GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Caldicellulosiruptor kronotskyensis 2002

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_041741958.1 CALKRO_RS07895 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_000166775.1:WP_041741958.1
          Length = 327

 Score =  323 bits (828), Expect = 4e-93
 Identities = 170/335 (50%), Positives = 228/335 (68%), Gaps = 15/335 (4%)

Query: 7   VAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFE- 65
           +A+VGATG VG+  LK LE++N  ++   L +S RSAGTKV F G+E TV+E   +SF+ 
Sbjct: 1   MAIVGATGMVGRTFLKVLEEKNLPVEEYFLFASSRSAGTKVEFMGKEYTVEELKEDSFDR 60

Query: 66  GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGII 125
           G++IALFSAG S S   AP A  +G IVIDN+SA+RM+++ PLVVPEVN  D+  H GII
Sbjct: 61  GIDIALFSAGASTSLHFAPIAASKGCIVIDNSSAWRMEKDVPLVVPEVNPEDIKWHKGII 120

Query: 126 ANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIEP 185
           ANPNCSTIQ V  L+P+   Y + +++ STYQAVSGAG +   +L             E 
Sbjct: 121 ANPNCSTIQAVVVLKPLHDRYKIKRIVYSTYQAVSGAGYQGYLDL-------------EE 167

Query: 186 EIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRLP 245
            +      K  Y IA N IP ID F +NGYT EEMKMINET+KI+H   +++ AT VR+P
Sbjct: 168 GLKGAPPKKFPYPIAGNVIPHIDVFLENGYTKEEMKMINETRKILHDDSIKITATTVRVP 227

Query: 246 IQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVGR 305
           +  GHSES+ +E ++    +E++K +LK A GV +QDDP+  LYPMP    GK++V+VGR
Sbjct: 228 VFNGHSESINVEFEK-QFDLEELKEILKNAKGVVVQDDPANLLYPMPIYVSGKDEVYVGR 286

Query: 306 IRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESL 340
           IR+D    +G +LWVV+DN+ KGAA N+VQIAE +
Sbjct: 287 IRRDESVESGVNLWVVADNIRKGAATNAVQIAEKV 321


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: 315
Number of extensions: 14
Number of successful extensions: 4
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: 327
Length adjustment: 28
Effective length of query: 318
Effective length of database: 299
Effective search space:    95082
Effective search space used:    95082
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_041741958.1 CALKRO_RS07895 (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.632969.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-147  477.1   0.1   3.9e-147  475.7   0.1    1.6  1  NCBI__GCF_000166775.1:WP_041741958.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_041741958.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  475.7   0.1  3.9e-147  3.9e-147       2     337 ..       1     322 [.       1     324 [. 0.98

  Alignments for each domain:
  == domain 1  score: 475.7 bits;  conditional E-value: 3.9e-147
                             TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfeg.idialfsaGgsv 73 
                                           +aivGatG vG+++lkvLee+n p+++  l+as+rsaG+kv+f gke++vee+++ sf++ idialfsaG+s+
  NCBI__GCF_000166775.1:WP_041741958.1   1 MAIVGATGMVGRTFLKVLEEKNLPVEEYFLFASSRSAGTKVEFMGKEYTVEELKEDSFDRgIDIALFSAGAST 73 
                                           59********************************************************977************ PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           s  fap aa++g+iviDn+sa+r+++dvPLvvpevn e++k +k  giianPnCstiq+vvvLkpl+d++k+k
  NCBI__GCF_000166775.1:WP_041741958.1  74 SLHFAPIAASKGCIVIDNSSAWRMEKDVPLVVPEVNPEDIKWHK--GIIANPNCSTIQAVVVLKPLHDRYKIK 144
                                           *****************************************998..*************************** PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           r+v stYqavsGaG +g  +L++ +k +             ++kkf+++ia n+ip+id + e+Gytkee+k+
  NCBI__GCF_000166775.1:WP_041741958.1 145 RIVYSTYQAVSGAGYQGYLDLEEGLKGA-------------PPKKFPYPIAGNVIPHIDVFLENGYTKEEMKM 204
                                           *********************9988764.............479***************************** PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292
                                           ++etrkil+++ +k++at+vrvPvf ghses+++efek++++ee+ke+Lk+a+gvvv+ddp + lyp+P+ ++
  NCBI__GCF_000166775.1:WP_041741958.1 205 INETRKILHDDSIKITATTVRVPVFNGHSESINVEFEKQFDLEELKEILKNAKGVVVQDDPANLLYPMPIYVS 277
                                           ************************************************************************* PP

                             TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337
                                           gkdev+vgrir+D s e g++l+vvaDn+rkGaa+navqiae++i
  NCBI__GCF_000166775.1:WP_041741958.1 278 GKDEVYVGRIRRDESVESGVNLWVVADNIRKGAATNAVQIAEKVI 322
                                           ******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (327 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: 7.97
//
[ok]

This GapMind analysis is from Jul 26 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