GapMind for Amino acid biosynthesis

 

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

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_106299112.1 MGEO_RS00490 diaminopimelate epimerase

Query= curated2:Q3IZB6
         (279 letters)



>NCBI__GCF_002115805.1:WP_106299112.1
          Length = 278

 Score =  344 bits (882), Expect = 1e-99
 Identities = 165/268 (61%), Positives = 208/268 (77%), Gaps = 2/268 (0%)

Query: 10  LGFMKMHGAGNDFVVIDSRGRGGALVTAGLARALGDRHRGVGFDQLAEIRDQEG-ADCAL 68
           + FMKMHG GNDFVV+D+R +   ++TA LA+A+GDRHRGVGFDQLA I    G AD  L
Sbjct: 8   IAFMKMHGLGNDFVVLDARVQP-VVMTAALAQAIGDRHRGVGFDQLALIERGAGDADARL 66

Query: 69  DFWNSDGSRSGTCGNATRCVSDYLMRDLGRDEVNLVTARGRLHARRREDGLVAVNMGAPQ 128
            F+NSDGS +G CGNATRC++ +LM + G   V L T RG+L AR   +GL +VNMG PQ
Sbjct: 67  VFYNSDGSTAGACGNATRCIARHLMDESGLTGVTLTTERGQLFARDAGNGLTSVNMGQPQ 126

Query: 129 LLWSEIPLARAMETDSLPLEGTPSAVGMGNPHCIYFVEDAEAVDLAGRGAAVETDPLFPE 188
           L W E+PLA  M+T  LP++G P+A GMGNPHC +FVEDAE+VDL  RGA +E  PL+P+
Sbjct: 127 LRWDEVPLAHEMDTLELPIDGAPTATGMGNPHCTFFVEDAESVDLETRGAEIEDHPLYPQ 186

Query: 189 RTNVEFASLIGPDRLRLRVWERGAGITLACGSGACATAVAAARRGLTGRQVRLEMDGGVL 248
           RTNV+FASLIGPD LR+RVWERG G+TLA GS +CATAVAAARRGLTGR+V +++DGG +
Sbjct: 187 RTNVQFASLIGPDHLRMRVWERGVGVTLASGSSSCATAVAAARRGLTGRRVSIDLDGGRI 246

Query: 249 EVDWRDEGVWLSGPVARVFEGHLSPEMM 276
           E+DWR++GVW++GP A VF G  + E +
Sbjct: 247 EIDWREDGVWMTGPTAHVFSGTFTAEWL 274


Lambda     K      H
   0.321    0.138    0.423 

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: 328
Number of extensions: 13
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: 279
Length of database: 278
Length adjustment: 25
Effective length of query: 254
Effective length of database: 253
Effective search space:    64262
Effective search space used:    64262
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate WP_106299112.1 MGEO_RS00490 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

# 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/TIGR00652.hmm
# target sequence database:        /tmp/gapView.669643.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00652  [M=270]
Accession:   TIGR00652
Description: DapF: diaminopimelate epimerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-75  240.2   0.0    1.5e-75  240.0   0.0    1.0  1  NCBI__GCF_002115805.1:WP_106299112.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_106299112.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.0   0.0   1.5e-75   1.5e-75       1     268 [.       8     269 ..       8     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 240.0 bits;  conditional E-value: 1.5e-75
                             TIGR00652   1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemC 73 
                                           ++F+kmhGlgNdFv++d + + +v + a+l++++ drh gvg+D++ l+e +  +ad++l ++NsDGS a  C
  NCBI__GCF_002115805.1:WP_106299112.1   8 IAFMKMHGLGNDFVVLDARVQPVVMT-AALAQAIGDRHRGVGFDQLALIERGAGDADARLVFYNSDGSTAGAC 79 
                                           57******************999999.9********************************************* PP

                             TIGR00652  74 GNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellale 146
                                           GN+ Rc+a++++++ +   + +++ t++g++ +    ++   +v+mg+p+++ +e+pl +e ++ +  +   +
  NCBI__GCF_002115805.1:WP_106299112.1  80 GNATRCIARHLMDESGL--TGVTLTTERGQLFARDAGNG-LTSVNMGQPQLRWDEVPLAHEMDTLELPID-GA 148
                                           **************999..79**********99999998.9******************97777744443.34 PP

                             TIGR00652 147 vlvvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTlaCGtGav 219
                                             +  +GnPH+ +fved e++dle+ g+++e h+ +p+++Nv+f+   ++d++++rv+ERG+g Tla G+ ++
  NCBI__GCF_002115805.1:WP_106299112.1 149 PTATGMGNPHCTFFVEDAESVDLETRGAEIEDHPLYPQRTNVQFASLIGPDHLRMRVWERGVGVTLASGSSSC 221
                                           469********************************************************************** PP

                             TIGR00652 220 AsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268
                                           A+av+a++ g+t ++v + l+gg++ei+++edg v++tGp  +v++g+ 
  NCBI__GCF_002115805.1:WP_106299112.1 222 ATAVAAARRGLTGRRVSIDLDGGRIEIDWREDG-VWMTGPTAHVFSGTF 269
                                           ********************************8.***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (278 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: 11.50
//
[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