GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gly1 in Pseudomonas fluorescens FW300-N1B4

Align glycine hydroxymethyltransferase (EC 2.1.2.1); low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate Pf1N1B4_2778 Serine hydroxymethyltransferase (EC 2.1.2.1)

Query= BRENDA::P0A825
         (417 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2778
          Length = 417

 Score =  630 bits (1626), Expect = 0.0
 Identities = 306/416 (73%), Positives = 357/416 (85%), Gaps = 1/416 (0%)

Query: 1   MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYP 60
           M  R++ IA YDA+L+ AMEQE  RQEEHIELIASENYTSP VM+AQGS LTNKYAEGYP
Sbjct: 1   MFSRDLTIAKYDADLFAAMEQEAQRQEEHIELIASENYTSPAVMEAQGSVLTNKYAEGYP 60

Query: 61  GKRYYGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLEPGDTVLGMN 120
           GKRYYGGCE+VD+VEQLAIDRAKELFGADYANVQPH+GSQAN AVY ALL+ GDT+LGM+
Sbjct: 61  GKRYYGGCEFVDVVEQLAIDRAKELFGADYANVQPHAGSQANSAVYLALLQAGDTILGMS 120

Query: 121 LAHGGHLTHGSPVNFSGKLYNIVPYGIDATGHIDYADLEKQAKEHKPKMIIGGFSAYSGV 180
           LAHGGHLTHG+ V+ SGKLYN V YGIDA G IDY ++E+ A EHKPKMI+ GFSAYS +
Sbjct: 121 LAHGGHLTHGASVSSSGKLYNAVQYGIDANGLIDYDEVERLAVEHKPKMIVAGFSAYSQI 180

Query: 181 VDWAKMREIADSIGAYLFVDMAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLIL 240
           +D+ + REIAD +GAYLFVDMAHVAGLVAAGVYPNPVP A VVTTTTHKTL GPRGGLIL
Sbjct: 181 LDFPRFREIADKVGAYLFVDMAHVAGLVAAGVYPNPVPFADVVTTTTHKTLRGPRGGLIL 240

Query: 241 AKGGSEELYKKLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVE 300
           A+  + ++ KKLNSAVFPG QGGPL HVIA KA+  KEA++PEFK YQQQV KNA+AM  
Sbjct: 241 ARANA-DIEKKLNSAVFPGAQGGPLEHVIAAKAICFKEALQPEFKAYQQQVVKNAQAMAG 299

Query: 301 VFLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTS 360
           VF+ERG+ VVSGGT NHLFL+ L+ + ++GK+ADAALG+A ITVNKNSVPNDP+SPFVTS
Sbjct: 300 VFIERGFDVVSGGTQNHLFLLSLIKQEISGKDADAALGKAFITVNKNSVPNDPRSPFVTS 359

Query: 361 GIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIERIKGKVLDICARYPVY 416
           G+R GTPA+T RGFKEAE KELAGW+CD+L  +++EAVI+ ++ KV  IC + PVY
Sbjct: 360 GLRFGTPAVTTRGFKEAECKELAGWICDILADLSNEAVIDAVREKVKAICKKLPVY 415


Lambda     K      H
   0.316    0.134    0.393 

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: 651
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 (21.6 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