GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Sinorhizobium meliloti 1021

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate SMc04410 SMc04410 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Smeli:SMc04410
          Length = 344

 Score =  324 bits (831), Expect = 2e-93
 Identities = 166/332 (50%), Positives = 229/332 (68%), Gaps = 5/332 (1%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64
           F +A+ GATG VG  ML +L ER FP DE+  LAS RS G    +  KT++V N++ +D+
Sbjct: 3   FKIAVAGATGNVGREMLNILSERGFPADEVVALASSRSVGTEVSYGDKTLKVTNLDTYDF 62

Query: 65  SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124
           S   I L SAGG +S K++P     G VVIDN+S +RYD D+PL+VPEVN +AIA+F  +
Sbjct: 63  SDTDICLMSAGGAVSQKYSPKIGREGCVVIDNSSAWRYDADVPLIVPEVNADAIAQFSKK 122

Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184
           NIIANPNCST Q++VALKP++D   I+RI V+TYQSVSGAGK G+DEL  QT  +    P
Sbjct: 123 NIIANPNCSTAQLVVALKPLHDHAKIKRIVVSTYQSVSGAGKDGMDELFNQTRAVFVADP 182

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

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

Query: 302 ISHHSGINLWVVADNVRKGAATNAVQIAELLV 333
            +  +G+N+W+V+DN+RKGAA NAVQIAELL+
Sbjct: 301 ATVENGLNMWIVSDNLRKGAALNAVQIAELLI 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: 316
Number of extensions: 11
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 SMc04410 SMc04410 (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.31435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-145  470.6   0.9   1.5e-145  470.5   0.9    1.0  1  lcl|FitnessBrowser__Smeli:SMc04410  SMc04410 aspartate-semialdehyde 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04410  SMc04410 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.5   0.9  1.5e-145  1.5e-145       1     338 [.       4     333 ..       4     334 .. 0.99

  Alignments for each domain:
  == domain 1  score: 470.5 bits;  conditional E-value: 1.5e-145
                           TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvsk 75 
                                         ++a+ GatG+vG+e+l++L er fp+d++v+las+rs G++v + +k l+v+++++ +f++ di l+saGg+vs+
  lcl|FitnessBrowser__Smeli:SMc04410   4 KIAVAGATGNVGREMLNILSERGFPADEVVALASSRSVGTEVSYGDKTLKVTNLDTYDFSDTDICLMSAGGAVSQ 78 
                                         69************************************************************************* PP

                           TIGR01296  76 efapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvv 150
                                         ++ pk+ ++g++viDn+sa+r d dvPL+vpevna+ ++++ kk+iianPnCst qlvv+Lkpl+d+ak+kr+vv
  lcl|FitnessBrowser__Smeli:SMc04410  79 KYSPKIGREGCVVIDNSSAWRYDADVPLIVPEVNADAIAQFSKKNIIANPNCSTAQLVVALKPLHDHAKIKRIVV 153
                                         *************************************************************************** PP

                           TIGR01296 151 stYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrk 225
                                         stYq+vsGaGk+g++eL nqt+av++   +e       +kkf+k+iafn+ip+id ++edGytkee k+l et+k
  lcl|FitnessBrowser__Smeli:SMc04410 154 STYQSVSGAGKDGMDELFNQTRAVFVADPIE-------SKKFTKRIAFNVIPHIDVFMEDGYTKEEWKVLAETKK 221
                                         ************************9976655.......7************************************ PP

                           TIGR01296 226 ilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvg 300
                                         +l+ +++kv+ t+vrvPvf+ghsesv+iefe+e++++e++e+L+eapg  v+d+ ++  y+tP e +g+d+++++
  lcl|FitnessBrowser__Smeli:SMc04410 222 MLD-PKIKVTCTAVRVPVFIGHSESVNIEFENEITADEAREILREAPGCLVVDKHENGGYVTPYECAGEDATYIS 295
                                         **9.*********************************************************************** PP

                           TIGR01296 301 rirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                         rir+D + e+gl++++v+DnlrkGaalnavqiaelli+
  lcl|FitnessBrowser__Smeli:SMc04410 296 RIREDATVENGLNMWIVSDNLRKGAALNAVQIAELLIN 333
                                         ************************************97 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.55
//
[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