GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Dyella japonica UNC79MFTsu3.2

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate N515DRAFT_0109 N515DRAFT_0109 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0109
          Length = 342

 Score =  407 bits (1047), Expect = e-118
 Identities = 210/335 (62%), Positives = 251/335 (74%), Gaps = 3/335 (0%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64
           + VA+ GATGAVGET+L +L ER+FPV EL  LASERS G    F GK+V V+N+ ++D+
Sbjct: 7   YKVAMVGATGAVGETLLAILAERKFPVGELVPLASERSAGGKVDFAGKSVTVRNLADYDF 66

Query: 65  SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124
           + V IA FSAGG +S + AP AA AG VVIDNTS FRY  DIPLVV EVNP AIA +  R
Sbjct: 67  TGVDIAFFSAGGSVSREHAPRAAAAGAVVIDNTSEFRYQDDIPLVVSEVNPHAIARYTVR 126

Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184
            IIANPNCST+QMLVAL PI+   GIERINV TYQSVSGAG++G++EL  QTA LLN   
Sbjct: 127 GIIANPNCSTMQMLVALAPIHRQAGIERINVATYQSVSGAGRSGMEELGKQTAALLNFQD 186

Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244
            E + F +QIAFN IP ID F DNGYTKEEMKMVWET+KI  D +I VNPT VRVPVFYG
Sbjct: 187 VERSKFPKQIAFNVIPHIDDFQDNGYTKEEMKMVWETRKILEDETIQVNPTAVRVPVFYG 246

Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDGI---ELFRGADFPTQVRDAGGKDHVLVGRVRND 301
           H+EAVH+ETR  I A Q   +LE+ +G+   +  +   +PT V DA GKD V VGR+R D
Sbjct: 247 HSEAVHIETRDKITAGQARALLEKAEGVVVQDERKAGGYPTPVGDAAGKDPVFVGRIRED 306

Query: 302 ISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336
           ISH  G++LW+V+DN+RKGAA NAVQIAE L+ DY
Sbjct: 307 ISHERGLDLWIVSDNIRKGAALNAVQIAERLIEDY 341


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: 372
Number of extensions: 12
Number of successful extensions: 2
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 N515DRAFT_0109 N515DRAFT_0109 (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.12514.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   9.4e-142  458.0   0.1   1.1e-141  457.8   0.1    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0109  N515DRAFT_0109 aspartate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0109  N515DRAFT_0109 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.8   0.1  1.1e-141  1.1e-141       1     338 [.       8     339 ..       8     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 457.8 bits;  conditional E-value: 1.1e-141
                                    TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidial 66 
                                                  +va+vGatGavG++ll +L+er+fp+ +lv+lasersaG kv f gk ++v+++   +f g+dia+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0109   8 KVAMVGATGAVGETLLAILAERKFPVGELVPLASERSAGGKVDFAGKSVTVRNLADYDFTGVDIAF 73 
                                                  69**************************************************************** PP

                                    TIGR01296  67 fsaGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiql 132
                                                  fsaGgsvs+e ap+aa+ag++viDnts fr ++d+PLvv+evn + ++    +giianPnCst+q+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0109  74 FSAGGSVSREHAPRAAAAGAVVIDNTSEFRYQDDIPLVVSEVNPHAIARYTVRGIIANPNCSTMQM 139
                                                  ****************************************************************** PP

                                    TIGR01296 133 vvvLkplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiaf 198
                                                  +v+L p++++a+++r+ v+tYq+vsGaG+ g+eeL +qt a l++++ e        +kf+kqiaf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 140 LVALAPIHRQAGIERINVATYQSVSGAGRSGMEELGKQTAALLNFQDVER-------SKFPKQIAF 198
                                                  *********************************************99885.......9******** PP

                                    TIGR01296 199 naiplidklkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveev 264
                                                  n+ip+id+++++Gytkee+k+++etrkil++e ++v  t+vrvPvf+ghse+v+ie+ +++++ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 199 NVIPHIDDFQDNGYTKEEMKMVWETRKILEDETIQVNPTAVRVPVFYGHSEAVHIETRDKITAGQA 264
                                                  ****************************************************************** PP

                                    TIGR01296 265 kelLkeapgvvviddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalna 329
                                                  + lL++a+gvvv+d+ +   yptP+ +a+gkd vfvgrir+D+s+e+gl+l++v+Dn+rkGaalna
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 265 RALLEKAEGVVVQDERKAGGYPTPVgDAAGKDPVFVGRIREDISHERGLDLWIVSDNIRKGAALNA 330
                                                  ************************9779************************************** PP

                                    TIGR01296 330 vqiaellik 338
                                                  vqiae li+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 331 VQIAERLIE 339
                                                  ******997 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: 00:00:00.01
# Mc/sec: 8.73
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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