GapMind for Amino acid biosynthesis

 

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

Align glycine hydroxymethyltransferase (EC 2.1.2.1) (characterized)
to candidate Pf1N1B4_2778 Serine hydroxymethyltransferase (EC 2.1.2.1)

Query= BRENDA::L7Y8B0
         (417 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2778 Serine
           hydroxymethyltransferase (EC 2.1.2.1)
          Length = 417

 Score =  668 bits (1723), Expect = 0.0
 Identities = 336/416 (80%), Positives = 367/416 (88%), Gaps = 1/416 (0%)

Query: 1   MFSKQDQIQGYDDALLAAMNAEEQRQEDHIELIASENYTSKRVMQAQGSGLTNKYAEGYP 60
           MFS+   I  YD  L AAM  E QRQE+HIELIASENYTS  VM+AQGS LTNKYAEGYP
Sbjct: 1   MFSRDLTIAKYDADLFAAMEQEAQRQEEHIELIASENYTSPAVMEAQGSVLTNKYAEGYP 60

Query: 61  GKRYYGGCEHVDKVEALAIERAKQLFGADYANVQPHSGSSANGAVYLALVQAGDTILGMS 120
           GKRYYGGCE VD VE LAI+RAK+LFGADYANVQPH+GS AN AVYLAL+QAGDTILGMS
Sbjct: 61  GKRYYGGCEFVDVVEQLAIDRAKELFGADYANVQPHAGSQANSAVYLALLQAGDTILGMS 120

Query: 121 LAHGGHLTHGAKVSSSGKLYNAVQYGIDTNTGLIDYDEVERLAVEHKPKMIVAGFSAYSK 180
           LAHGGHLTHGA VSSSGKLYNAVQYGID N GLIDYDEVERLAVEHKPKMIVAGFSAYS+
Sbjct: 121 LAHGGHLTHGASVSSSGKLYNAVQYGIDAN-GLIDYDEVERLAVEHKPKMIVAGFSAYSQ 179

Query: 181 TLDFPRFRAIADKVGALLFVDMAHVAGLVAAGLYPNPIPFADVVTTTTHKTLRGPRGGLI 240
            LDFPRFR IADKVGA LFVDMAHVAGLVAAG+YPNP+PFADVVTTTTHKTLRGPRGGLI
Sbjct: 180 ILDFPRFREIADKVGAYLFVDMAHVAGLVAAGVYPNPVPFADVVTTTTHKTLRGPRGGLI 239

Query: 241 LAKANEEIEKKLNAAVFPGAQGGPLMHVIAAKAVCFKEALEPEFKAYQQQVIENAQAMAQ 300
           LA+AN +IEKKLN+AVFPGAQGGPL HVIAAKA+CFKEAL+PEFKAYQQQV++NAQAMA 
Sbjct: 240 LARANADIEKKLNSAVFPGAQGGPLEHVIAAKAICFKEALQPEFKAYQQQVVKNAQAMAG 299

Query: 301 VFVDRGYDVVSGGTDNHLFLVSLIRQGLTGKDADAALGCAHITVNKNAVPNDPQSPFVTS 360
           VF++RG+DVVSGGT NHLFL+SLI+Q ++GKDADAALG A ITVNKN+VPNDP+SPFVTS
Sbjct: 300 VFIERGFDVVSGGTQNHLFLLSLIKQEISGKDADAALGKAFITVNKNSVPNDPRSPFVTS 359

Query: 361 GLRIGTPAVTTRGFKVAQCVALAGWICDILDNLGDADVEADVAKNVAALCADFPVY 416
           GLR GTPAVTTRGFK A+C  LAGWICDIL +L +  V   V + V A+C   PVY
Sbjct: 360 GLRFGTPAVTTRGFKEAECKELAGWICDILADLSNEAVIDAVREKVKAICKKLPVY 415


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: 683
Number of extensions: 20
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: 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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