GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Enterococcus termitis LMG 8895

Align dihydrodipicolinate reductase subunit (EC 1.17.1.8) (characterized)
to candidate WP_069665198.1 BCR25_RS19050 4-hydroxy-tetrahydrodipicolinate reductase

Query= metacyc::MONOMER-6568
         (267 letters)



>NCBI__GCF_001730305.1:WP_069665198.1
          Length = 262

 Score =  285 bits (728), Expect = 9e-82
 Identities = 143/262 (54%), Positives = 197/262 (75%), Gaps = 2/262 (0%)

Query: 6   IKLVIAGPRGRMGQEAVKLAERTPHFDLVGAIDHTYDQQKLSDVMPVES-DAFIYTDIHA 64
           IK+++AG +G+MG  A K+      F+LVG +D   ++  L ++    + D  I+     
Sbjct: 2   IKILVAGFKGKMGATATKMVIDHEGFELVGVLDPFEEKDNLQELPEYATLDVPIFKTKEE 61

Query: 65  CFTETQPDVLIDLTTPEIGKVHTKIALEHGVRPVVGTTGFSEADLKELTSLTEEKGIGAI 124
             +  QPDV ID T P++   +T+ A+EH + PVVGTTG +E  L+ELT+ +EE  +G +
Sbjct: 62  VIS-VQPDVWIDFTIPKVAYENTRFAIEHHISPVVGTTGLTEEQLEELTARSEELQVGGL 120

Query: 125 IAPNFALGAILMMKFSKMAANYFEDVEIIELHHDQKLDAPSGTALKTAEMISEVRKEKQQ 184
           IAPNFA+GA+LMM+F++ AA YF DVEIIELHHD KLDAPSGTA+KTAEM+SEVRK+K Q
Sbjct: 121 IAPNFAVGAVLMMQFAQKAAEYFPDVEIIELHHDNKLDAPSGTAIKTAEMMSEVRKKKTQ 180

Query: 185 GHPDEKEILPGARGAEQNGIRLHSVRLPGLIAHQEVMFGMDGQTLQIRHDSYNRASFMSG 244
           GHP+EKE+L GARGA+ +G+++HSVRLPGLIAHQ+V FG  G+ L IRHDSY+R+SFM+G
Sbjct: 181 GHPEEKELLAGARGADFDGMKIHSVRLPGLIAHQQVQFGGIGEGLTIRHDSYDRSSFMTG 240

Query: 245 VKLSVEQVMKIDQLVYGLENII 266
           V L  E+V++++ LVYGLEN++
Sbjct: 241 VALGCEKVVQLNTLVYGLENLL 262


Lambda     K      H
   0.317    0.135    0.379 

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: 247
Number of extensions: 7
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: 267
Length of database: 262
Length adjustment: 25
Effective length of query: 242
Effective length of database: 237
Effective search space:    57354
Effective search space used:    57354
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_069665198.1 BCR25_RS19050 (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.3404841.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    8.5e-83  264.0   0.2    9.5e-83  263.8   0.2    1.0  1  NCBI__GCF_001730305.1:WP_069665198.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001730305.1:WP_069665198.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.8   0.2   9.5e-83   9.5e-83       1     269 [.       1     262 []       1     262 [] 0.96

  Alignments for each domain:
  == domain 1  score: 263.8 bits;  conditional E-value: 9.5e-83
                             TIGR00036   1 likvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekka 73 
                                           +ik+ vaG +G+mG  + k v ++e++elv++l+ + ++    ++ el + + ++vp+ +  e v      ++
  NCBI__GCF_001730305.1:WP_069665198.1   1 MIKILVAGFKGKMGATATKMVIDHEGFELVGVLD-PFEE--KDNLQELPEYATLDVPIFKTKEEV---ISVQP 67 
                                           69********************************.3333..34678***********99888865...7899* PP

                             TIGR00036  74 dvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaa 146
                                           dv iDft+p+ ++en+++a+e+ + +VvGTTG++ee+l+el++ +e+ +v+ +iapNfa+G++l++++++kaa
  NCBI__GCF_001730305.1:WP_069665198.1  68 DVWIDFTIPKVAYENTRFAIEHHISPVVGTTGLTEEQLEELTARSEELQVGGLIAPNFAVGAVLMMQFAQKAA 140
                                           ************************************************************************* PP

                             TIGR00036 147 kvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiG..iaavRggdv 217
                                           +++ dv  EiiElHH++K DaPSGTA+k+ae+++++r+ ++ + + ee+e l+G+r+++  G  i++vR++++
  NCBI__GCF_001730305.1:WP_069665198.1 141 EYFPDV--EIIELHHDNKLDAPSGTAIKTAEMMSEVRK-KKTQGHPEEKELLAGARGADFDGmkIHSVRLPGL 210
                                           ****99..******************************.59999******************99********* PP

                             TIGR00036 218 vgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvl 269
                                           +++++v F+++Ge l+i+H++++R++f++Gv ++ +++++++++vy+le++l
  NCBI__GCF_001730305.1:WP_069665198.1 211 IAHQQVQFGGIGEGLTIRHDSYDRSSFMTGVALGCEKVVQLNTLVYGLENLL 262
                                           *************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (262 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: 15.37
//
[ok]

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

Links

Downloads

Related tools

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