Alignments for a candidate for asd in Rhizobium johnstonii 3841

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Rhizobium johnstonii 3841

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_003543997.1 RL_RS24260 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>NCBI__GCF_000009265.1:WP_003543997.1
          Length = 344

 Score =  333 bits (855), Expect = 3e-96
 Identities = 171/332 (51%), Positives = 231/332 (69%), Gaps = 5/332 (1%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64
           F VA+ GATG VG  ML +L ER FP DE+  LAS RS+G    +  +T++V N+E +D+
Sbjct: 3   FKVAVAGATGNVGREMLNILSERGFPADEVVALASSRSQGTEVSYGDRTLKVSNLENYDF 62

Query: 65  SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124
           S   I L SAGGE+S K++P   + G +VIDN+S +RYD D+PL+VPEVNP+AI++F  R
Sbjct: 63  SDTDICLMSAGGEVSKKYSPKIGQQGCIVIDNSSAWRYDADVPLIVPEVNPDAISQFTKR 122

Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184
           NIIANPNCST Q++VALKP++D   I+R+ ++TYQSVSGAGK G+DEL  QT  +    P
Sbjct: 123 NIIANPNCSTAQLVVALKPLHDFAKIKRVVISTYQSVSGAGKDGMDELFNQTRAVFVADP 182

Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244
            E   F+++IAFN IP ID FM++GYTKEE K++ ET+K+  DP I V  T VRVPVF G
Sbjct: 183 IENKKFTKRIAFNVIPHIDVFMEDGYTKEEWKVLAETKKML-DPKIKVTCTAVRVPVFIG 241

Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDG---IELFRGADFPTQVRDAGGKDHVLVGRVRND 301
           H+E+V++E    I A+Q  D+L    G   I+      + T    A G+D   + R+R D
Sbjct: 242 HSESVNIEFENEITADQARDILRDAPGCLVIDKREDGGYITPYESA-GEDATYISRIRED 300

Query: 302 ISHHSGINLWVVADNVRKGAATNAVQIAELLV 333
            +  +G+N+WVV+DN+RKGAA NA+QIAELLV
Sbjct: 301 ATVENGLNIWVVSDNLRKGAALNAIQIAELLV 332


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: 332
Number of extensions: 13
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: 344
Length adjustment: 28
Effective length of query: 309
Effective length of database: 316
Effective search space:    97644
Effective search space used:    97644
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_003543997.1 RL_RS24260 (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.3706295.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-143  464.2   0.4   1.4e-143  464.0   0.4    1.0  1  NCBI__GCF_000009265.1:WP_003543997.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000009265.1:WP_003543997.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.0   0.4  1.4e-143  1.4e-143       1     338 [.       4     333 ..       4     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 464.0 bits;  conditional E-value: 1.4e-143
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           +va+ GatG+vG+e+l++L er fp+d++v+las+rs+G++v + ++ l+v+++e+ +f++ di l+saGg v
  NCBI__GCF_000009265.1:WP_003543997.1   4 KVAVAGATGNVGREMLNILSERGFPADEVVALASSRSQGTEVSYGDRTLKVSNLENYDFSDTDICLMSAGGEV 76 
                                           69*********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           sk++ pk+ ++g+iviDn+sa+r d dvPL+vpevn + + ++ k++iianPnCst qlvv+Lkpl+d ak+k
  NCBI__GCF_000009265.1:WP_003543997.1  77 SKKYSPKIGQQGCIVIDNSSAWRYDADVPLIVPEVNPDAISQFTKRNIIANPNCSTAQLVVALKPLHDFAKIK 149
                                           ************************************************************************* PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           rvv+stYq+vsGaGk+g++eL nqt+av++   +e        kkf+k+iafn+ip+id ++edGytkee k+
  NCBI__GCF_000009265.1:WP_003543997.1 150 RVVISTYQSVSGAGKDGMDELFNQTRAVFVADPIE-------NKKFTKRIAFNVIPHIDVFMEDGYTKEEWKV 215
                                           ****************************9976655.......69***************************** PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292
                                           l et+k+l+ +++kv+ t+vrvPvf+ghsesv+iefe+e+++++++++L++apg  vid+ ++  y+tP e +
  NCBI__GCF_000009265.1:WP_003543997.1 216 LAETKKMLD-PKIKVTCTAVRVPVFIGHSESVNIEFENEITADQARDILRDAPGCLVIDKREDGGYITPYESA 287
                                           ********9.*************************************************************** PP

                             TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                           g+d+++++rir+D + e+gl+++vv+DnlrkGaalna+qiaell++
  NCBI__GCF_000009265.1:WP_003543997.1 288 GEDATYISRIREDATVENGLNIWVVSDNLRKGAALNAIQIAELLVN 333
                                           *******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (344 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: 29.94
//
[ok]

This GapMind analysis is from Jul 25 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:

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