GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Streptacidiphilus oryzae TH49

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_037568868.1 BS73_RS02665 aspartate-semialdehyde dehydrogenase

Query= BRENDA::P9WNX5
         (345 letters)



>NCBI__GCF_000744815.1:WP_037568868.1
          Length = 342

 Score =  421 bits (1083), Expect = e-122
 Identities = 227/343 (66%), Positives = 258/343 (75%), Gaps = 3/343 (0%)

Query: 3   LSIGIVGATGQVGQVMRTLLDERDFPASAVRFFASARSQGRKLAFRGQEIEVEDAETADP 62
           + +GIVGATGQVG VMR +L+ERDFP   +R FASARS GR L ++G EI VEDA  AD 
Sbjct: 1   MKVGIVGATGQVGGVMRRVLEERDFPVEQLRLFASARSAGRTLPWKGSEITVEDAAAADY 60

Query: 63  SGLDIALFSAGSAMSKVQAPRFAAAGVTVIDNSSAWRKDPDVPLVVSEVNFERDAHRRPK 122
           SGLDI LFSAG A SK  A + A  G  VIDNSSAWR DP VPLVV+EVN       RPK
Sbjct: 61  SGLDIVLFSAGGATSKALAEKVARDGAVVIDNSSAWRMDPQVPLVVAEVN-PHAVVDRPK 119

Query: 123 GIIANPNCTTMAAMPVLKVLHDEARLVRLVVSSYQAVSGSGLAGVAELAEQARAVIGGAE 182
           GIIANPNCTTMAAMPVLK LH EA L  LV ++YQAVSGSGLAGVAEL  Q +     A 
Sbjct: 120 GIIANPNCTTMAAMPVLKPLHQEAGLKALVATTYQAVSGSGLAGVAELEAQIQKGADRAA 179

Query: 183 QLVYDGGALEFPPPNTYVAPIAFNVVPLAGSLVDDGSGETDEDQKLRFESRKILGIPDLL 242
            L +DG A++ P P+ Y  PIAFNV+PLAG +VDDG  ETDE++KLR ESRKIL IP+L 
Sbjct: 180 ALTHDGSAIDLPAPSVYARPIAFNVLPLAGKIVDDGLNETDEEKKLRNESRKILEIPELK 239

Query: 243 VSGTCVRVPVFTGHSLSINAEFAQPLSPERARELLDGATGVQLVDVPTPLAAAGVDESLV 302
           VSGTCVRVPVFTGHSL +NA F +P++P+RA ELL GA GV L ++PTPL AAG D S V
Sbjct: 240 VSGTCVRVPVFTGHSLQVNARFERPITPDRAAELLAGAPGVALSEIPTPLQAAGQDPSYV 299

Query: 303 GRIRRDPGVPDGRGLALFVSGDNLRKGAALNTIQIAELLTADL 345
           GRIR D  V +  GLALF+S DNLRKGAALN IQIAEL+ ADL
Sbjct: 300 GRIRVDETVDN--GLALFLSNDNLRKGAALNAIQIAELVAADL 340


Lambda     K      H
   0.317    0.135    0.382 

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: 412
Number of extensions: 15
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: 345
Length of database: 342
Length adjustment: 29
Effective length of query: 316
Effective length of database: 313
Effective search space:    98908
Effective search space used:    98908
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 WP_037568868.1 BS73_RS02665 (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.1918983.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-132  428.1   0.0   1.4e-132  427.9   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037568868.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037568868.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.9   0.0  1.4e-132  1.4e-132       1     337 [.       2     337 ..       2     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 427.9 bits;  conditional E-value: 1.4e-132
                             TIGR01296   1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 
                                           +v+ivGatG+vG ++++vLeer+fp+++l+l+as+rsaG+ +  kg e++ve+a  ++++g+di lfsaGg++
  NCBI__GCF_000744815.1:WP_037568868.1   2 KVGIVGATGQVGGVMRRVLEERDFPVEQLRLFASARSAGRTLPWKGSEITVEDAAAADYSGLDIVLFSAGGAT 74 
                                           599********************************************************************** PP

                             TIGR01296  74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146
                                           sk++a k+a++g++viDn+sa+r+d++vPLvv+evn + + +++ kgiianPnC+t+++++vLkpl++ea+lk
  NCBI__GCF_000744815.1:WP_037568868.1  75 SKALAEKVARDGAVVIDNSSAWRMDPQVPLVVAEVNPHAVVDRP-KGIIANPNCTTMAAMPVLKPLHQEAGLK 146
                                           ******************************************99.**************************** PP

                             TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeida....lkakkfakqiafnaiplidklkedG..yt 213
                                            +v  tYqavsG+G +gv+eL+ q++   + +   +++++    + ++ +a++iafn++pl++k+++dG  +t
  NCBI__GCF_000744815.1:WP_037568868.1 147 ALVATTYQAVSGSGLAGVAELEAQIQKGADRAAALTHDGSaidlPAPSVYARPIAFNVLPLAGKIVDDGlnET 219
                                           ************************99887777666655533454999***********************99* PP

                             TIGR01296 214 keelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyp 286
                                           +ee+kl++e+rkil+i++lkvs+tcvrvPvftghs+ v++ fe++++++++ elL +apgv++ + p      
  NCBI__GCF_000744815.1:WP_037568868.1 220 DEEKKLRNESRKILEIPELKVSGTCVRVPVFTGHSLQVNARFERPITPDRAAELLAGAPGVALSEIP------ 286
                                           ***************************************************************9988...... PP

                             TIGR01296 287 tPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337
                                           tPl+a+g+d ++vgrir D + ++glalf++ DnlrkGaalna+qiael+ 
  NCBI__GCF_000744815.1:WP_037568868.1 287 TPLQAAGQDPSYVGRIRVDETVDNGLALFLSNDNLRKGAALNAIQIAELVA 337
                                           ************************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (339 nodes)
Target sequences:                          1  (342 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: 24.48
//
[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