GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Caldicellulosiruptor kronotskyensis 2002

Align Diaminopimelate epimerase; DAP epimerase; PLP-independent amino acid racemase; EC 5.1.1.7 (characterized)
to candidate WP_013429569.1 CALKRO_RS02625 diaminopimelate epimerase

Query= SwissProt::Q81XR2
         (288 letters)



>NCBI__GCF_000166775.1:WP_013429569.1
          Length = 278

 Score =  252 bits (644), Expect = 6e-72
 Identities = 121/278 (43%), Positives = 187/278 (67%), Gaps = 5/278 (1%)

Query: 6   FTKMHGLGNSYIYVNMFEEQIPEEDLALVAEKVSNINTGIGADGMILICPSDVAPVKMRM 65
           F+KMHGLGN +I ++   ++  + D  L+A+++ + + G+GADG++L+  S +A ++MR+
Sbjct: 3   FSKMHGLGNDFIVIDARGKE--DIDYNLLAKRMCHRHIGVGADGLLLVLDSKLADIRMRI 60

Query: 66  FNNDGSEGKSCGNGLRCVAKYAYEHKLVEDTVFTIETLAGIVTAEVTVEE-GKVTLAKID 124
            N+DGSE + CGNG+RC AKY +E  +V+ T F +ETLAGI+  E+ + E G V   K++
Sbjct: 61  INSDGSEAEMCGNGIRCFAKYVFERGIVKATKFKVETLAGIIEPELFINEYGLVDKVKVN 120

Query: 125 MGAPRLTRAEIPMLGEGETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTTL 184
           MG P   R +IPM G+ ++  I  + + + + Y  T++ MG PH ++FVDD+E+  + TL
Sbjct: 121 MGKPSFKRKDIPMQGDPKSDAINTSIVVDGNEYRITSLLMGVPHTILFVDDLEKVDIYTL 180

Query: 185 GPVLETHEMFPERVNVEFIEILNEEEMNFRVWERGSGVTQACGTGACAAVVASILNGKME 244
           GP +E HE+FP + NV F++++++  +  R WERG+G T ACGTG+CA+V+A+ LNG  E
Sbjct: 181 GPKIEKHEIFPRKTNVNFVQVIDKNNIKVRTWERGAGATFACGTGSCASVIAANLNGLTE 240

Query: 245 RGKEITVHLAGGDLMIAWTEEGNVLMKGPAEVICRGVY 282
           R  +  VHL  G L I W E+G V M GPAE +  G Y
Sbjct: 241 R--KANVHLYFGILEIEWREDGIVFMTGPAEEVFVGEY 276


Lambda     K      H
   0.318    0.136    0.398 

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: 237
Number of extensions: 13
Number of successful extensions: 4
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: 288
Length of database: 278
Length adjustment: 26
Effective length of query: 262
Effective length of database: 252
Effective search space:    66024
Effective search space used:    66024
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_013429569.1 CALKRO_RS02625 (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.659850.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-100  320.2   0.1   6.3e-100  320.0   0.1    1.0  1  NCBI__GCF_000166775.1:WP_013429569.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166775.1:WP_013429569.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.0   0.1  6.3e-100  6.3e-100       1     268 [.       1     276 [.       1     278 [] 0.93

  Alignments for each domain:
  == domain 1  score: 320.0 bits;  conditional E-value: 6.3e-100
                             TIGR00652   1 meFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvepsseeadvklrifNsDGSeaemC 73 
                                           m F+kmhGlgNdF+++d + +e +   + l++++c+rh gvgaDg+llv  +s+ ad+++ri NsDGSeaemC
  NCBI__GCF_000166775.1:WP_013429569.1   1 MLFSKMHGLGNDFIVIDARGKEDIDY-NLLAKRMCHRHIGVGADGLLLVL-DSKLADIRMRIINSDGSEAEMC 71 
                                           78*********************999.79*********************.5********************* PP

                             TIGR00652  74 GNgiRcfakfvyekglkekkelsvetlaglikveveeen....kkvkvdmgepkfkkeeipltvekeeekeel 142
                                           GNgiRcfak+v e+g+++ ++++vetlag+i+ e+  ++     kvkv+mg+p+fk+++ip+++++++   + 
  NCBI__GCF_000166775.1:WP_013429569.1  72 GNGIRCFAKYVFERGIVKATKFKVETLAGIIEPELFINEyglvDKVKVNMGKPSFKRKDIPMQGDPKSDAINT 144
                                           ************************************99999*99*******************7655442222 PP

                             TIGR00652 143 lalev.......l.vvdvGnPHlvvfvedvekldleelgklleaheefpegvNvefvevkkedeiklrvyERG 207
                                               v       +  + +G+PH ++fv+d+ek+d+ +lg+++e+he fp ++Nv+fv+v ++++ik+r++ERG
  NCBI__GCF_000166775.1:WP_013429569.1 145 SI--VvdgneyrItSLLMGVPHTILFVDDLEKVDIYTLGPKIEKHEIFPRKTNVNFVQVIDKNNIKVRTWERG 215
                                           11..1123454526999******************************************************** PP

                             TIGR00652 208 ageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedgkvyltGpavlvlegel 268
                                           ag T aCGtG++As+++a+  g+t++k++vhl  g Leie++edg v++tGpa+ v+ ge+
  NCBI__GCF_000166775.1:WP_013429569.1 216 AGATFACGTGSCASVIAANLNGLTERKANVHLYFGILEIEWREDGIVFMTGPAEEVFVGEY 276
                                           *********************************************************9997 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 15.31
//
[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