Alignments for a candidate for asd in Phaeobacter inhibens BS107

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.18648.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.65
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis