Alignments for a candidate for metY in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for metY in Rhodospirillum rubrum ATCC 11170

Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate WP_011389589.1 RRU_RS09535 PLP-dependent transferase

Query= metacyc::MONOMER-17873
         (438 letters)



>NCBI__GCF_000013085.1:WP_011389589.1
          Length = 430

 Score =  587 bits (1513), Expect = e-172
 Identities = 292/423 (69%), Positives = 336/423 (79%), Gaps = 1/423 (0%)

Query: 14  HQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEEIGFAYTRIGNPTQ 73
           H +TL LH G YR+D  T AVAVPIYQTTSYQ  DT  AA L  L+E+G  YTRI NPT 
Sbjct: 7   HPETLVLHAG-YRSDEATNAVAVPIYQTTSYQFRDTEQAANLFALKELGNIYTRIMNPTC 65

Query: 74  DAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLYGGTWNLFANTLRT 133
           DA EQR+AALEGGVAALA++SGQ AS  AVL L QAGDN VTSTDLYGGTWNLFANT + 
Sbjct: 66  DALEQRVAALEGGVAALAVSSGQTASTFAVLNLCQAGDNFVTSTDLYGGTWNLFANTFKQ 125

Query: 134 LGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAAIGRSLGVPLIIDN 193
           +GIEARFVDP+DPEAFRRATD +TR YY ETLPNPKL VFPIAEVAAIGR+LGVPLI+DN
Sbjct: 126 MGIEARFVDPSDPEAFRRATDEKTRCYYAETLPNPKLHVFPIAEVAAIGRALGVPLIVDN 185

Query: 194 TATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADHAERHALLTGPEPS 253
           TA P++ RP   GAAVVVYS TKYIGGHGT+IGG ++DGG F W  H  R   LT P+PS
Sbjct: 186 TAAPVLCRPLALGAAVVVYSATKYIGGHGTSIGGIVVDGGNFDWEAHGARFPTLTNPDPS 245

Query: 254 YHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLETLPLRLARHNANA 313
           YH A WT+   P GP+AYILR R  +LRD+GA+++P +AF LIQGLETLPLR+  H  NA
Sbjct: 246 YHGAVWTEAVKPLGPIAYILRMRVILLRDIGAALSPFNAFLLIQGLETLPLRMRAHCENA 305

Query: 314 IKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELAGGEEAGRRFIEAL 373
           +KV D+L SHP+V++V  P +Q+GE  RR D  L  G G L+GFEL GG EAGR FI+AL
Sbjct: 306 LKVVDFLKSHPQVTTVIHPSVQTGELARRRDGALAHGQGALVGFELKGGLEAGRAFIDAL 365

Query: 374 RLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIGIEHPDDIIGDIAQ 433
           ++ YHV NIGDARSLAIHPA+TTHSQLS EDQ ATGV+ G+VRLSIGIEH DDIIGD+ Q
Sbjct: 366 KMLYHVANIGDARSLAIHPASTTHSQLSAEDQLATGVSQGYVRLSIGIEHADDIIGDLKQ 425

Query: 434 ALD 436
           AL+
Sbjct: 426 ALE 428


Lambda     K      H
   0.319    0.136    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: 602
Number of extensions: 16
Number of successful extensions: 1
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: 438
Length of database: 430
Length adjustment: 32
Effective length of query: 406
Effective length of database: 398
Effective search space:   161588
Effective search space used:   161588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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 original 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