GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glyA in Pseudomonas fluorescens FW300-N1B4

Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate Pf1N1B4_2454 Serine hydroxymethyltransferase (EC 2.1.2.1)

Query= BRENDA::L7Y8B0
         (417 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2454
          Length = 417

 Score =  788 bits (2035), Expect = 0.0
 Identities = 395/417 (94%), Positives = 405/417 (97%)

Query: 1   MFSKQDQIQGYDDALLAAMNAEEQRQEDHIELIASENYTSKRVMQAQGSGLTNKYAEGYP 60
           MFSKQDQI+GYDDALLAAMNAEEQRQEDHIELIASENYTSKRVM+AQGSGLTNKYAEGYP
Sbjct: 1   MFSKQDQIKGYDDALLAAMNAEEQRQEDHIELIASENYTSKRVMEAQGSGLTNKYAEGYP 60

Query: 61  GKRYYGGCEHVDKVEALAIERAKQLFGADYANVQPHSGSSANGAVYLALVQAGDTILGMS 120
           GKRYYGGCEHVDKVEALAIERAKQLFGADYANVQPHSGSSAN AVYLAL+QAGDTILGMS
Sbjct: 61  GKRYYGGCEHVDKVEALAIERAKQLFGADYANVQPHSGSSANSAVYLALLQAGDTILGMS 120

Query: 121 LAHGGHLTHGAKVSSSGKLYNAVQYGIDTNTGLIDYDEVERLAVEHKPKMIVAGFSAYSK 180
           LAHGGHLTHGAKVSSSGKLYNAVQYGIDT TGLIDYDEVERLAVE KPKMIVAGFSAYSK
Sbjct: 121 LAHGGHLTHGAKVSSSGKLYNAVQYGIDTKTGLIDYDEVERLAVECKPKMIVAGFSAYSK 180

Query: 181 TLDFPRFRAIADKVGALLFVDMAHVAGLVAAGLYPNPIPFADVVTTTTHKTLRGPRGGLI 240
           TLDFPRFR IADKVGALLFVDMAHVAGLVAAGLYPNP+P+ADVVTTTTHKTLRGPRGGLI
Sbjct: 181 TLDFPRFRQIADKVGALLFVDMAHVAGLVAAGLYPNPLPYADVVTTTTHKTLRGPRGGLI 240

Query: 241 LAKANEEIEKKLNAAVFPGAQGGPLMHVIAAKAVCFKEALEPEFKAYQQQVIENAQAMAQ 300
           LAKANEEIEKKLNAAVFPGAQGGPLMHVIA KAVCFKEALEP FKAYQQQVI+NAQAMA 
Sbjct: 241 LAKANEEIEKKLNAAVFPGAQGGPLMHVIAGKAVCFKEALEPGFKAYQQQVIDNAQAMAG 300

Query: 301 VFVDRGYDVVSGGTDNHLFLVSLIRQGLTGKDADAALGCAHITVNKNAVPNDPQSPFVTS 360
           VF+ RGYDVVSGGTDNHLFLVSLIRQGLTGK+ADAALG AHITVNKNAVPNDPQSPFVTS
Sbjct: 301 VFIKRGYDVVSGGTDNHLFLVSLIRQGLTGKEADAALGRAHITVNKNAVPNDPQSPFVTS 360

Query: 361 GLRIGTPAVTTRGFKVAQCVALAGWICDILDNLGDADVEADVAKNVAALCADFPVYR 417
           GLRIGTPAVTTRGFKV QCV LAGWICDILDNLGDADVEA+VA+ VAALCADFPVYR
Sbjct: 361 GLRIGTPAVTTRGFKVTQCVELAGWICDILDNLGDADVEANVAQQVAALCADFPVYR 417


Lambda     K      H
   0.318    0.134    0.390 

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: 759
Number of extensions: 21
Number of successful extensions: 1
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: 417
Length of database: 417
Length adjustment: 31
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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