GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Phaeobacter inhibens BS107

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate GFF3097 PGA1_c31480 aspartate-semialdehyde dehydrogenase Asd

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Phaeo:GFF3097
          Length = 340

 Score =  319 bits (818), Expect = 6e-92
 Identities = 170/335 (50%), Positives = 231/335 (68%), Gaps = 6/335 (1%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64
           + V I GATG VG  ML +L ER+FPVDE+ +LAS +S G    F  KT+  Q+++ FD+
Sbjct: 3   YRVVIAGATGNVGREMLNILAERQFPVDEIAVLASRKSLGTEVTFGDKTLTTQDLDTFDF 62

Query: 65  SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124
           +   +ALF+ G + + K+AP AA AG VVIDN+S +RYD+D+PL+VPEVNP+A+  +  +
Sbjct: 63  AGWDMALFAVGSDATKKYAPKAAAAGCVVIDNSSLYRYDHDVPLIVPEVNPQAVHGYAKK 122

Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLN-GY 183
           NIIANPNCST QM+VALKP++D   I+R+ V+TYQSVSG+GK  IDEL  QT  + N   
Sbjct: 123 NIIANPNCSTAQMVVALKPLHDRAKIKRVVVSTYQSVSGSGKDAIDELWDQTKAVYNPTQ 182

Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243
               + +++QIAFN IP ID F+D+G TKEE KMV ET+KI  DPSI V  TCVRVPVF 
Sbjct: 183 DVPPSVYTKQIAFNVIPHIDVFLDDGSTKEEWKMVAETKKII-DPSIKVTATCVRVPVFV 241

Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVRN 300
           GH+EA+++E    +D ++  D+L +  GI +        + T V +  G     + R+R 
Sbjct: 242 GHSEAINIEFEDFLDEDEARDILREAPGIMVIDKREDGGYVTPV-ECVGDFATFISRIRQ 300

Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVRD 335
           D +  +G+NLW V+DN+RKGAA NAVQIAELL R+
Sbjct: 301 DSTLDNGLNLWCVSDNLRKGAALNAVQIAELLGRE 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: 356
Number of extensions: 15
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: 337
Length of database: 340
Length adjustment: 28
Effective length of query: 309
Effective length of database: 312
Effective search space:    96408
Effective search space used:    96408
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 GFF3097 PGA1_c31480 (aspartate-semialdehyde dehydrogenase Asd)
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.1014.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.5e-143  461.8   0.1   7.4e-143  461.6   0.1    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3097  PGA1_c31480 aspartate-semialdehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3097  PGA1_c31480 aspartate-semialdehyde dehydrogenase Asd
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.6   0.1  7.4e-143  7.4e-143       2     337 ..       5     333 ..       4     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 461.6 bits;  conditional E-value: 7.4e-143
                          TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskef 77 
                                        v i GatG+vG+e+l++L+er+fp+d++ +las++s G++v+f +k l+ +++++++f g d+alf+ G+   k++
  lcl|FitnessBrowser__Phaeo:GFF3097   5 VVIAGATGNVGREMLNILAERQFPVDEIAVLASRKSLGTEVTFGDKTLTTQDLDTFDFAGWDMALFAVGSDATKKY 80 
                                        8899************************************************************************ PP

                          TIGR01296  78 apkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstY 153
                                        apkaa+ag++viDn+s++r d+dvPL+vpevn + ++   kk+iianPnCst q+vv+Lkpl+d+ak+krvvvstY
  lcl|FitnessBrowser__Phaeo:GFF3097  81 APKAAAAGCVVIDNSSLYRYDHDVPLIVPEVNPQAVHGYAKKNIIANPNCSTAQMVVALKPLHDRAKIKRVVVSTY 156
                                        **************************************************************************** PP

                          TIGR01296 154 qavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgi 229
                                        q+vsG+Gk++++eL +qtkav++ +         +++ ++kqiafn+ip+id + +dG tkee k++ et+ki++ 
  lcl|FitnessBrowser__Phaeo:GFF3097 157 QSVSGSGKDAIDELWDQTKAVYNPTQDV------PPSVYTKQIAFNVIPHIDVFLDDGSTKEEWKMVAETKKIID- 225
                                        **********************977655......599**************************************. PP

                          TIGR01296 230 edlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrirkD 305
                                        + +kv+atcvrvPvf+ghse+++iefe+ l+ +e++++L+eapg++vid+ ++  y+tP+e vg  ++f++rir+D
  lcl|FitnessBrowser__Phaeo:GFF3097 226 PSIKVTATCVRVPVFVGHSEAINIEFEDFLDEDEARDILREAPGIMVIDKREDGGYVTPVECVGDFATFISRIRQD 301
                                        **************************************************************************** PP

                          TIGR01296 306 lskekglalfvvaDnlrkGaalnavqiaelli 337
                                         + ++gl+l++v+DnlrkGaalnavqiaell 
  lcl|FitnessBrowser__Phaeo:GFF3097 302 STLDNGLNLWCVSDNLRKGAALNAVQIAELLG 333
                                        *****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (340 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: 00:00:00.00
# Mc/sec: 11.68
//
[ok]

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