Alignments for a candidate for metX in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Pedobacter sp. GW460-11-11-14-LB5

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate CA265_RS08175 CA265_RS08175 homoserine O-acetyltransferase

Query= SwissProt::K4ICC9
         (336 letters)



>FitnessBrowser__Pedo557:CA265_RS08175
          Length = 352

 Score =  375 bits (964), Expect = e-109
 Identities = 180/332 (54%), Positives = 239/332 (71%), Gaps = 1/332 (0%)

Query: 5   FKYQDPFQLENGEVLPELEVSYSTLGKLNKEKSNVIWVCHALTANAQPEDWWRGLIGNEK 64
           + Y   F+LE+G+ +  L+++Y T GKLN  K NVIWVCHALTANA   +WW GL G   
Sbjct: 7   YHYNKQFKLESGKKIRNLQIAYQTYGKLNANKDNVIWVCHALTANADVFEWWEGLFGQNS 66

Query: 65  GIDTEKYFIVCANIIGSCYGSTNPKSINPETGEVYGLNFPLFSIRDVTKSLELLSEALEI 124
             + E+++IVCAN++GS YGS+NP S NP TG  Y L+FP F+IRD+  + +LL+  L I
Sbjct: 67  LFNPEEHYIVCANVLGSHYGSSNPLSTNPVTGLPYYLSFPQFTIRDLVSAHQLLASHLGI 126

Query: 125 EHIQFLIGGSMGGMQAMEWAIEKPDKIKNLILLATNAKHSSWGIALNETQRMAIEADSTF 184
           ++I+ LIGGS+GG QA+EW+I +P+KI+NLIL+ATNA HS WGIA NE+QR+AI  D TF
Sbjct: 127 DYIKLLIGGSLGGQQAVEWSISEPNKIENLILIATNAAHSPWGIAFNESQRLAITTDRTF 186

Query: 185 YKKETNSGKKGLEAARAIALLSYRNYNTYRHTQVDQ-EHTADHFRASTYQKYQGEKLSKR 243
           Y  + N G KGL+ AR+IALLSYR Y+ Y  TQV+      D+FR+S+YQ YQGEKL  R
Sbjct: 187 YANQPNGGSKGLKTARSIALLSYRTYSAYGSTQVESVNDKTDNFRSSSYQNYQGEKLINR 246

Query: 244 FNAKCYWYLSKAMDSHNVGRNRGDCKKALAKIKAETLVIAVQSDLLFPVEEQRFLAQYIP 303
           FNA  Y+YL+KAMDSHNVGRNR     AL  I A TLVI +++D+LFP+ EQ++LA +IP
Sbjct: 247 FNAYSYYYLTKAMDSHNVGRNRKSIADALKLITANTLVIGIENDVLFPLSEQKYLADHIP 306

Query: 304 KGKLEIIDSIYGHDGFLIEVEKIKSLVHKHFK 335
             +   + S YGHDGFLIE + + +++    K
Sbjct: 307 GAEFSALHSDYGHDGFLIETDALTNVIGNFIK 338


Lambda     K      H
   0.317    0.134    0.397 

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: 376
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: 336
Length of database: 352
Length adjustment: 29
Effective length of query: 307
Effective length of database: 323
Effective search space:    99161
Effective search space used:    99161
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate CA265_RS08175 CA265_RS08175 (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.4258.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.3e-107  344.2   0.1     5e-107  343.9   0.1    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS08175  CA265_RS08175 homoserine O-acety


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS08175  CA265_RS08175 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.9   0.1    5e-107    5e-107       3     350 ..      11     337 ..       9     338 .. 0.95

  Alignments for each domain:
  == domain 1  score: 343.9 bits;  conditional E-value: 5e-107
                                  TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgraldt 70 
                                                ++++lesG++++++++ay+tyG+lna++dN++ vcHalt++a+v    +     WW+ l+G++  +++
  lcl|FitnessBrowser__Pedo557:CA265_RS08175  11 KQFKLESGKKIRNLQIAYQTYGKLNANKDNVIWVCHALTANADVF---E-----WWEGLFGQNSLFNP 70 
                                                79******************************************9...6.....************** PP

                                  TIGR01392  71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlG 138
                                                +++++vc+NvlGs +Gs+ Pls+np tg py  +fP++tirDlv a++ l+ +Lg++ +++ +GgSlG
  lcl|FitnessBrowser__Pedo557:CA265_RS08175  71 EEHYIVCANVLGSHYGSSNPLSTNPVTGLPYYLSFPQFTIRDLVSAHQLLASHLGIDYIKLLIGGSLG 138
                                                ******************************************************************** PP

                                  TIGR01392 139 GmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARm 206
                                                G qa+ew++s+p+++++++ +at a++s++ iafne qr ai++D  +   + +     +kGL++AR 
  lcl|FitnessBrowser__Pedo557:CA265_RS08175 139 GQQAVEWSISEPNKIENLILIATNAAHSPWGIAFNESQRLAITTDRTFYANQPNG---GSKGLKTARS 203
                                                ************************************************8887777...67******** PP

                                  TIGR01392 207 lalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274
                                                +all+Yr+ +++ +   ++++++       +++f  +sy +yqg+k+++rF+A sY +ltka+d+h++
  lcl|FitnessBrowser__Pedo557:CA265_RS08175 204 IALLSYRTYSAYGSTQVESVNDK-------TDNFRSSSYQNYQGEKLINRFNAYSYYYLTKAMDSHNV 264
                                                ********988765544333333.......57899********************************* PP

                                  TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakleyaeieseeGHDaFllekekv 342
                                                +r+ r+s+++alk i+a++lv+gie D+lf+l+eq+ la++++ a+ +   ++s++GHD+Fl+e++++
  lcl|FitnessBrowser__Pedo557:CA265_RS08175 265 GRN-RKSIADALKLITANTLVIGIENDVLFPLSEQKYLADHIPGAEFS--ALHSDYGHDGFLIETDAL 329
                                                **9.9**************************************99887..****************** PP

                                  TIGR01392 343 eelirefl 350
                                                +++i +f+
  lcl|FitnessBrowser__Pedo557:CA265_RS08175 330 TNVIGNFI 337
                                                ****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (352 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.46
//
[ok]

This GapMind analysis is from Apr 09 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