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

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.22271.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.45
//
[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:

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