GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Sulfurihydrogenibium subterraneum DSM 15120

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_028950286.1 Q385_RS0103220 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_000619805.1:WP_028950286.1
          Length = 337

 Score =  370 bits (951), Expect = e-107
 Identities = 186/344 (54%), Positives = 250/344 (72%), Gaps = 8/344 (2%)

Query: 3   RGLHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPE 62
           +  +VA++GATGAVGQ M+K LE+RNF ++ +  L+S+RSAG +V + G +  V+  S +
Sbjct: 2   KSYNVAILGATGAVGQTMIKVLEERNFPINEIKFLASERSAGKEVEYMGVKYKVEAVSED 61

Query: 63  SFEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHN 122
           +F+G++IALFSAGG  S+  AP AV +GA+VIDN+SAFRMD + PLVVPEVN  D+  H 
Sbjct: 62  AFKGIDIALFSAGGERSKKWAPIAVSKGAVVIDNSSAFRMDSDVPLVVPEVNPEDVKWHK 121

Query: 123 GIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEE 182
           GIIANPNCSTIQMV AL PI K   + ++IV+TYQAVSGAG  A+ +L ++T+A++    
Sbjct: 122 GIIANPNCSTIQMVVALYPIHKVKKIKRIIVATYQAVSGAGATAIADLENETKAVMEGRY 181

Query: 183 IEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCV 242
             P+ +P       + IAFN IP+ID F+ NGYT EEMKMINET+KIMH PD++V+ TCV
Sbjct: 182 YYPQALP-------HHIAFNVIPRIDNFEPNGYTKEEMKMINETRKIMHEPDIKVSPTCV 234

Query: 243 RLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVF 302
           R+P+  GHSE+V IE +    T E+ + +L +APGV ++DDP   +YP+P +  GK+DVF
Sbjct: 235 RVPVYVGHSEAVTIETEL-PITAEEAREILMKAPGVIVEDDPINNVYPVPIEVAGKDDVF 293

Query: 303 VGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           VGRIRKD    NG  +W+V DNL KGAA N+VQIAE L K  L+
Sbjct: 294 VGRIRKDAGFENGLSMWIVGDNLRKGAATNAVQIAELLIKYELI 337


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: 346
Number of extensions: 12
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: 346
Length of database: 337
Length adjustment: 29
Effective length of query: 317
Effective length of database: 308
Effective search space:    97636
Effective search space used:    97636
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_028950286.1 Q385_RS0103220 (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.677514.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-154  499.5   1.3   2.5e-154  499.3   1.3    1.0  1  NCBI__GCF_000619805.1:WP_028950286.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000619805.1:WP_028950286.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  499.3   1.3  2.5e-154  2.5e-154       1     338 [.       5     333 ..       5     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 499.3 bits;  conditional E-value: 2.5e-154
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           nvai+GatGavGq+++kvLeernfpi+++++lasersaGk+v++ g +++ve++++  f+gidialfsaGg  
  NCBI__GCF_000619805.1:WP_028950286.1   5 NVAILGATGAVGQTMIKVLEERNFPINEIKFLASERSAGKEVEYMGVKYKVEAVSEDAFKGIDIALFSAGGER 77 
                                           79*********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           sk++ap a+++g++viDn+safr+d dvPLvvpevn e++k +k  giianPnCstiq+vv+L p+++  k+k
  NCBI__GCF_000619805.1:WP_028950286.1  78 SKKWAPIAVSKGAVVIDNSSAFRMDSDVPLVVPEVNPEDVKWHK--GIIANPNCSTIQMVVALYPIHKVKKIK 148
                                           *****************************************998..*************************** PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           r++v+tYqavsGaG+ ++++L+n+tkav+eg+   p       ++ ++ iafn+ip id+++ +Gytkee+k+
  NCBI__GCF_000619805.1:WP_028950286.1 149 RIIVATYQAVSGAGATAIADLENETKAVMEGRYYYP-------QALPHHIAFNVIPRIDNFEPNGYTKEEMKM 214
                                           *******************************99997.......99**************************** PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292
                                           ++etrki++ +d+kvs tcvrvPv++ghse+v+ie+e ++++ee++e+L +apgv+v ddp +n+yp+P+e++
  NCBI__GCF_000619805.1:WP_028950286.1 215 INETRKIMHEPDIKVSPTCVRVPVYVGHSEAVTIETELPITAEEAREILMKAPGVIVEDDPINNVYPVPIEVA 287
                                           ************************************************************************* PP

                             TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                           gkd+vfvgrirkD   e+gl++++v+DnlrkGaa+navqiaellik
  NCBI__GCF_000619805.1:WP_028950286.1 288 GKDDVFVGRIRKDAGFENGLSMWIVGDNLRKGAATNAVQIAELLIK 333
                                           ********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (337 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: 00:00:00.00
# Mc/sec: 14.14
//
[ok]

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

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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