GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Lentibacillus jeotgali Grbi

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_010530677.1 ON01_RS08875 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_000224785.1:WP_010530677.1
          Length = 348

 Score =  473 bits (1217), Expect = e-138
 Identities = 231/336 (68%), Positives = 285/336 (84%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64
           ++VAVVGATGAVG+++++ LE+++  +  L LLSSKRSAG KVTF  QELTV+EA PESF
Sbjct: 7   VNVAVVGATGAVGEKIIEILENKDLPIKELKLLSSKRSAGKKVTFNNQELTVEEALPESF 66

Query: 65  EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124
             ++IALFSAGGSVS+ LAPEAVKRGA+V+DNTSA+RM E+ PLVVPEVNE+D+  HNGI
Sbjct: 67  SNIDIALFSAGGSVSKKLAPEAVKRGAVVVDNTSAYRMAEDVPLVVPEVNESDIQSHNGI 126

Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184
           IANPNCSTIQMVAAL+PI++A+GL++VIVSTYQAVSGAGN+A +EL +Q +  +N E++ 
Sbjct: 127 IANPNCSTIQMVAALKPIQEAFGLSRVIVSTYQAVSGAGNKANEELDNQVKQYVNNEDMT 186

Query: 185 PEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRL 244
            E++PVKGD+KHY IAFNA+PQID FQ+NGYTFEEMKMINE+KKI+H  DL VAATCVRL
Sbjct: 187 AELLPVKGDEKHYPIAFNALPQIDVFQENGYTFEEMKMINESKKILHAQDLPVAATCVRL 246

Query: 245 PIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVG 304
           P  T H+ESVYI+++++  +VEDI N L+ A GVTLQDDP+ Q YP P  A  K DVFVG
Sbjct: 247 PFFTSHAESVYIDVEKEGLSVEDIWNALRGADGVTLQDDPATQTYPTPLSAANKEDVFVG 306

Query: 305 RIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESL 340
           R+RKDLD   GFHLWVVSDNL+KGAAWN++QIAE L
Sbjct: 307 RVRKDLDSNKGFHLWVVSDNLIKGAAWNTIQIAERL 342


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: 414
Number of extensions: 5
Number of successful extensions: 1
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: 348
Length adjustment: 29
Effective length of query: 317
Effective length of database: 319
Effective search space:   101123
Effective search space used:   101123
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_010530677.1 ON01_RS08875 (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.3875959.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-156  505.9   2.1     3e-156  505.7   2.1    1.0  1  NCBI__GCF_000224785.1:WP_010530677.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010530677.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.7   2.1    3e-156    3e-156       1     339 []       8     345 ..       8     345 .. 0.99

  Alignments for each domain:
  == domain 1  score: 505.7 bits;  conditional E-value: 3e-156
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           nva+vGatGavG++++++Le+++ pi++l+ll+s+rsaGkkv+f+++el+veea  esf++idialfsaGgsv
  NCBI__GCF_000224785.1:WP_010530677.1   8 NVAVVGATGAVGEKIIEILENKDLPIKELKLLSSKRSAGKKVTFNNQELTVEEALPESFSNIDIALFSAGGSV 80 
                                           79*********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           sk++ap+a+k+g++v+Dntsa+r+ edvPLvvpevn+++++ ++  giianPnCstiq+v++Lkp++++++l 
  NCBI__GCF_000224785.1:WP_010530677.1  81 SKKLAPEAVKRGAVVVDNTSAYRMAEDVPLVVPEVNESDIQSHN--GIIANPNCSTIQMVAALKPIQEAFGLS 151
                                           ********************************************..*************************** PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           rv+vstYqavsGaG+k+ eeL nq+k  ++ +++++e  ++k+++++++iafna+p+id ++e+Gyt+ee+k+
  NCBI__GCF_000224785.1:WP_010530677.1 152 RVIVSTYQAVSGAGNKANEELDNQVKQYVNNEDMTAELLPVKGDEKHYPIAFNALPQIDVFQENGYTFEEMKM 224
                                           ************************************999********************************** PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefek.elsveevkelLkeapgvvviddpsenlyptPlea 291
                                           ++e++kil+ +dl+v+atcvr+P ft+h+esv+i++ek  lsve++ + L++a+gv+++ddp  ++yptPl+a
  NCBI__GCF_000224785.1:WP_010530677.1 225 INESKKILHAQDLPVAATCVRLPFFTSHAESVYIDVEKeGLSVEDIWNALRGADGVTLQDDPATQTYPTPLSA 297
                                           *************************************9669******************************** PP

                             TIGR01296 292 vgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339
                                           ++k++vfvgr+rkDl+++kg++l+vv+Dnl kGaa+n++qiae li++
  NCBI__GCF_000224785.1:WP_010530677.1 298 ANKEDVFVGRVRKDLDSNKGFHLWVVSDNLIKGAAWNTIQIAERLIAN 345
                                           *********************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (348 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: 15.49
//
[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