GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Sphingomonas indica Dd16

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_085218993.1 B9N75_RS11920 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>NCBI__GCF_900177405.1:WP_085218993.1
          Length = 342

 Score =  321 bits (822), Expect = 2e-92
 Identities = 177/335 (52%), Positives = 230/335 (68%), Gaps = 7/335 (2%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRF--NGKTVRVQNVEEF 62
           + V + GATG VG  ML +L ER+FPVDE+  +AS RS G    F  +G+ ++V+N+E F
Sbjct: 3   YRVVVVGATGNVGREMLNILAERQFPVDEIAAVASPRSTGDVIDFGDSGQELKVRNIEHF 62

Query: 63  DWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFR 122
           D++   IALF+AG   S  +AP AA AG  VIDN+S FR D D+PL+VPEVN  AI  +R
Sbjct: 63  DFAGWDIALFAAGSAASKAYAPGAAAAGCTVIDNSSLFRMDPDVPLIVPEVNAHAIDGYR 122

Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182
            +NIIANPNCST QM+VALKP++D   I+R+ V TYQSVSGAGK+G+DEL  Q+  +  G
Sbjct: 123 AKNIIANPNCSTAQMVVALKPLHDFARIKRVVVATYQSVSGAGKSGMDELFEQSRNIFVG 182

Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242
             AE+ TF++QIAFN IP ID F+D+G TKEE KMV ET+KI  DP I V  TCVRVPVF
Sbjct: 183 DSAESKTFTKQIAFNVIPHIDAFLDDGSTKEEWKMVVETKKIL-DPKIKVTATCVRVPVF 241

Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVR 299
            GH+EA+++E    I A+    +L +  G+ L        + T V +A G+    V RVR
Sbjct: 242 VGHSEAINIEFENEISAKDAQRILREAPGVMLVDKREDGGYVTPV-EAVGEYATYVSRVR 300

Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVR 334
            D +  +G++LW V+DN+RKGAA NAVQIAELL R
Sbjct: 301 EDPTVDNGLSLWCVSDNLRKGAALNAVQIAELLGR 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: 341
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: 342
Length adjustment: 28
Effective length of query: 309
Effective length of database: 314
Effective search space:    97026
Effective search space used:    97026
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_085218993.1 B9N75_RS11920 (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.3851713.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-144  466.4   0.3     3e-144  466.2   0.3    1.0  1  NCBI__GCF_900177405.1:WP_085218993.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085218993.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.2   0.3    3e-144    3e-144       2     336 ..       5     333 ..       4     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 466.2 bits;  conditional E-value: 3e-144
                             TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfk..gkeleveeaekesfegidialfsaGgs 72 
                                           v +vGatG+vG+e+l++L+er+fp+d++ ++as rs+G  + f   g+el+v+++e+++f g dialf+aG++
  NCBI__GCF_900177405.1:WP_085218993.1   5 VVVVGATGNVGREMLNILAERQFPVDEIAAVASPRSTGDVIDFGdsGQELKVRNIEHFDFAGWDIALFAAGSA 77 
                                           89*****************************************63379************************* PP

                             TIGR01296  73 vskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeakl 145
                                            sk++ap aa+ag++viDn+s+fr+d+dvPL+vpevna+ +   + k+iianPnCst q+vv+Lkpl+d a++
  NCBI__GCF_900177405.1:WP_085218993.1  78 ASKAYAPGAAAAGCTVIDNSSLFRMDPDVPLIVPEVNAHAIDGYRAKNIIANPNCSTAQMVVALKPLHDFARI 150
                                           ************************************************************************* PP

                             TIGR01296 146 krvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelk 218
                                           krvvv+tYq+vsGaGk g++eL +q + +++g   e       +k+f+kqiafn+ip+id + +dG tkee k
  NCBI__GCF_900177405.1:WP_085218993.1 151 KRVVVATYQSVSGAGKSGMDELFEQSRNIFVGDSAE-------SKTFTKQIAFNVIPHIDAFLDDGSTKEEWK 216
                                           ******************************999888.......59**************************** PP

                             TIGR01296 219 llfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPlea 291
                                           ++ et+kil+ +++kv+atcvrvPvf+ghse+++iefe+e+s+++++ +L+eapgv+++d+ ++  y+tP+ea
  NCBI__GCF_900177405.1:WP_085218993.1 217 MVVETKKILD-PKIKVTATCVRVPVFVGHSEAINIEFENEISAKDAQRILREAPGVMLVDKREDGGYVTPVEA 288
                                           **********.************************************************************** PP

                             TIGR01296 292 vgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaell 336
                                           vg+ +++v+r+r+D + ++gl+l++v+DnlrkGaalnavqiaell
  NCBI__GCF_900177405.1:WP_085218993.1 289 VGEYATYVSRVREDPTVDNGLSLWCVSDNLRKGAALNAVQIAELL 333
                                           *******************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (342 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: 00:00:00.00
# Mc/sec: 14.42
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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