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.3700424.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.59
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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