Alignments for a candidate for asd in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Shewanella oneidensis MR-1

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 202188 SO3070 aspartate semialdehyde dehydrogenese (NCBI ptt file)

Query= SwissProt::P23247
         (337 letters)



>FitnessBrowser__MR1:202188
          Length = 338

 Score =  482 bits (1240), Expect = e-141
 Identities = 236/338 (69%), Positives = 271/338 (80%), Gaps = 1/338 (0%)

Query: 1   MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60
           MSQ+FNV + GA+GAVG+TM+E+L+ER FPV  L+ LAS RS G+T  F+GK + + +VE
Sbjct: 1   MSQEFNVVVLGASGAVGQTMIEILEERNFPVANLYPLASSRSAGETVSFHGKQITILDVE 60

Query: 61  EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120
            FDWSQ  +  FSAGG++SAKWAPIAAEAG VVIDNTSHFRYD DIPLVVPEVNP AIA+
Sbjct: 61  TFDWSQAQLGFFSAGGDVSAKWAPIAAEAGCVVIDNTSHFRYDIDIPLVVPEVNPHAIAD 120

Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180
           FRNRNIIANPNCSTIQMLVALKPIYD  GI RINV TYQSVSG GK  I+ELA Q  KLL
Sbjct: 121 FRNRNIIANPNCSTIQMLVALKPIYDTYGISRINVATYQSVSGTGKKAIEELARQCTKLL 180

Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240
            G PAE   + +QIAFN +PQID+FMDNGYTKEEMKMVWETQKIF D  I+VN T VRVP
Sbjct: 181 QGLPAEAEVYPKQIAFNVLPQIDKFMDNGYTKEEMKMVWETQKIFGDDDILVNATAVRVP 240

Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGAD-FPTQVRDAGGKDHVLVGRVR 299
           VFYGH+EAVH+ETR P DAE +  +L   +G+ LF   D +PT V  A G D V VGRVR
Sbjct: 241 VFYGHSEAVHIETRQPADAEDIKALLRNAEGVVLFESDDEYPTAVTHAAGTDPVYVGRVR 300

Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDYF 337
            DISH  GINLWVV+DN+RKGAA N+VQIAE+LVRDY+
Sbjct: 301 KDISHAHGINLWVVSDNIRKGAALNSVQIAEILVRDYY 338


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: 392
Number of extensions: 5
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: 338
Length adjustment: 28
Effective length of query: 309
Effective length of database: 310
Effective search space:    95790
Effective search space used:    95790
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 202188 SO3070 (aspartate semialdehyde dehydrogenese (NCBI ptt file))
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.1705.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-137  444.3   0.1   1.6e-137  444.1   0.1    1.0  1  lcl|FitnessBrowser__MR1:202188  SO3070 aspartate semialdehyde de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:202188  SO3070 aspartate semialdehyde dehydrogenese (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.1   0.1  1.6e-137  1.6e-137       1     338 [.       6     335 ..       6     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 444.1 bits;  conditional E-value: 1.6e-137
                       TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskefap 79 
                                     nv ++Ga+GavGq+++++Leernfp+ +l++las+rsaG+ v f+gk++++ ++e+++ ++ ++ +fsaGg vs ++ap
  lcl|FitnessBrowser__MR1:202188   6 NVVVLGASGAVGQTMIEILEERNFPVANLYPLASSRSAGETVSFHGKQITILDVETFDWSQAQLGFFSAGGDVSAKWAP 84 
                                     689**************************************************************************** PP

                       TIGR01296  80 kaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYqavsG 158
                                      aa+ag++viDnts fr d d+PLvvpevn + ++++++++iianPnCstiq++v+Lkp++d +++ r+ v+tYq+vsG
  lcl|FitnessBrowser__MR1:202188  85 IAAEAGCVVIDNTSHFRYDIDIPLVVPEVNPHAIADFRNRNIIANPNCSTIQMLVALKPIYDTYGISRINVATYQSVSG 163
                                     ******************************************************************************* PP

                       TIGR01296 159 aGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgiedlkvsat 237
                                     +Gkk++eeL+ q    l+g   e       a+ ++kqiafn++p+idk++++Gytkee+k+++et+ki+g++d+ v at
  lcl|FitnessBrowser__MR1:202188 164 TGKKAIEELARQCTKLLQGLPAE-------AEVYPKQIAFNVLPQIDKFMDNGYTKEEMKMVWETQKIFGDDDILVNAT 235
                                     ************99999987766.......799********************************************** PP

                       TIGR01296 238 cvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPl.eavgkdevfvgrirkDlskekglalf 315
                                     +vrvPvf+ghse+v+ie+ +++++e++k lL++a+gvv+ + +  ++ypt + +a+g+d v+vgr+rkD+s+++g++l+
  lcl|FitnessBrowser__MR1:202188 236 AVRVPVFYGHSEAVHIETRQPADAEDIKALLRNAEGVVLFESD--DEYPTAVtHAAGTDPVYVGRVRKDISHAHGINLW 312
                                     ***************************************9977..89**9973699*********************** PP

                       TIGR01296 316 vvaDnlrkGaalnavqiaellik 338
                                     vv+Dn+rkGaaln+vqiae l++
  lcl|FitnessBrowser__MR1:202188 313 VVSDNIRKGAALNSVQIAEILVR 335
                                     ********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (338 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: 9.97
//
[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