Aligments for a candidate for gly1 in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Aligments for a candidate for gly1 in Pseudomonas fluorescens FW300-N2C3

Align glycine hydroxymethyltransferase (EC 2.1.2.1); low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate AO356_15725 AO356_15725 serine hydroxymethyltransferase

Query= BRENDA::P0A825
         (417 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_15725
          Length = 417

 Score =  632 bits (1629), Expect = 0.0
 Identities = 306/416 (73%), Positives = 356/416 (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
           GKRYYGGCEYVD+VEQLAIDRAKELFGADYANVQPH+GSQAN AVY ALL  GDT+LGM+
Sbjct: 61  GKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHAGSQANAAVYLALLSAGDTILGMS 120

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

Query: 181 VDWAKMREIADSIGAYLFVDMAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLIL 240
           +D+ + R IAD +GAYLFVDMAHVAGLVAAGVYPNPVP A VVTTTTHKTL GPRGGLIL
Sbjct: 181 LDFPRFRAIADKVGAYLFVDMAHVAGLVAAGVYPNPVPFADVVTTTTHKTLRGPRGGLIL 240

Query: 241 AKGGSEELYKKLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVE 300
           A+  + ++ KKLNSAVFPG QGGPL HVIA KA+  KEA++PEFK YQQQV KNAKAM  
Sbjct: 241 ARANA-DIEKKLNSAVFPGAQGGPLEHVIAAKAICFKEALQPEFKAYQQQVVKNAKAMAG 299

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

Query: 361 GIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIERIKGKVLDICARYPVY 416
           G+R GTPA+T RGFKEAE KELAGW+CD+L  +N+EAVI+ ++ KV  IC + PVY
Sbjct: 360 GLRFGTPAVTTRGFKEAECKELAGWICDILADLNNEAVIDAVREKVKAICKKLPVY 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: 645
Number of extensions: 19
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for Amino acid biosynthesis