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_014626023.1 RRU_RS04110 PLP-dependent transferase

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



>NCBI__GCF_000013085.1:WP_014626023.1
          Length = 439

 Score =  645 bits (1664), Expect = 0.0
 Identities = 316/429 (73%), Positives = 358/429 (83%)

Query: 8   PKAAQYHQDTLALHGGSYRADPTTGAVAVPIYQTTSYQVHDTAHAARLAGLEEIGFAYTR 67
           P     + +TLALHGG+YRADPTTG+VAVPIYQTTSYQ  +T  AARL  L+E+G  Y+R
Sbjct: 9   PLTGLKNPETLALHGGTYRADPTTGSVAVPIYQTTSYQFENTGQAARLFALQELGNIYSR 68

Query: 68  IGNPTQDAFEQRLAALEGGVAALALASGQAASAIAVLTLAQAGDNIVTSTDLYGGTWNLF 127
           + NPT DAFEQR+AA+EGGVAALA++SGQAAS  AVL LAQAGDNIV+STDLYGGTW LF
Sbjct: 69  LTNPTTDAFEQRIAAIEGGVAALAVSSGQAASTFAVLNLAQAGDNIVSSTDLYGGTWALF 128

Query: 128 ANTLRTLGIEARFVDPADPEAFRRATDARTRLYYGETLPNPKLTVFPIAEVAAIGRSLGV 187
           A+T +  GIE RFVDP DPE FR+ATD RTR YY ETLPNPKL VFPI EVA IGRSLGV
Sbjct: 129 ASTFKQFGIEVRFVDPTDPENFRKATDERTRAYYAETLPNPKLNVFPIREVADIGRSLGV 188

Query: 188 PLIIDNTATPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGAIIDGGTFPWADHAERHALL 247
           PLI+DNTA PLIARPFDHGAAVVVYSTTKYIGGHGTTIGG IID GTFPW D  +R   L
Sbjct: 189 PLIVDNTAAPLIARPFDHGAAVVVYSTTKYIGGHGTTIGGVIIDSGTFPWEDFPDRFPTL 248

Query: 248 TGPEPSYHNASWTDLAAPFGPLAYILRARAGVLRDLGASIAPVSAFNLIQGLETLPLRLA 307
           T P+ SYH A WT+   P GP+AYI+RAR  +LRD+GA+I+P++ F LIQGLETLPLR+ 
Sbjct: 249 TEPDESYHGAVWTEATKPLGPVAYIIRARVKLLRDVGAAISPLAVFQLIQGLETLPLRIR 308

Query: 308 RHNANAIKVADYLASHPKVSSVTFPGLQSGEARRRADAYLKGGYGGLIGFELAGGEEAGR 367
           +HN NA+KVA +L  HPK++ V +PGLQ+GE RRRADAYL GGYGGL+GFEL GG EAGR
Sbjct: 309 QHNENALKVATFLKDHPKIARVIYPGLQTGELRRRADAYLTGGYGGLVGFELHGGAEAGR 368

Query: 368 RFIEALRLFYHVFNIGDARSLAIHPATTTHSQLSPEDQRATGVTPGFVRLSIGIEHPDDI 427
            FIE+LRLFYHV NIGDARSLAIHPATTTHSQLS EDQ  TGVTPG+VRLSIGIEHP DI
Sbjct: 369 AFIESLRLFYHVANIGDARSLAIHPATTTHSQLSEEDQLLTGVTPGYVRLSIGIEHPADI 428

Query: 428 IGDIAQALD 436
           I D++QALD
Sbjct: 429 IEDLSQALD 437


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: 687
Number of extensions: 18
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: 439
Length adjustment: 32
Effective length of query: 406
Effective length of database: 407
Effective search space:   165242
Effective search space used:   165242
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)
SQLite3 databases

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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