GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metX in Caldicellulosiruptor kronotskyensis 2002

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_015907626.1 CALKRO_RS07945 homoserine O-acetyltransferase

Query= SwissProt::D3P9D1
         (377 letters)



>NCBI__GCF_000166775.1:WP_015907626.1
          Length = 381

 Score =  399 bits (1024), Expect = e-116
 Identities = 200/366 (54%), Positives = 252/366 (68%), Gaps = 5/366 (1%)

Query: 12  KYVTF--KDDFYFESGRILSPITVAYETYGKLNEKKDNAILICHALTGSAHAAGYNSPDD 69
           K+V F    DF  ESG+   PITVAYE YG++N++K+N ILI HALTG +H A + S DD
Sbjct: 13  KFVRFAHNKDFVLESGKTFGPITVAYEVYGEINKEKNNIILITHALTGDSHVAKH-SEDD 71

Query: 70  QKPGWWDDMIGPGKAFDTDKYFIICSNFLGSCYGTTGPASIDPSTGKPYGLKFPVFTVKD 129
            KPGWWD  +GPGK  DT+KYF+ICSN  G C GTTGP+SIDP TGKPYG +FP+ T+KD
Sbjct: 72  PKPGWWDKFVGPGKMIDTNKYFVICSNVFGGCQGTTGPSSIDPETGKPYGARFPIITIKD 131

Query: 130 MVKLQKKLIDYLGIEKLLCVAGGSMGGMQALEWAVTFPEKTYSIIPIATAGRITPMAIAF 189
           MV +QKKL++ L I+ +LCV GGSMGGMQALEWAV++P+    +I IA+  ++   +IAF
Sbjct: 132 MVNVQKKLLEALKIDHILCVVGGSMGGMQALEWAVSYPDFMDGVINIASPLKLNAQSIAF 191

Query: 190 NTIGRFAIMKDPNWMNGDYYGKTFPRDGLAIARMAGHITYMSDKSFHKKFGRRYA-TFGG 248
           N + R AIM DPNW  GDYY KT P  GL+IARM G ITY SDK   KKF RR       
Sbjct: 192 NEVMRRAIMADPNWHGGDYYDKTGPSQGLSIARMLGMITYQSDKLMDKKFNRRMKDPVES 251

Query: 249 IYDFFG-YFEVENYLRYNGYKFTERFDANSYLYIIKAMDIFDLSYGYGSYEEAIGRIEAD 307
            ++ F   FEVE+YL Y G K  +RFDAN+YLY+ +AMD++DL   YGS EEA+ RI+A 
Sbjct: 252 FFESFNTEFEVESYLHYQGMKLVQRFDANTYLYLTRAMDLYDLGRTYGSEEEALRRIKAK 311

Query: 308 SLFITFTSDFLFPSYQTEEIVNIMKNHGKNPEWVNIESDYGHDAFLLEFDTQTSCIKEFL 367
            L I  TSD LFP  Q   + + +   G +  +  IESDYGHD+FL+E +   + I EFL
Sbjct: 312 FLLIAITSDILFPLSQMRYMRDKLLEAGVDLVYKEIESDYGHDSFLVEEEKYRNIISEFL 371

Query: 368 SKIYNK 373
             +YNK
Sbjct: 372 ELLYNK 377


Lambda     K      H
   0.321    0.140    0.432 

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: 555
Number of extensions: 26
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: 377
Length of database: 381
Length adjustment: 30
Effective length of query: 347
Effective length of database: 351
Effective search space:   121797
Effective search space used:   121797
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: 50 (23.9 bits)

Align candidate WP_015907626.1 CALKRO_RS07945 (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.3882060.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-150  485.6   0.0   4.7e-150  485.4   0.0    1.0  1  NCBI__GCF_000166775.1:WP_015907626.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_015907626.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  485.4   0.0  4.7e-150  4.7e-150       2     350 ..      20     371 ..      19     372 .. 0.97

  Alignments for each domain:
  == domain 1  score: 485.4 bits;  conditional E-value: 4.7e-150
                             TIGR01392   2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsry 73 
                                           +++++lesG++   ++vay+ yG++n+e++N++l+ Haltg++hva++ +++ k GWWd+++Gpg+ +dt++y
  NCBI__GCF_000166775.1:WP_015907626.1  20 NKDFVLESGKTFGPITVAYEVYGEINKEKNNIILITHALTGDSHVAKHSEDDPKpGWWDKFVGPGKMIDTNKY 92 
                                           6899******************************************887777668****************** PP

                             TIGR01392  74 fvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewa 146
                                           fv+c+Nv+G+c+G+tgP+si+petgkpyga+fP +ti+D+v++qk+ll++L ++++ +vvGgS+GGmqalewa
  NCBI__GCF_000166775.1:WP_015907626.1  93 FVICSNVFGGCQGTTGPSSIDPETGKPYGARFPIITIKDMVNVQKKLLEALKIDHILCVVGGSMGGMQALEWA 165
                                           ************************************************************************* PP

                             TIGR01392 147 lsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlalltYrseesle 219
                                           +syp++++ ++++a++++++aq iafnev+r+ai++Dp++++G+y++++ P++GL++ARml+++tY+s++ ++
  NCBI__GCF_000166775.1:WP_015907626.1 166 VSYPDFMDGVINIASPLKLNAQSIAFNEVMRRAIMADPNWHGGDYYDKTGPSQGLSIARMLGMITYQSDKLMD 238
                                           ************************************************************************* PP

                             TIGR01392 220 erfgreakse.eslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkika 291
                                           ++f+r++k+  es   s+++ef+vesyl+yqg k+v+rFdAn+Yl+lt+a+d +dl+r   +s +eal++ika
  NCBI__GCF_000166775.1:WP_015907626.1 239 KKFNRRMKDPvESFFESFNTEFEVESYLHYQGMKLVQRFDANTYLYLTRAMDLYDLGRT-YGSEEEALRRIKA 310
                                           *****9998714455567****************************************8.9************ PP

                             TIGR01392 292 pvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350
                                           ++l+++i+sD+lf+l++ + ++++l +a+++  y+eies++GHD+Fl+e+ek++++i+efl
  NCBI__GCF_000166775.1:WP_015907626.1 311 KFLLIAITSDILFPLSQMRYMRDKLLEAGVDlvYKEIESDYGHDSFLVEEEKYRNIISEFL 371
                                           **************************9999999**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (381 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 22.53
//
[ok]

This GapMind analysis is from Jul 26 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