GapMind for Amino acid biosynthesis

 

Aligments for a candidate for asd in Synechococcus elongatus PCC 7942

Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate Synpcc7942_1848 Synpcc7942_1848 aspartate-semialdehyde dehydrogenase

Query= SwissProt::P23247
         (337 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1848 Synpcc7942_1848
           aspartate-semialdehyde dehydrogenase
          Length = 354

 Score =  282 bits (722), Expect = 8e-81
 Identities = 155/337 (45%), Positives = 209/337 (62%), Gaps = 6/337 (1%)

Query: 1   MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60
           +SQ + VAI GATGAVG  +L++L+ER+FP+ EL LLAS RS G+T  F G+T+ +Q   
Sbjct: 10  LSQGYRVAILGATGAVGTELLQILEERQFPIAELRLLASPRSAGQTLTFAGETLTIQEAT 69

Query: 61  EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120
              +  + I L SAGG  S   A     AG V+IDN+S FR D  +PLVVPEVNPEA A+
Sbjct: 70  PSAFQGLDIVLASAGGSTSKALAEAIVAAGAVMIDNSSAFRMDPTVPLVVPEVNPEAAAQ 129

Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180
             ++ IIANPNC+TI M +AL P+     I RI V+TYQS SGAG   + E+  Q+  +L
Sbjct: 130 --HQGIIANPNCTTILMAIALWPLQQRHPIRRIVVSTYQSASGAGARAMAEVQEQSRAIL 187

Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240
            G PA        +AFN  P      ++GY +EE+KM+ E++KIF  P + +  TCVRVP
Sbjct: 188 AGQPAIAEILPYPLAFNLFPHNSPLTESGYCEEELKMLNESRKIFGLPDLKLTATCVRVP 247

Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGAD---FPTQVRDAGGKDHVLVGR 297
           V   H+EA++VE   P    +  + +    G  L    D   FP  + +A G+D VLVGR
Sbjct: 248 VLRAHSEAINVEFTEPFSVAEAREAIAAAPGARLLEDWDRNYFPMPI-EASGEDDVLVGR 306

Query: 298 VRNDISHHSGINLWVVADNVRKGAATNAVQIAELLVR 334
           +R D+S  + + LW+  D +RKGAA NAVQIAELLV+
Sbjct: 307 IRQDLSEPNALELWICGDQIRKGAALNAVQIAELLVK 343


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: 302
Number of extensions: 16
Number of successful extensions: 3
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: 354
Length adjustment: 29
Effective length of query: 308
Effective length of database: 325
Effective search space:   100100
Effective search space used:   100100
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 Synpcc7942_1848 Synpcc7942_1848 (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.9454.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-129  416.2   0.0   5.5e-129  416.0   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1848  Synpcc7942_1848 aspartate-semial


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1848  Synpcc7942_1848 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.0   0.0  5.5e-129  5.5e-129       1     338 [.      15     343 ..      15     344 .. 0.99

  Alignments for each domain:
  == domain 1  score: 416.0 bits;  conditional E-value: 5.5e-129
                                 TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 
                                               +vai+GatGavG ell++Leer+fpi +l+llas rsaG+ ++f g+ l+++ea+   f+g+di l sa
  lcl|FitnessBrowser__SynE:Synpcc7942_1848  15 RVAILGATGAVGTELLQILEERQFPIAELRLLASPRSAGQTLTFAGETLTIQEATPSAFQGLDIVLASA 83 
                                               69******************************************************************* PP

                                 TIGR01296  70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138
                                               Ggs+sk++a  +++ag+++iDn+safr+d+ vPLvvpevn e  ++++  giianPnC+ti +  +L p
  lcl|FitnessBrowser__SynE:Synpcc7942_1848  84 GGSTSKALAEAIVAAGAVMIDNSSAFRMDPTVPLVVPEVNPEAAAQHQ--GIIANPNCTTILMAIALWP 150
                                               *******************************************99999..******************* PP

                                 TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207
                                               l+++  ++r+vvstYq+ sGaG+++++e+++q +a+l g+          a+  ++++afn++p+   l
  lcl|FitnessBrowser__SynE:Synpcc7942_1848 151 LQQRHPIRRIVVSTYQSASGAGARAMAEVQEQSRAILAGQPAI-------AEILPYPLAFNLFPHNSPL 212
                                               *************************************997655.......6899*************** PP

                                 TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276
                                               +e Gy +eelk+l+e+rki+g +dlk++atcvrvPv+++hse++++ef +++sv e++e +  apg  +
  lcl|FitnessBrowser__SynE:Synpcc7942_1848 213 TESGYCEEELKMLNESRKIFGLPDLKLTATCVRVPVLRAHSEAINVEFTEPFSVAEAREAIAAAPGARL 281
                                               ********************************************************************* PP

                                 TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                               ++d ++n +p+P+ea+g+d+v+vgrir+Dls+ ++l+l++ +D++rkGaalnavqiaell+k
  lcl|FitnessBrowser__SynE:Synpcc7942_1848 282 LEDWDRNYFPMPIEASGEDDVLVGRIRQDLSEPNALELWICGDQIRKGAALNAVQIAELLVK 343
                                               ************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (354 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.18
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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