Alignments for a candidate for metY in Geotalea uraniireducens Rf4

GapMind for Amino acid biosynthesis

Alignments for a candidate for metY in Geotalea uraniireducens Rf4

Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_011940073.1 GURA_RS16550 homocysteine synthase

Query= BRENDA::P94890
         (442 letters)



>NCBI__GCF_000016745.1:WP_011940073.1
          Length = 428

 Score =  560 bits (1444), Expect = e-164
 Identities = 269/428 (62%), Positives = 341/428 (79%), Gaps = 9/428 (2%)

Query: 13  FKPETIALHGGQEPDPTTTSRAVPLYQTTSYVFKDTDHAARLFGLQEFGNIYTRLMNPTT 72
           F  +T+ALH GQ PDPTT SRAVP+YQT+SYVFK ++HAA LFGL+EFGNIYTR+MNPTT
Sbjct: 6   FNFDTLALHAGQTPDPTTLSRAVPIYQTSSYVFKSSEHAANLFGLKEFGNIYTRIMNPTT 65

Query: 73  DVLEKRVAALEGGVAALATASGQSAEMLALLNIVEAGQEIVASSSLYGGTYNLLHYTFPK 132
           DVLE+R+A L+GGV ALA ASGQ+A   A+LNI +AGQ IV+++ LYGGTYNL HYT PK
Sbjct: 66  DVLEQRMAQLDGGVGALAVASGQAAISYAVLNITQAGQNIVSTNYLYGGTYNLFHYTLPK 125

Query: 133 LGIKVHFVDQSDPENFRKASNDKTRAFYAETLGNPKLDTLDIAAVSKVAKEVGVPLVIDN 192
           LGI V FVD SDPEN R+A +DKTR  Y+E++GNPK +  D  A++++A   G+P V+DN
Sbjct: 126 LGIMVKFVDTSDPENVRRAIDDKTRLVYSESVGNPKNNVDDFEAIAQIAHAAGIPFVVDN 185

Query: 193 TMPSPYLVNPLKHGADIVVHSLTKFLGGHGTSIGGIIIDGGSFNWGNGKFKNFTEPDPSY 252
           T+ +PYL  PL+HGADIV +SLTKF+GGHGTSIGG ++DGG F W NGKF  FTEPDPSY
Sbjct: 186 TVTTPYLFKPLEHGADIVAYSLTKFIGGHGTSIGGCVVDGGKFPWNNGKFPEFTEPDPSY 245

Query: 253 HGLKFWEVFGKFEPFGGVNIAFILKARVQGLRDLGPAISPFNAWQILQGVETLPLRMERH 312
           HGLK+WE  G        N+++I+K RV  LRD+G A+SPFNA+Q + G+ETL +RM RH
Sbjct: 246 HGLKYWEALG--------NLSYIIKMRVSLLRDMGAALSPFNAFQFILGLETLHVRMPRH 297

Query: 313 SGNALKVAEFLQKHPKIEWVNYPGLSTDKNYATAKKYHERGLFGAIVGFEIKGGVEKAKK 372
             NA KVAE+L+K+P + WVNYPGL++ K+YA A+KY  +G  GAI+GF IKGGVE  K+
Sbjct: 298 VENAQKVAEWLEKNPLVTWVNYPGLASHKDYARARKYLTKGA-GAIIGFGIKGGVEAGKR 356

Query: 373 FIDGLELFSLLANIGDAKSLAIHPASTTHQQLTGPEQISAGVTPGFVRLSVGLENIDDIL 432
           FID ++L S LANIGDAKSL IHPASTTHQQL+  EQ+++GVT  F+RLS+G+E+  DI+
Sbjct: 357 FIDNVKLLSHLANIGDAKSLVIHPASTTHQQLSEAEQLASGVTADFIRLSIGIEDAGDIM 416

Query: 433 VDLEEALK 440
            D+++ALK
Sbjct: 417 ADIDQALK 424


Lambda     K      H
   0.317    0.137    0.402 

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: 586
Number of extensions: 17
Number of successful extensions: 3
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: 442
Length of database: 428
Length adjustment: 32
Effective length of query: 410
Effective length of database: 396
Effective search space:   162360
Effective search space used:   162360
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: 51 (24.3 bits)

This GapMind analysis is from Apr 12 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:

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
the source code
instructions for running GapMind on your computer
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