GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Magnetospirillum magneticum AMB-1

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_011383030.1 AMB_RS03035 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>NCBI__GCF_000009985.1:WP_011383030.1
          Length = 338

 Score =  332 bits (850), Expect = 1e-95
 Identities = 173/334 (51%), Positives = 233/334 (69%), Gaps = 3/334 (0%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64
           + VA+ GATG VG  ML++L +R+FP DE+  LASERS G+   +  K ++ +++  FD+
Sbjct: 3   YKVAVIGATGNVGRAMLQILVDRKFPADEVVALASERSVGREVSYGDKVLKCKDLATFDF 62

Query: 65  SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124
               IAL S G ++SA  +P AA AG VVIDNTSHFR + D+PLVVPEVNP+AIA+++ R
Sbjct: 63  KGCDIALSSPGAKVSAIHSPRAAAAGCVVIDNTSHFRMEPDVPLVVPEVNPDAIAQYKKR 122

Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184
            IIANPNCSTIQM+VALKP++    I+R+ V+TYQSVSGAGK G+DEL  QT  +L    
Sbjct: 123 GIIANPNCSTIQMVVALKPLHKLGKIKRVVVSTYQSVSGAGKEGMDELYDQTKGILVHDA 182

Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244
            +   F++QIAFN IPQID FM++G TKEE KMV ET KI  DP I VN TCVRVPVF  
Sbjct: 183 IKPQKFAKQIAFNLIPQIDVFMEDGSTKEEWKMVVETHKIL-DPDIAVNATCVRVPVFVS 241

Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVR--DAGGKDHVLVGRVRNDI 302
           H+E+++VE   P+   +  + L + +G+ +    +    +   D  G+D V + R+R D 
Sbjct: 242 HSESINVEFERPVSVAEATEALREAEGVVVMDTREPGGYITPLDTTGEDPVYISRIRKDP 301

Query: 303 SHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336
           +  +G++ W VADN+RKGAA NAVQIAE+L+RDY
Sbjct: 302 TVKNGLSFWCVADNLRKGAALNAVQIAEVLIRDY 335


Lambda     K      H
   0.319    0.135    0.395 

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: 320
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: 337
Length of database: 338
Length adjustment: 28
Effective length of query: 309
Effective length of database: 310
Effective search space:    95790
Effective search space used:    95790
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: 49 (23.5 bits)

Align candidate WP_011383030.1 AMB_RS03035 (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.15333.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-145  469.1   0.5   4.5e-145  468.9   0.5    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383030.1  AMB_RS03035 aspartate-semialdehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383030.1  AMB_RS03035 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.9   0.5  4.5e-145  4.5e-145       1     338 [.       4     333 ..       4     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 468.9 bits;  conditional E-value: 4.5e-145
                                 TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 
                                               +va++GatG+vG+ +l++L +r+fp+d++v+lasers G++v + +k l+ +++ +++f+g dial s 
  lcl|NCBI__GCF_000009985.1:WP_011383030.1   4 KVAVIGATGNVGRAMLQILVDRKFPADEVVALASERSVGREVSYGDKVLKCKDLATFDFKGCDIALSSP 72 
                                               69******************************************************************* PP

                                 TIGR01296  70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138
                                               G+ vs    p+aa+ag++viDnts fr+++dvPLvvpevn + +++ kk+giianPnCstiq+vv+Lkp
  lcl|NCBI__GCF_000009985.1:WP_011383030.1  73 GAKVSAIHSPRAAAAGCVVIDNTSHFRMEPDVPLVVPEVNPDAIAQYKKRGIIANPNCSTIQMVVALKP 141
                                               ********************************************************************* PP

                                 TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207
                                               l++  k+krvvvstYq+vsGaGk+g++eL++qtk +l+   ++       ++kfakqiafn+ip+id +
  lcl|NCBI__GCF_000009985.1:WP_011383030.1 142 LHKLGKIKRVVVSTYQSVSGAGKEGMDELYDQTKGILVHDAIK-------PQKFAKQIAFNLIPQIDVF 203
                                               ************************************9876655.......6****************** PP

                                 TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276
                                               +edG tkee k++ et+kil+ +d+ v atcvrvPvf++hses+++efe+++sv e+ e L+ea+gvvv
  lcl|NCBI__GCF_000009985.1:WP_011383030.1 204 MEDGSTKEEWKMVVETHKILD-PDIAVNATCVRVPVFVSHSESINVEFERPVSVAEATEALREAEGVVV 271
                                               *********************.*********************************************** PP

                                 TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                               +d  +   y+tPl+++g+d v+++rirkD + ++gl+ ++vaDnlrkGaalnavqiae li+
  lcl|NCBI__GCF_000009985.1:WP_011383030.1 272 MDTREPGGYITPLDTTGEDPVYISRIRKDPTVKNGLSFWCVADNLRKGAALNAVQIAEVLIR 333
                                               ***********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (338 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: 00:00:00.01
# Mc/sec: 8.36
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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