GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Desulfovibrio vulgaris Hildenborough

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate 208563 DVU3048 aspartate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-6564
         (346 letters)



>MicrobesOnline__882:208563
          Length = 349

 Score =  358 bits (920), Expect = e-104
 Identities = 190/342 (55%), Positives = 243/342 (71%), Gaps = 8/342 (2%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64
           L VAVVGATGAVG++MLKTLE R+F    +   +S RSAG+KV F+  ELTV+E + + F
Sbjct: 6   LVVAVVGATGAVGREMLKTLEGRDFPAAEVIPFASARSAGSKVPFRDGELTVRELTEDCF 65

Query: 65  EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124
            G++IALFSAGGS S+  AP A K G +VIDN+SA+RMD   PLVVPEVN   L  HNGI
Sbjct: 66  TGIDIALFSAGGSTSEKFAPHAAKAGCVVIDNSSAWRMDARCPLVVPEVNPHHLEAHNGI 125

Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184
           IANPNCSTIQMV AL+P+  A  + +VIVSTYQAVSG G +A+ EL  Q + + N  E E
Sbjct: 126 IANPNCSTIQMVVALKPLHDAARIKRVIVSTYQAVSGTGQKAIDELDRQVRQMFNMMEPE 185

Query: 185 PEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRL 244
            ++ P       ++IAFN +P ID F DN YT EEMKM++ET KIM  P ++V ATCVR+
Sbjct: 186 VQVYP-------HRIAFNCLPHIDVFLDNDYTKEEMKMVHETVKIMDDPSVKVTATCVRV 238

Query: 245 PIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVG 304
           P+  GHSESV IE ++   T  D + +L +APGV + D+P Q++YPMP DA G++  FVG
Sbjct: 239 PVFYGHSESVNIETEK-KLTARDARAILSQAPGVQVYDNPGQKMYPMPIDAAGEDATFVG 297

Query: 305 RIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           RIR+D    NG +LW+V+DN+ KGAA N+VQIAE L   +LV
Sbjct: 298 RIREDETIENGLNLWIVADNIRKGAALNAVQIAEELIDRDLV 339


Lambda     K      H
   0.314    0.131    0.366 

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: 329
Number of extensions: 6
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: 346
Length of database: 349
Length adjustment: 29
Effective length of query: 317
Effective length of database: 320
Effective search space:   101440
Effective search space used:   101440
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: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate 208563 DVU3048 (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.3262316.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     4e-153  495.4   0.1   4.7e-153  495.2   0.1    1.0  1  lcl|MicrobesOnline__882:208563  DVU3048 aspartate-semialdehyde d


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208563  DVU3048 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.2   0.1  4.7e-153  4.7e-153       2     338 ..       8     335 ..       7     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 495.2 bits;  conditional E-value: 4.7e-153
                       TIGR01296   2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskefapk 80 
                                     va+vGatGavG+e+lk+Le r+fp+ +++++as+rsaG kv f++ el+v+e+++  f gidialfsaGgs+s++fap+
  lcl|MicrobesOnline__882:208563   8 VAVVGATGAVGREMLKTLEGRDFPAAEVIPFASARSAGSKVPFRDGELTVRELTEDCFTGIDIALFSAGGSTSEKFAPH 86 
                                     8****************************************************************************** PP

                       TIGR01296  81 aakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYqavsGa 159
                                     aakag++viDn+sa+r+d   PLvvpevn ++l+ ++  giianPnCstiq+vv+Lkpl+d+a++krv+vstYqavsG+
  lcl|MicrobesOnline__882:208563  87 AAKAGCVVIDNSSAWRMDARCPLVVPEVNPHHLEAHN--GIIANPNCSTIQMVVALKPLHDAARIKRVIVSTYQAVSGT 163
                                     ************************************9..**************************************** PP

                       TIGR01296 160 GkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgiedlkvsatc 238
                                     G+k+++eL  q++ ++++ e e+       + ++++iafn +p+id + ++ ytkee+k+++et ki++++ +kv+atc
  lcl|MicrobesOnline__882:208563 164 GQKAIDELDRQVRQMFNMMEPEV-------QVYPHRIAFNCLPHIDVFLDNDYTKEEMKMVHETVKIMDDPSVKVTATC 235
                                     *******************9997.......99*********************************************** PP

                       TIGR01296 239 vrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrirkDlskekglalfvv 317
                                     vrvPvf+ghsesv+ie+ek+l++++++ +L +apgv+v d+p +++yp+P++a+g+d++fvgrir+D + e+gl+l++v
  lcl|MicrobesOnline__882:208563 236 VRVPVFYGHSESVNIETEKKLTARDARAILSQAPGVQVYDNPGQKMYPMPIDAAGEDATFVGRIREDETIENGLNLWIV 314
                                     ******************************************************************************* PP

                       TIGR01296 318 aDnlrkGaalnavqiaellik 338
                                     aDn+rkGaalnavqiae li+
  lcl|MicrobesOnline__882:208563 315 ADNIRKGAALNAVQIAEELID 335
                                     *****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (349 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.78
//
[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:

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