Alignments for a candidate for asd in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Dinoroseobacter shibae DFL-12

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 3609858 Dshi_3240 aspartate-semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__Dino:3609858
          Length = 340

 Score =  309 bits (791), Expect = 8e-89
 Identities = 167/332 (50%), Positives = 226/332 (68%), Gaps = 6/332 (1%)

Query: 5   FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64
           + V + GATG VG  ML +L ER+FPVDE+ +LAS +S G    F  KT++ ++++ FD+
Sbjct: 3   YKVVVVGATGNVGREMLNILAERQFPVDEIAVLASRKSLGTEVSFGDKTLKTKDLDTFDF 62

Query: 65  SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124
           +   IA F+ G   + ++AP AA A  VVIDN+S +RYD  IPLVVPEVNPEA+ +++N+
Sbjct: 63  TGWDIAFFAVGSTATKEYAPRAAAAKCVVIDNSSLYRYDPQIPLVVPEVNPEAVEDYKNK 122

Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKL-LNGY 183
            IIANPNCST QM+VALKP++D   I+R+ V+TYQSVSG GK  IDEL  QT  + + G 
Sbjct: 123 YIIANPNCSTAQMVVALKPLHDRARIKRVVVSTYQSVSGTGKEAIDELWDQTKGMYVPGQ 182

Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243
               + + +QIAFN IP ID F+++G TKEE KMV ET+KI  DP+I V  TCVRVPVF 
Sbjct: 183 EKAPSVYPKQIAFNVIPHIDVFLEDGSTKEEWKMVAETKKIV-DPAIKVTATCVRVPVFV 241

Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVRN 300
           GH+EA+++E    ID ++V D+L +  GI +        + T V +  G     + R+R 
Sbjct: 242 GHSEAINIEFEEFIDEDEVRDILREAPGIMVVDKREDGGYVTPV-ECVGDFATFISRIRQ 300

Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELL 332
           D +  +GINLW V+DN+RKGAA NAVQIAE L
Sbjct: 301 DSTIDNGINLWCVSDNLRKGAALNAVQIAETL 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: 340
Number of extensions: 11
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: 340
Length adjustment: 28
Effective length of query: 309
Effective length of database: 312
Effective search space:    96408
Effective search space used:    96408
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 3609858 Dshi_3240 (aspartate-semialdehyde dehydrogenase (RefSeq))
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.15005.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.7e-142  459.4   0.2   4.2e-142  459.2   0.2    1.0  1  lcl|FitnessBrowser__Dino:3609858  Dshi_3240 aspartate-semialdehyde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609858  Dshi_3240 aspartate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  459.2   0.2  4.2e-142  4.2e-142       2     337 ..       5     333 ..       4     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 459.2 bits;  conditional E-value: 4.2e-142
                         TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskefa 78 
                                       v +vGatG+vG+e+l++L+er+fp+d++ +las++s G++v f +k l+ +++++++f g dia+f+ G++  ke+a
  lcl|FitnessBrowser__Dino:3609858   5 VVVVGATGNVGREMLNILAERQFPVDEIAVLASRKSLGTEVSFGDKTLKTKDLDTFDFTGWDIAFFAVGSTATKEYA 81 
                                       89*************************************************************************** PP

                         TIGR01296  79 pkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYqa 155
                                       p+aa+a ++viDn+s++r d+++PLvvpevn e +++ k+k iianPnCst q+vv+Lkpl+d+a++krvvvstYq+
  lcl|FitnessBrowser__Dino:3609858  82 PRAAAAKCVVIDNSSLYRYDPQIPLVVPEVNPEAVEDYKNKYIIANPNCSTAQMVVALKPLHDRARIKRVVVSTYQS 158
                                       ***************************************************************************** PP

                         TIGR01296 156 vsGaGkkgveeLknqtkavle.gkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgied 231
                                       vsG+Gk++++eL +qtk +++ g+ek        ++ ++kqiafn+ip+id + edG tkee k++ et+ki++ + 
  lcl|FitnessBrowser__Dino:3609858 159 VSGTGKEAIDELWDQTKGMYVpGQEKA-------PSVYPKQIAFNVIPHIDVFLEDGSTKEEWKMVAETKKIVD-PA 227
                                       *****************9987255665.......599************************************9.** PP

                         TIGR01296 232 lkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrirkDlsk 308
                                       +kv+atcvrvPvf+ghse+++iefe+ ++ +ev+++L+eapg++v+d+ ++  y+tP+e vg  ++f++rir+D + 
  lcl|FitnessBrowser__Dino:3609858 228 IKVTATCVRVPVFVGHSEAINIEFEEFIDEDEVRDILREAPGIMVVDKREDGGYVTPVECVGDFATFISRIRQDSTI 304
                                       ***************************************************************************** PP

                         TIGR01296 309 ekglalfvvaDnlrkGaalnavqiaelli 337
                                       ++g++l++v+DnlrkGaalnavqiae+l 
  lcl|FitnessBrowser__Dino:3609858 305 DNGINLWCVSDNLRKGAALNAVQIAETLG 333
                                       **************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (340 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: 9.04
//
[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