GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Marinobacter adhaerens HP15

Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate GFF2610 HP15_2554 D-3-phosphoglycerate dehydrogenase-like protein

Query= uniprot:L0G228_ECHVK
         (630 letters)



>FitnessBrowser__Marino:GFF2610
          Length = 409

 Score =  441 bits (1135), Expect = e-128
 Identities = 216/405 (53%), Positives = 293/405 (72%), Gaps = 1/405 (0%)

Query: 227 SYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSKTQ 285
           S  KS+I +LLLE VH   ++ +   GY N+E +S +++EEEL EKI +   +GIRS+TQ
Sbjct: 5   SLEKSKIRILLLEGVHQSAIDTLNAAGYTNIEYLSHSLAEEELIEKIADAHFVGIRSRTQ 64

Query: 286 ITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIFLM 345
           +T+KV E A +L+AVG FCIGTNQ+DL+    +GIAVFNAPFSNTRSV EL +++ I L+
Sbjct: 65  LTEKVFEAAKKLVAVGCFCIGTNQVDLQAATRRGIAVFNAPFSNTRSVAELVLAQAILLL 124

Query: 346 RNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDIVE 405
           R + +K  K H+G W KSA  S+E+RGKKLGIIGYGNIG Q SVLAE +GM+V++YD+V 
Sbjct: 125 RGVPEKNAKAHRGEWLKSAKDSYEIRGKKLGIIGYGNIGTQFSVLAEGLGMDVYFYDVVS 184

Query: 406 RLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGHVV 465
           +L++GNAT++ +L ELL   D++SLHV      K +   E+  +MK G+IL+N SRG VV
Sbjct: 185 KLSIGNATQVGTLQELLNIADVVSLHVPETPATKYMFKAEQFAQMKPGSILMNASRGTVV 244

Query: 466 DVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQENI 525
           D+ AL DAL SG L GAA+DVFP EPK+NDE F S L    N ILTPH+GGST+EAQ NI
Sbjct: 245 DIDALADALGSGKLLGAAIDVFPVEPKSNDEEFVSPLREFDNVILTPHVGGSTIEAQANI 304

Query: 526 AQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASYKI 585
            + V  K+  Y ++G + +SVNFP + LP   + HRL+HIH+N PGV+++INQV +   I
Sbjct: 305 GREVAEKLAMYSDNGTSVSSVNFPEVALPSHPNQHRLLHIHENVPGVMSEINQVFSENGI 364

Query: 586 NIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630
           N+ GQYL+T E IGYV+ D++K Y     + L +++GTIR R+L+
Sbjct: 365 NVCGQYLQTKEDIGYVVVDVNKEYGELAQEKLLKVKGTIRCRVLF 409


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: 641
Number of extensions: 24
Number of successful extensions: 2
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: 409
Length adjustment: 34
Effective length of query: 596
Effective length of database: 375
Effective search space:   223500
Effective search space used:   223500
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: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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