GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Marivita geojedonensis DPG-138

Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_085634936.1 MGEO_RS01580 4-hydroxy-tetrahydrodipicolinate reductase

Query= BRENDA::Q2YJN7
         (268 letters)



>NCBI__GCF_002115805.1:WP_085634936.1
          Length = 272

 Score =  306 bits (785), Expect = 2e-88
 Identities = 157/267 (58%), Positives = 193/267 (72%), Gaps = 1/267 (0%)

Query: 1   MGLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDD 60
           +G+VV G  GRMGQ L+  I       L GA+ER+G  ++GKD G   G    GV + DD
Sbjct: 5   IGVVVTGVSGRMGQMLVSEIAKHPRMHLAGAVERAGHDWVGKDVGTAMGGAANGVIVADD 64

Query: 61  PLPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVK 120
           PL  FA+A  V+DFT+PAA+V FA LAAQAR VHVIGTTG S ED  +I+ AARHA +V+
Sbjct: 65  PLDCFARAQAVIDFTAPAATVAFAELAAQARAVHVIGTTGLSDEDLTRIKTAARHAVVVR 124

Query: 121 SGNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDI 180
           +GNMSLGVNLL+VL +K A AL   D+DIE++E HH  KVDAPSGTAL+LGEAAA+GR +
Sbjct: 125 AGNMSLGVNLLTVLTRKVAAALDA-DYDIEVIEYHHNKKVDAPSGTALMLGEAAAQGRGV 183

Query: 181 ALADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFA 240
            L + S R RDG TG R+ G IGF+ +RGG +IGDH V+ A  GER+ L H A DR++FA
Sbjct: 184 ELREVSDRGRDGITGARKRGDIGFSAIRGGDIIGDHDVLFAAEGERITLRHVASDRALFA 243

Query: 241 RGAIKAALWAHGKKPGLYSMLDVLGLN 267
           RGA+KAALW   K PG Y MLDVLGL+
Sbjct: 244 RGALKAALWGQDKAPGEYDMLDVLGLS 270


Lambda     K      H
   0.318    0.136    0.387 

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: 264
Number of extensions: 10
Number of successful extensions: 2
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: 268
Length of database: 272
Length adjustment: 25
Effective length of query: 243
Effective length of database: 247
Effective search space:    60021
Effective search space used:    60021
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: 47 (22.7 bits)

Align candidate WP_085634936.1 MGEO_RS01580 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

# 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/TIGR00036.hmm
# target sequence database:        /tmp/gapView.3816319.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00036  [M=270]
Accession:   TIGR00036
Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.2e-81  258.4   4.9    4.8e-81  258.2   4.9    1.0  1  NCBI__GCF_002115805.1:WP_085634936.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085634936.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  258.2   4.9   4.8e-81   4.8e-81       2     270 .]       5     268 ..       4     268 .. 0.96

  Alignments for each domain:
  == domain 1  score: 258.2 bits;  conditional E-value: 4.8e-81
                             TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkad 74 
                                           i v+v+G +GrmG+ ++ ++++++ ++l++a+er g++ +gkD+G  +g +  gv v d   ++   +  +a+
  NCBI__GCF_002115805.1:WP_085634936.1   5 IGVVVTGVSGRMGQMLVSEIAKHPRMHLAGAVERAGHDWVGKDVGTAMGGAANGVIVAD-DPLD---CFARAQ 73 
                                           679****************************************************5555.5556...678889 PP

                             TIGR00036  75 vliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaak 147
                                            +iDft p a++  +++a+++    V+GTTG+s+edl ++k +a +  + +v a N+++Gvnll+ l++k+a 
  NCBI__GCF_002115805.1:WP_085634936.1  74 AVIDFTAPAATVAFAELAAQARAVHVIGTTGLSDEDLTRIKTAARH--AVVVRAGNMSLGVNLLTVLTRKVAA 144
                                           99*******************************************9..899******************9999 PP

                             TIGR00036 148 vle.dvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvg 219
                                            l+ d+DiE+iE HH++K+DaPSGTAl l+e+ a+ rg +l+e+   +r+g+tG+rk+ +iG++a+Rggd++g
  NCBI__GCF_002115805.1:WP_085634936.1 145 ALDaDYDIEVIEYHHNKKVDAPSGTALMLGEAAAQGRGVELREVSDRGRDGITGARKRGDIGFSAIRGGDIIG 217
                                           996599******************************************************************* PP

                             TIGR00036 220 ehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                           +h vlFa +Ger++++H as+Ra fa+G+++a+ w +dk+ + yd+ dvl+
  NCBI__GCF_002115805.1:WP_085634936.1 218 DHDVLFAAEGERITLRHVASDRALFARGALKAALWGQDKAPGEYDMLDVLG 268
                                           *************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (272 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.62
//
[ok]

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