Alignments for a candidate for metX in Geobacter metallireducens GS-15

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Geobacter metallireducens GS-15

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_004511679.1 GMET_RS13945 homoserine O-acetyltransferase

Query= SwissProt::B3E278
         (367 letters)



>NCBI__GCF_000012925.1:WP_004511679.1
          Length = 369

 Score =  637 bits (1643), Expect = 0.0
 Identities = 299/365 (81%), Positives = 330/365 (90%)

Query: 1   MSIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAG 60
           MS+G+V EQ++TF+  +RLESGRIL PITL YE YG +NAD SN I+V HAWTG+AHLAG
Sbjct: 1   MSVGIVQEQSVTFDTELRLESGRILGPITLAYETYGELNADRSNAILVAHAWTGNAHLAG 60

Query: 61  KRREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFP 120
           K  E+D KPGWWDAIVGPGRLLDTDR  V+CSNVIGSCYGSTGPASINP+TGKRYNL+FP
Sbjct: 61  KNSEEDTKPGWWDAIVGPGRLLDTDRCFVICSNVIGSCYGSTGPASINPKTGKRYNLTFP 120

Query: 121 VITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPS 180
           VITVRDMVRAQ LLLDHLGI RLL V+GGSMGGMQALEWATQ+P+R+ S +ALATT RPS
Sbjct: 121 VITVRDMVRAQALLLDHLGIDRLLTVLGGSMGGMQALEWATQFPDRIRSAIALATTSRPS 180

Query: 181 PQAISLNAVARWAIYNDPTWKKGEYKHNPKDGLALARGIGHITFLSDESMWQKFERRFSA 240
           PQAISLNAVARWAI+NDPTWKKGEY+ NPKDGLALARGIGHITFLSDESMWQKF RRF+A
Sbjct: 181 PQAISLNAVARWAIFNDPTWKKGEYRKNPKDGLALARGIGHITFLSDESMWQKFGRRFNA 240

Query: 241 KDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYESMTDAFSRIT 300
           +DGLFDFFGQFEVERYL+YNGYNFVDRFD N FLYLAKALDLYD AWGYES+ +AFSR+ 
Sbjct: 241 RDGLFDFFGQFEVERYLSYNGYNFVDRFDTNSFLYLAKALDLYDTAWGYESLEEAFSRVK 300

Query: 301 APIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPMVRS 360
           APIQFFAF+SDWLYPPYQTEEM T L+ LGK VEYHLI+SAYGHDAFLLEHETF PMVR 
Sbjct: 301 APIQFFAFTSDWLYPPYQTEEMATILRSLGKPVEYHLIESAYGHDAFLLEHETFAPMVRE 360

Query: 361 LLERV 365
            L++V
Sbjct: 361 FLDKV 365


Lambda     K      H
   0.323    0.138    0.439 

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: 550
Number of extensions: 11
Number of successful extensions: 2
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: 367
Length of database: 369
Length adjustment: 30
Effective length of query: 337
Effective length of database: 339
Effective search space:   114243
Effective search space used:   114243
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: 49 (23.5 bits)

Align candidate WP_004511679.1 GMET_RS13945 (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.28654.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.3e-135  435.1   0.0   1.1e-134  434.9   0.0    1.0  1  lcl|NCBI__GCF_000012925.1:WP_004511679.1  GMET_RS13945 homoserine O-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012925.1:WP_004511679.1  GMET_RS13945 homoserine O-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  434.9   0.0  1.1e-134  1.1e-134       3     350 ..      15     362 ..      13     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 434.9 bits;  conditional E-value: 1.1e-134
                                 TIGR01392   3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgrald 69 
                                               +el lesG +l  +++ay+tyG+lna+r+Na+lv Ha tg+ah+agk++eed+  GWWd ++Gpgr ld
  lcl|NCBI__GCF_000012925.1:WP_004511679.1  15 TELRLESGRILGPITLAYETYGELNADRSNAILVAHAWTGNAHLAGKNSEEDTkpGWWDAIVGPGRLLD 83 
                                               789*******************************************999887779************** PP

                                 TIGR01392  70 tsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlG 138
                                               t+r fv+c+Nv+Gsc+GstgP+sinp+tgk+y   fP++t+rD+v+aq+ lld+Lg+++l +v+GgS+G
  lcl|NCBI__GCF_000012925.1:WP_004511679.1  84 TDRCFVICSNVIGSCYGSTGPASINPKTGKRYNLTFPVITVRDMVRAQALLLDHLGIDRLLTVLGGSMG 152
                                               ********************************************************************* PP

                                 TIGR01392 139 GmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARml 207
                                               Gmqalewa++ p+r++++++lat+ r s+qai++n+v+r ai +Dp +++Gey++  +P+ GLalAR +
  lcl|NCBI__GCF_000012925.1:WP_004511679.1 153 GMQALEWATQFPDRIRSAIALATTSRPSPQAISLNAVARWAIFNDPTWKKGEYRK--NPKDGLALARGI 219
                                               ******************************************************9..9*********** PP

                                 TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlar 276
                                               +++t++s+es+ ++fgr+ ++++   + +  +f+ve yl+y+g +fv+rFd ns+l+l+kald +d a 
  lcl|NCBI__GCF_000012925.1:WP_004511679.1 220 GHITFLSDESMWQKFGRRFNARDG-LFDFFGQFEVERYLSYNGYNFVDRFDTNSFLYLAKALDLYDTAW 287
                                               *****************9999965.677999************************************** PP

                                 TIGR01392 277 grrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekve 343
                                               g  +sl+ea++++kap+ + +++sD+l+++ ++ee+a+ l++ ++   y+ ies++GHDaFlle+e+++
  lcl|NCBI__GCF_000012925.1:WP_004511679.1 288 G-YESLEEAFSRVKAPIQFFAFTSDWLYPPYQTEEMATILRSLGKPveYHLIESAYGHDAFLLEHETFA 355
                                               *.8***************************************999888********************* PP

                                 TIGR01392 344 elirefl 350
                                                ++refl
  lcl|NCBI__GCF_000012925.1:WP_004511679.1 356 PMVREFL 362
                                               *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (369 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.27
//
[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