GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Synechococcus elongatus PCC 7942

Align aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate Synpcc7942_1848 Synpcc7942_1848 aspartate-semialdehyde dehydrogenase

Query= metacyc::AT1G14810-MONOMER
         (375 letters)



>FitnessBrowser__SynE:Synpcc7942_1848
          Length = 354

 Score =  335 bits (859), Expect = 1e-96
 Identities = 166/335 (49%), Positives = 235/335 (70%), Gaps = 8/335 (2%)

Query: 41  LAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTVEELTADSFNG 100
           +A++G TGAVG E L +L +R FP + +++LAS RSAG+ + F G   T++E T  +F G
Sbjct: 16  VAILGATGAVGTELLQILEERQFPIAELRLLASPRSAGQTLTFAGETLTIQEATPSAFQG 75

Query: 101 VDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPEAMKGIKVGMG 160
           +DI L SAGGS SK         G +++DNSSAFRM   VPLV+PEVNPEA    +    
Sbjct: 76  LDIVLASAGGSTSKALAEAIVAAGAVMIDNSSAFRMDPTVPLVVPEVNPEAAAQHQ---- 131

Query: 161 KGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEELVQQTREVLEG 220
              +IANPNC+TI+  +A+ PL     ++R+VVSTYQ+ASGAGA AM E+ +Q+R +L G
Sbjct: 132 --GIIANPNCTTILMAIALWPLQQRHPIRRIVVSTYQSASGAGARAMAEVQEQSRAILAG 189

Query: 221 KPPTCNIFGQQYAFNLFSHNAPILDNGYNEEEMKLVKETRKIWNDTEVKVTATCIRVPVM 280
           +P    I     AFNLF HN+P+ ++GY EEE+K++ E+RKI+   ++K+TATC+RVPV+
Sbjct: 190 QPAIAEILPYPLAFNLFPHNSPLTESGYCEEELKMLNESRKIFGLPDLKLTATCVRVPVL 249

Query: 281 RAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNKDDVAVGRIRR 340
           RAH+E++N++F  P     ARE +  APG  +++D   N FP P++ S +DDV VGRIR+
Sbjct: 250 RAHSEAINVEFTEPFSVAEAREAIAAAPGARLLEDWDRNYFPMPIEASGEDDVLVGRIRQ 309

Query: 341 DVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEMLL 375
           D+S+     L++++CGDQIRKGAALNAVQIAE+L+
Sbjct: 310 DLSEPN--ALELWICGDQIRKGAALNAVQIAELLV 342


Lambda     K      H
   0.318    0.133    0.380 

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: 303
Number of extensions: 7
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: 375
Length of database: 354
Length adjustment: 29
Effective length of query: 346
Effective length of database: 325
Effective search space:   112450
Effective search space used:   112450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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.18272.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.15
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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