GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Enterococcus termitis LMG 8895

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_069661975.1 BCR25_RS02295 aspartate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-6564
         (346 letters)



>NCBI__GCF_001730305.1:WP_069661975.1
          Length = 351

 Score =  432 bits (1111), Expect = e-126
 Identities = 216/344 (62%), Positives = 268/344 (77%), Gaps = 3/344 (0%)

Query: 6   HVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFE 65
           +VAVVGATGAVG +M++ L +    ++ + LL+SKRSAG + TFKGQ L ++E  PESFE
Sbjct: 6   NVAVVGATGAVGTKMIEMLAESTLPLNQVKLLASKRSAGKERTFKGQTLVIEELVPESFE 65

Query: 66  GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGII 125
           G++IALFSAGGS+S+  APEAVKRGA+V+DNTS FRMD + PLVVPEVN   L  H GII
Sbjct: 66  GIDIALFSAGGSISKQFAPEAVKRGAVVVDNTSHFRMDPDVPLVVPEVNPDALKRHKGII 125

Query: 126 ANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILN---KEE 182
           ANPNCSTIQ++ ALEPIRKAYGL+++IVSTYQAVSGAG  A++EL +Q    +N    E+
Sbjct: 126 ANPNCSTIQLMVALEPIRKAYGLDRLIVSTYQAVSGAGIHAMEELKTQATEYINGTPAEK 185

Query: 183 IEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCV 242
           +   I+P  GDKKHY IAFNA+PQID F D+ YT+EE KMINETKKIM    ++V ATCV
Sbjct: 186 LAANILPCGGDKKHYPIAFNALPQIDVFSDDDYTYEEWKMINETKKIMEDDGIKVVATCV 245

Query: 243 RLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVF 302
           R+P+ +GHSESVYIE+  D A V  IK L++ APG  LQDDPSQQ+YP    ++ + + F
Sbjct: 246 RIPVLSGHSESVYIEVKEDGADVAKIKKLIETAPGAVLQDDPSQQVYPQALMSIDRKETF 305

Query: 303 VGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           VGRIRKD+D   GFH+WVVSDNLLKGAAWNSVQIAE+L  ++LV
Sbjct: 306 VGRIRKDIDIEKGFHMWVVSDNLLKGAAWNSVQIAETLHAMDLV 349


Lambda     K      H
   0.314    0.131    0.366 

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: 386
Number of extensions: 15
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: 346
Length of database: 351
Length adjustment: 29
Effective length of query: 317
Effective length of database: 322
Effective search space:   102074
Effective search space used:   102074
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: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate WP_069661975.1 BCR25_RS02295 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

# 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/TIGR01296.hmm
# target sequence database:        /tmp/gapView.3893397.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01296  [M=339]
Accession:   TIGR01296
Description: asd_B: aspartate-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.8e-144  466.3   0.2   3.2e-144  466.1   0.2    1.0  1  NCBI__GCF_001730305.1:WP_069661975.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069661975.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.1   0.2  3.2e-144  3.2e-144       1     337 [.       6     344 ..       6     346 .. 0.96

  Alignments for each domain:
  == domain 1  score: 466.1 bits;  conditional E-value: 3.2e-144
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           nva+vGatGavG +++++L+e++ p+++++llas+rsaGk+ +fkg+ l +ee+  esfegidialfsaGgs+
  NCBI__GCF_001730305.1:WP_069661975.1   6 NVAVVGATGAVGTKMIEMLAESTLPLNQVKLLASKRSAGKERTFKGQTLVIEELVPESFEGIDIALFSAGGSI 78 
                                           79*********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           sk+fap+a+k+g++v+Dnts fr+d+dvPLvvpevn + lk +k  giianPnCstiql+v+L+p++++++l 
  NCBI__GCF_001730305.1:WP_069661975.1  79 SKQFAPEAVKRGAVVVDNTSHFRMDPDVPLVVPEVNPDALKRHK--GIIANPNCSTIQLMVALEPIRKAYGLD 149
                                           ****************************************9988..*************************** PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeida...lkakkfakqiafnaiplidklkedGytkee 216
                                           r++vstYqavsGaG +++eeLk q+   ++g+  e          ++k++++iafna+p+id +++d yt ee
  NCBI__GCF_001730305.1:WP_069661975.1 150 RLIVSTYQAVSGAGIHAMEELKTQATEYINGTPAEKLAANilpCGGDKKHYPIAFNALPQIDVFSDDDYTYEE 222
                                           *****************************98655433322234899*************************** PP

                             TIGR01296 217 lkllfetrkilgiedlkvsatcvrvPvftghsesvsiefek.elsveevkelLkeapgvvviddpsenlyptP 288
                                            k+++et+ki++++ +kv atcvr+Pv+ ghsesv+ie+++  ++v ++k+l++ apg v++ddps+++yp  
  NCBI__GCF_001730305.1:WP_069661975.1 223 WKMINETKKIMEDDGIKVVATCVRIPVLSGHSESVYIEVKEdGADVAKIKKLIETAPGAVLQDDPSQQVYPQA 295
                                           ***************************************88579***************************** PP

                             TIGR01296 289 leavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337
                                           l+  ++ e+fvgrirkD++ ekg++++vv+Dnl+kGaa+n+vqiae+l 
  NCBI__GCF_001730305.1:WP_069661975.1 296 LMSIDRKETFVGRIRKDIDIEKGFHMWVVSDNLLKGAAWNSVQIAETLH 344
                                           **********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (351 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.47
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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