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_2778 Serine hydroxymethyltransferase (EC 2.1.2.1)

Query= BRENDA::L7Y8B0
         (417 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2778
          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:

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