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.34367.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  NCBI__GCF_000012925.1:WP_004511679.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012925.1:WP_004511679.1  
   #    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..GWWdellGpgraldtsry 73 
                                           +el lesG +l  +++ay+tyG+lna+r+Na+lv Ha tg+ah+agk++eed+  GWWd ++Gpgr ldt+r 
  NCBI__GCF_000012925.1:WP_004511679.1  15 TELRLESGRILGPITLAYETYGELNADRSNAILVAHAWTGNAHLAGKNSEEDTkpGWWDAIVGPGRLLDTDRC 87 
                                           789*******************************************999887779****************** PP

                             TIGR01392  74 fvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewa 146
                                           fv+c+Nv+Gsc+GstgP+sinp+tgk+y   fP++t+rD+v+aq+ lld+Lg+++l +v+GgS+GGmqalewa
  NCBI__GCF_000012925.1:WP_004511679.1  88 FVICSNVIGSCYGSTGPASINPKTGKRYNLTFPVITVRDMVRAQALLLDHLGIDRLLTVLGGSMGGMQALEWA 160
                                           ************************************************************************* PP

                             TIGR01392 147 lsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlalltYrseesle 219
                                           ++ p+r++++++lat+ r s+qai++n+v+r ai +Dp +++Gey++  +P+ GLalAR ++++t++s+es+ 
  NCBI__GCF_000012925.1:WP_004511679.1 161 TQFPDRIRSAIALATTSRPSPQAISLNAVARWAIFNDPTWKKGEYRK--NPKDGLALARGIGHITFLSDESMW 231
                                           **********************************************9..9*********************** PP

                             TIGR01392 220 erfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikap 292
                                           ++fgr+ ++++   + +  +f+ve yl+y+g +fv+rFd ns+l+l+kald +d a g  +sl+ea++++kap
  NCBI__GCF_000012925.1:WP_004511679.1 232 QKFGRRFNARDG-LFDFFGQFEVERYLSYNGYNFVDRFDTNSFLYLAKALDLYDTAWG-YESLEEAFSRVKAP 302
                                           *****9999965.677999***************************************.8************* PP

                             TIGR01392 293 vlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                           + + +++sD+l+++ ++ee+a+ l++ ++   y+ ies++GHDaFlle+e+++ ++refl
  NCBI__GCF_000012925.1:WP_004511679.1 303 IQFFAFTSDWLYPPYQTEEMATILRSLGKPveYHLIESAYGHDAFLLEHETFAPMVREFL 362
                                           **************************999888**************************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.69
//
[ok]

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

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:

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:

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:

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