydrogenase (RefSeq)

Query= uniprot:L0G228_ECHVK
         (630 letters)



>FitnessBrowser__Dino:3609936
          Length = 531

 Score =  204 bits (518), Expect = 1e-56
 Identities = 122/321 (38%), Positives = 177/321 (55%), Gaps = 10/321 (3%)

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

Query: 294 ANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLMRNLHDKTL 353
           A+ L  VG   IGT+ +D     +KG+ V N PF N  +  E AI+ +  + R + + + 
Sbjct: 65  ADNLKVVGRAGIGTDNVDKVAASKKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEASA 124

Query: 354 KMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYD---IVERLALG 410
             H G W KS     E+  K LG+IG GNIG  +   A  + M V  YD     ER    
Sbjct: 125 STHAGKWEKSKFMGVELTAKTLGVIGAGNIGGIVCERALGLKMKVIAYDPFLSEERADKL 184

Query: 411 NATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVVDVPAL 470
              K+D LD LL   D I+LHV    + +NIL++E + K KKG  ++N +RG +VD  AL
Sbjct: 185 GVEKVD-LDTLLARADFITLHVPLTDQTRNILSREALEKTKKGVRIINCARGGLVDEQAL 243

Query: 471 RDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENIAQFVP 530
            D L+SGH+AGAA DVF  EP       E+ L G PN + TPH+G ST EAQEN+A  V 
Sbjct: 244 ADLLKSGHVAGAAFDVFAEEPAT-----ENPLFGLPNVVCTPHLGASTTEAQENVALQVA 298

Query: 531 GKIIEYINSGNTFNSVNFPNI 551
            ++  Y+ SG   N++N P++
Sbjct: 299 EQMSNYLLSGAVENALNMPSV 319



 Score = 26.6 bits (57), Expect = 0.003
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 560 HRLIHIHQNAPGVLAKINQVLASYKINIVGQYLKTNEKIGYVIT--DIDKRYSNDVIDAL 617
           H L   +++ PG++  +  +L   ++NI    L  NE  G  I    +D     DV D L
Sbjct: 455 HMLYTTNKDTPGMIGTLGGILGENQVNIANFTLGRNETNGDAIAMLYLDAPLPRDVQDKL 514


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: 691
Number of extensions: 33
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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