Alignments for a candidate for metX in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Rhodospirillum rubrum ATCC 11170

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate YP_428348.1 Rru_A3266 homoserine O-acetyltransferase

Query= SwissProt::Q9AAS1
         (382 letters)



>NCBI__GCF_000013085.1:YP_428348.1
          Length = 391

 Score =  513 bits (1320), Expect = e-150
 Identities = 248/361 (68%), Positives = 292/361 (80%), Gaps = 2/361 (0%)

Query: 22  PLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGWWQRLV 81
           P+RLDSG  +  L +AYQT G+LNA+++NA+LICHALTGDQHV  PHP TG+PGWW+ LV
Sbjct: 22  PMRLDSGLELGPLTVAYQTIGRLNAERTNAILICHALTGDQHVIGPHPVTGRPGWWETLV 81

Query: 82  GPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQAMLVS 141
           GPGK +D  R+FIICSNV+GGC+G+TGP  INPATGK +GL FPVITI DMVRAQA+L+ 
Sbjct: 82  GPGKTIDTDRYFIICSNVLGGCLGTTGPKEINPATGKPWGLGFPVITIGDMVRAQALLLD 141

Query: 142 ALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGRQAIMA 201
            LG+E LF  +GGSMG MQV QWAV YPER+ + V +A + RHSAQNIAFHEVGRQAIMA
Sbjct: 142 HLGIERLFCAIGGSMGAMQVLQWAVSYPERVRAVVPIAGSWRHSAQNIAFHEVGRQAIMA 201

Query: 202 DPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGFDADFQ 260
           DPDW GG Y   G  P +GLAVARM AHITYLSEPALQ KFGR+LQ R  +++GFDADFQ
Sbjct: 202 DPDWNGGDYLNQGTVPRRGLAVARMTAHITYLSEPALQSKFGRKLQDRASITYGFDADFQ 261

Query: 261 VESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCVLSFSS 320
           VESYLRHQG++FV RFDANSYLYITRAMDYFD+AA H GVLA+AF +   VRFCV+SF+S
Sbjct: 262 VESYLRHQGANFVKRFDANSYLYITRAMDYFDLAAEHDGVLARAF-QGTKVRFCVVSFTS 320

Query: 321 DWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLASAERDRG 380
           DWL+PTAE+R +VRA+ AA A  +F E+ +DKGHDAFLLDEP     L+GFL  A    G
Sbjct: 321 DWLFPTAESRAVVRAMNAAAADVSFVEVTTDKGHDAFLLDEPEFHDTLQGFLDGAADMFG 380

Query: 381 L 381
           L
Sbjct: 381 L 381


Lambda     K      H
   0.321    0.135    0.417 

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: 517
Number of extensions: 21
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: 382
Length of database: 391
Length adjustment: 30
Effective length of query: 352
Effective length of database: 361
Effective search space:   127072
Effective search space used:   127072
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate YP_428348.1 Rru_A3266 (homoserine O-acetyltransferase)
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01392.hmm
# target sequence database:        /tmp/gapView.7686.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01392  [M=351]
Accession:   TIGR01392
Description: homoserO_Ac_trn: homoserine O-acetyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                              Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
     1e-146  474.5   0.0   1.2e-146  474.3   0.0    1.0  1  lcl|NCBI__GCF_000013085.1:YP_428348.1  Rru_A3266 homoserine O-acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_428348.1  Rru_A3266 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.3   0.0  1.2e-146  1.2e-146       3     350 ..      21     372 ..      19     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: 474.3 bits;  conditional E-value: 1.2e-146
                              TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsry 73 
                                             ++ l+sG +l  ++vay+t G+lnaer Na+l+cHaltg++hv g +  + + GWW++l+Gpg+++dt+ry
  lcl|NCBI__GCF_000013085.1:YP_428348.1  21 APMRLDSGLELGPLTVAYQTIGRLNAERTNAILICHALTGDQHVIGPHPVTGRpGWWETLVGPGKTIDTDRY 92 
                                            57899*****************************************99876666****************** PP

                              TIGR01392  74 fvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalew 145
                                            f++c+NvlG+c G+tgP  inp+tgkp+g  fP++ti D+v+aq+ lld+Lg+e+l++ +GgS+G mq+l+w
  lcl|NCBI__GCF_000013085.1:YP_428348.1  93 FIICSNVLGGCLGTTGPKEINPATGKPWGLGFPVITIGDMVRAQALLLDHLGIERLFCAIGGSMGAMQVLQW 164
                                            ************************************************************************ PP

                              TIGR01392 146 alsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrsee 216
                                            a+syperv+++v++a s r+saq+iaf+ev rqai++Dp++n+G+y +++  P++GLa+ARm+a++tY+se 
  lcl|NCBI__GCF_000013085.1:YP_428348.1 165 AVSYPERVRAVVPIAGSWRHSAQNIAFHEVGRQAIMADPDWNGGDYLNQGtVPRRGLAVARMTAHITYLSEP 236
                                            ************************************************999********************* PP

                              TIGR01392 217 sleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkk 288
                                            +l+++fgr+ ++++s+++ ++++f+vesylr+qg +fv+rFdAnsYl++t+a+d++dla+++++ l++a++ 
  lcl|NCBI__GCF_000013085.1:YP_428348.1 237 ALQSKFGRKLQDRASITYGFDADFQVESYLRHQGANFVKRFDANSYLYITRAMDYFDLAAEHDGVLARAFQG 308
                                            ************************************************************************ PP

                              TIGR01392 289 ikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                            +k++++vv+++sD+lf+++e++ +++a++aa+++  ++e+++++GHDaFll++ +++++++ fl
  lcl|NCBI__GCF_000013085.1:YP_428348.1 309 TKVRFCVVSFTSDWLFPTAESRAVVRAMNAAAADvsFVEVTTDKGHDAFLLDEPEFHDTLQGFL 372
                                            ****************************99988888************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (391 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.01
//
[ok]

This GapMind analysis is from Apr 10 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