GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Pontibacter ramchanderi LP43

Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_101444144.1 BD749_RS09560 aspartate-semialdehyde dehydrogenase

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



>NCBI__GCF_002846395.1:WP_101444144.1
          Length = 329

 Score =  291 bits (746), Expect = 1e-83
 Identities = 160/343 (46%), Positives = 224/343 (65%), Gaps = 15/343 (4%)

Query: 5   LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64
           + VAVVGATG VG ++LK L +R+F +  L L++S+RS G ++ FKG+++ V        
Sbjct: 1   MKVAVVGATGLVGGEILKVLAERDFPVTELLLVASERSVGKQMEFKGKQIKVIGMQDAIA 60

Query: 65  EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124
               IA+FSAGGS S   AP+  + G +V+DN+SA+RMD +  LVVPE+N  +L + + I
Sbjct: 61  AAPQIAIFSAGGSTSTEWAPKFAEVGTVVVDNSSAWRMDPSKKLVVPEINAKELTKEDKI 120

Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184
           IANPNCSTIQMV AL  + +     +++VSTYQ+V+G G +AV++L ++ +         
Sbjct: 121 IANPNCSTIQMVVALNKLHEELKAKRIVVSTYQSVTGTGVKAVEQLMNEREG-------- 172

Query: 185 PEIMPVKGDKKH-YQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVR 243
                 +G+K + Y I  N +P ID FQDNGYT EEMKMI ETKKIM    ++V AT VR
Sbjct: 173 -----KEGEKAYPYTIDLNVLPHIDVFQDNGYTKEEMKMILETKKIMGDDSIRVTATAVR 227

Query: 244 LPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFV 303
           +P+  GHSESV +E ++ D T++++  +L E  GV + DD     YPMP DA GK++V V
Sbjct: 228 IPVIGGHSESVNVEFEK-DFTLDEVYRILNETEGVKVVDDVKNLQYPMPKDAHGKDEVLV 286

Query: 304 GRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346
           GR+R D  +    +LW+V+DNL KGAA N+VQIAE L K  LV
Sbjct: 287 GRVRLDETQPRTLNLWIVADNLRKGAATNAVQIAEYLVKQGLV 329


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: 285
Number of extensions: 10
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: 346
Length of database: 329
Length adjustment: 28
Effective length of query: 318
Effective length of database: 301
Effective search space:    95718
Effective search space used:    95718
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 WP_101444144.1 BD749_RS09560 (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.668489.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-132  427.8   2.7   1.9e-132  427.4   2.7    1.1  1  NCBI__GCF_002846395.1:WP_101444144.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101444144.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.4   2.7  1.9e-132  1.9e-132       1     338 [.       2     325 ..       2     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 427.4 bits;  conditional E-value: 1.9e-132
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           +va+vGatG vG e+lkvL+er+fp+ +l l+asers Gk+++fkgk+++v  ++ +     +ia+fsaGgs+
  NCBI__GCF_002846395.1:WP_101444144.1   2 KVAVVGATGLVGGEILKVLAERDFPVTELLLVASERSVGKQMEFKGKQIKVIGMQDAIAAAPQIAIFSAGGST 74 
                                           69*********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           s e+apk+a+ g++v+Dn+sa+r+d+   Lvvpe+na+el++     iianPnCstiq+vv+L+ l++e+k k
  NCBI__GCF_002846395.1:WP_101444144.1  75 STEWAPKFAEVGTVVVDNSSAWRMDPSKKLVVPEINAKELTKED--KIIANPNCSTIQMVVALNKLHEELKAK 145
                                           ****************************************9988..8************************** PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219
                                           r+vvstYq+v G+G k+ve+L n+     egke e        k++++ i  n++p+id ++++Gytkee+k+
  NCBI__GCF_002846395.1:WP_101444144.1 146 RIVVSTYQSVTGTGVKAVEQLMNER----EGKEGE--------KAYPYTIDLNVLPHIDVFQDNGYTKEEMKM 206
                                           **********************986....566766........79**************************** PP

                             TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292
                                           + et+ki+g++ ++v+at+vr+Pv+ ghsesv++efek+++++ev+ +L+e +gv+v+dd ++ +yp+P +a 
  NCBI__GCF_002846395.1:WP_101444144.1 207 ILETKKIMGDDSIRVTATAVRIPVIGGHSESVNVEFEKDFTLDEVYRILNETEGVKVVDDVKNLQYPMPKDAH 279
                                           ************************************************************************* PP

                             TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338
                                           gkdev+vgr+r D ++ ++l+l++vaDnlrkGaa+navqiae l+k
  NCBI__GCF_002846395.1:WP_101444144.1 280 GKDEVLVGRVRLDETQPRTLNLWIVADNLRKGAATNAVQIAEYLVK 325
                                           ********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (329 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: 15.13
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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