GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Sinorhizobium fredii NGR234

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate WP_193377911.1 NGR_RS27260 diaminopimelate epimerase

Query= curated2:Q8YJF0
         (303 letters)



>NCBI__GCF_000018545.1:WP_193377911.1
          Length = 301

 Score =  454 bits (1167), Expect = e-132
 Identities = 220/297 (74%), Positives = 244/297 (82%), Gaps = 1/297 (0%)

Query: 1   MATKAAFARMNGLGNQIIVADMRGRADSITSAAAIRLASDSETAFDQIMAIHDPRTPGTD 60
           MA    FARMNGLGN+I+V DMRGR D +T  AAI L +D  T FDQIMAIHDPR PGTD
Sbjct: 1   MADHVQFARMNGLGNKILVVDMRGRKDRVTPGAAIALNADPATEFDQIMAIHDPRAPGTD 60

Query: 61  YYIAIINCDGTQAQACGNGTRCVVQALAAETGRHAFTFETRAGILTATEHDDGLISVDMG 120
            +I I+N DG+ AQACGNGTRCVVQALAAETG+ AF F T AG+L A EHDDGLISVDMG
Sbjct: 61  AWIDIVNSDGSMAQACGNGTRCVVQALAAETGKKAFLFHTVAGLLEAREHDDGLISVDMG 120

Query: 121 TPRFDWQDIPLAQAVADTRKIELQVDPADAPVLHSPSIASMGNPHAVFWVDKDVWSYELD 180
           +PRF W +IPLA+   DTR+IELQ+ P D PVLHSPS+ASMGNPHA+FWV+ DVWSYELD
Sbjct: 121 SPRFGWNEIPLAEEFHDTRRIELQIGPIDDPVLHSPSVASMGNPHAIFWVENDVWSYELD 180

Query: 181 KFGPLLENHPIFPERANISIAHVTSSDTIDLRTWERGAGLTRACGSAACAAAVSAARTGR 240
           +FGPLLENHPIFPERANISIAHV S   +DLRTWERGAGLT ACGSAACAAAVS ARTGR
Sbjct: 181 RFGPLLENHPIFPERANISIAHVRSRQEMDLRTWERGAGLTLACGSAACAAAVSGARTGR 240

Query: 241 TGRKVTVNVPGGPLLIEWRD-DDHVMMTGPAEWEFSGTFDPATGEWSRDTQGLQGSG 296
           T R VTVNVPGGPL IEWR+ DDHV+MTGPAEWE++GT DPATG + RD      SG
Sbjct: 241 TDRIVTVNVPGGPLKIEWRESDDHVIMTGPAEWEWTGTVDPATGAFERDAAATSESG 297


Lambda     K      H
   0.318    0.132    0.408 

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: 425
Number of extensions: 14
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: 303
Length of database: 301
Length adjustment: 27
Effective length of query: 276
Effective length of database: 274
Effective search space:    75624
Effective search space used:    75624
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: 48 (23.1 bits)

Align candidate WP_193377911.1 NGR_RS27260 (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.1745118.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.9e-64  203.0   0.0    3.5e-64  202.8   0.0    1.0  1  NCBI__GCF_000018545.1:WP_193377911.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:WP_193377911.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.8   0.0   3.5e-64   3.5e-64       2     263 ..       6     274 ..       5     280 .. 0.90

  Alignments for each domain:
  == domain 1  score: 202.8 bits;  conditional E-value: 3.5e-64
                             TIGR00652   2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemC 73 
                                           +F++m+GlgN+ ++vd + ++   + +  + ++ +    + +D+++ ++    + +d+ ++i NsDGS a+ C
  NCBI__GCF_000018545.1:WP_193377911.1   6 QFARMNGLGNKILVVDMRGRKDRVT-PGAAIAL-NADPATEFDQIMAIHDpRAPGTDAWIDIVNSDGSMAQAC 76 
                                           8****************99888888.5555555.5667889******9976899******************* PP

                             TIGR00652  74 GNgiRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellale 146
                                           GNg Rc+++ ++++++k  k + ++t agl+++  ++++  ++vdmg+p+f  +eipl +e + +++  l+  
  NCBI__GCF_000018545.1:WP_193377911.1  77 GNGTRCVVQALAAETGK--KAFLFHTVAGLLEAREHDDG-LISVDMGSPRFGWNEIPLAEEFHDTRRIELQ-- 144
                                           ***************99..8**************99999.*******************876666443333.. PP

                             TIGR00652 147 v.......l....vvdvGnPHlvvfved.vekldleelgklleaheefpegvNvefvevkkedeiklrvyERG 207
                                           +       l    v ++GnPH+++ ve+ v + +l++ g+lle+h+ fpe+ N+ +++v +++e+ lr++ERG
  NCBI__GCF_000018545.1:WP_193377911.1 145 IgpiddpvLhspsVASMGNPHAIFWVENdVWSYELDRFGPLLENHPIFPERANISIAHVRSRQEMDLRTWERG 217
                                           2234777625677***********998769******************************************* PP

                             TIGR00652 208 ageTlaCGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlv 263
                                           ag TlaCG+ a+A+av ++++g+t++ vtv+++gg L+ie++e++ +v++tGpa+  
  NCBI__GCF_000018545.1:WP_193377911.1 218 AGLTLACGSAACAAAVSGARTGRTDRIVTVNVPGGPLKIEWRESDdHVIMTGPAEWE 274
                                           ******************************************9998*******9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (301 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: 14.64
//
[ok]

This GapMind analysis is from Jul 25 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