GapMind for Amino acid biosynthesis

 

Aligments for a candidate for asd in Shewanella sp. ANA-3

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 7024285 Shewana3_1477 aspartate semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::P23247
         (337 letters)



>lcl|FitnessBrowser__ANA3:7024285 Shewana3_1477 aspartate
           semialdehyde dehydrogenase (RefSeq)
          Length = 338

 Score =  481 bits (1239), 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 V + +VE
Sbjct: 1   MSQEFNVVVLGASGAVGQTMIEILEERNFPVANLYPLASSRSAGETVSFHGKQVTILDVE 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 FRNRNIIANPNCSTIQMLVALKPIYDTYGISRINVATYQSVSGTGKKAIEELAKQCTKLL 180

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

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

Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDYF 337
            DISH  GINLWVV+DN+RKGAA N+VQIAE+LVRDY+
Sbjct: 301 KDISHSHGINLWVVSDNIRKGAALNSVQIAEILVRDYY 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: 395
Number of extensions: 6
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 7024285 Shewana3_1477 (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.15200.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.4e-137  442.1   0.1   7.2e-137  441.9   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7024285  Shewana3_1477 aspartate semialde


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024285  Shewana3_1477 aspartate semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.9   0.1  7.2e-137  7.2e-137       1     338 [.       6     335 ..       6     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 441.9 bits;  conditional E-value: 7.2e-137
                         TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskef 77 
                                       nv ++Ga+GavGq+++++Leernfp+ +l++las+rsaG+ v f+gk++++ ++e+++ ++ ++ +fsaGg vs ++
  lcl|FitnessBrowser__ANA3:7024285   6 NVVVLGASGAVGQTMIEILEERNFPVANLYPLASSRSAGETVSFHGKQVTILDVETFDWSQAQLGFFSAGGDVSAKW 82 
                                       689************************************************************************** PP

                         TIGR01296  78 apkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYq 154
                                       ap aa+ag++viDnts fr d d+PLvvpevn + ++++++++iianPnCstiq++v+Lkp++d +++ r+ v+tYq
  lcl|FitnessBrowser__ANA3:7024285  83 APIAAEAGCVVIDNTSHFRYDIDIPLVVPEVNPHAIADFRNRNIIANPNCSTIQMLVALKPIYDTYGISRINVATYQ 159
                                       ***************************************************************************** PP

                         TIGR01296 155 avsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgied 231
                                       +vsG+Gkk++eeL++q    l+g   +       a+ ++kqiafn++p+idk++++Gytkee+k+++et+ki+g+++
  lcl|FitnessBrowser__ANA3:7024285 160 SVSGTGKKAIEELAKQCTKLLQGLPAD-------AEVYPKQIAFNVLPQIDKFMDNGYTKEEMKMVWETQKIFGDDE 229
                                       *****************9999988776.......799**************************************** PP

                         TIGR01296 232 lkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPl.eavgkdevfvgrirkDls 307
                                       + v at+vrvPvf+ghse+v+ie+ +++++e++k lL++a+gvv+ + +  ++ypt + +a+g+d v+vgr+rkD+s
  lcl|FitnessBrowser__ANA3:7024285 230 ILVNATAVRVPVFYGHSEAVHIETRQPADAEDIKALLRDAEGVVLFESD--DEYPTAVtHAAGTDPVYVGRVRKDIS 304
                                       *********************************************9977..89**9973699*************** PP

                         TIGR01296 308 kekglalfvvaDnlrkGaalnavqiaellik 338
                                       +++g++l+vv+Dn+rkGaaln+vqiae l++
  lcl|FitnessBrowser__ANA3:7024285 305 HSHGINLWVVSDNIRKGAALNSVQIAEILVR 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: 6.81
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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