Alignments for a candidate for dapF in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapF in Sinorhizobium meliloti 1021

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate SMc03856 SMc03856 diaminopimelate epimerase

Query= curated2:B5ZTH4
         (301 letters)



>FitnessBrowser__Smeli:SMc03856
          Length = 306

 Score =  467 bits (1201), Expect = e-136
 Identities = 229/303 (75%), Positives = 259/303 (85%), Gaps = 6/303 (1%)

Query: 1   MSATVEFARMNGLGNKILVVDMRGRPDKVTPAAAVALNADPQTEFDQIMAIHDPKADGTD 60
           M   V+FARMNGLGNKILVVDMRGR D+VTP AA+ALNADP TEFDQIMAIHDPK+ GTD
Sbjct: 6   MGDQVQFARMNGLGNKILVVDMRGRKDRVTPQAAIALNADPATEFDQIMAIHDPKSAGTD 65

Query: 61  AFIDILNSDGSKAQACGNGTRCVVQALAAETGRKAFTFQTVAGILNAVEHEDGTISVDMG 120
           A+IDI+NSDGS AQACGNGTRCVVQALAAETGRKAF F TVAG+L A EH++GTISVDMG
Sbjct: 66  AWIDIVNSDGSMAQACGNGTRCVVQALAAETGRKAFLFHTVAGLLEAKEHDNGTISVDMG 125

Query: 121 RPVFDWNRIPLAEEFHDTSRIELQIGPIDNPVLHSPSAMSMGNPHAIFWVDRDVMSYDLA 180
           +P F W++IPLAEEFHDT RIELQIGPID PVLHSPS  SMGNPHAIFWV+ DV SY+L 
Sbjct: 126 KPRFGWDQIPLAEEFHDTRRIELQIGPIDAPVLHSPSVASMGNPHAIFWVENDVWSYELD 185

Query: 181 RFGPLLENHPMFPERANITLAQVTSPTSMTTRTWERGAGLTLACGSAACSAAVSAARTGR 240
           RFGPLLENHP+FPERANI++A++ S   M  RTWERGAGLTLACGSAAC+AAV+ ARTGR
Sbjct: 186 RFGPLLENHPIFPERANISIARIRSRQEMDLRTWERGAGLTLACGSAACAAAVNGARTGR 245

Query: 241 TGRKVTINVASAKPPATLSIEWRERDDHVIMTGPAEWEWSGSLDPSTGLWSRDGTQ--EA 298
           T R VT+NV    P   L IEWRERDDHVIMTGPAEWEWSG++DP TG+++R+  +  + 
Sbjct: 246 TERMVTVNV----PGGPLKIEWRERDDHVIMTGPAEWEWSGTVDPVTGIFARNEPESGDN 301

Query: 299 GAR 301
           GAR
Sbjct: 302 GAR 304


Lambda     K      H
   0.317    0.131    0.400 

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: 450
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: 301
Length of database: 306
Length adjustment: 27
Effective length of query: 274
Effective length of database: 279
Effective search space:    76446
Effective search space used:    76446
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 SMc03856 SMc03856 (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.19636.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    6.7e-66  208.4   0.0    7.9e-66  208.2   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc03856  SMc03856 diaminopimelate epimera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03856  SMc03856 diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2   0.0   7.9e-66   7.9e-66       2     265 ..      11     281 ..      10     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 7.9e-66
                           TIGR00652   2 eFlkmhGlgNdFvlvdevdeelvkeeaelvrkvcdrhtgvgaDgvllvep.sseeadvklrifNsDGSeaemCGN 75 
                                         +F++m+GlgN+ ++vd + ++   + ++ + ++ +    + +D+++ ++  +s  +d+ ++i NsDGS a+ CGN
  lcl|FitnessBrowser__Smeli:SMc03856  11 QFARMNGLGNKILVVDMRGRKDRVT-PQAAIAL-NADPATEFDQIMAIHDpKSAGTDAWIDIVNSDGSMAQACGN 83 
                                         8****************99888887.5665555.5677899******9977999********************* PP

                           TIGR00652  76 giRcfakfvyekglkekkelsvetlaglikveveeenkkvkvdmgepkfkkeeipltvekeeekeellalev... 147
                                         g Rc+++ ++++++   k + ++t agl++++ ++++ +++vdmg+p+f  ++ipl +e + +++  l+  +   
  lcl|FitnessBrowser__Smeli:SMc03856  84 GTRCVVQALAAETGR--KAFLFHTVAGLLEAKEHDNG-TISVDMGKPRFGWDQIPLAEEFHDTRRIELQ--Igpi 153
                                         ***********9999..8**************99999.*******************766655433333..2234 PP

                           TIGR00652 148 ....l....vvdvGnPHlvvfved.vekldleelgklleaheefpegvNvefvevkkedeiklrvyERGageTla 213
                                             l    v ++GnPH+++ ve+ v + +l++ g+lle+h+ fpe+ N+ ++++ +++e+ lr++ERGag Tla
  lcl|FitnessBrowser__Smeli:SMc03856 154 dapvLhspsVASMGNPHAIFWVENdVWSYELDRFGPLLENHPIFPERANISIARIRSRQEMDLRTWERGAGLTLA 228
                                         667625677***********998769************************************************* PP

                           TIGR00652 214 CGtGavAsavvalklgktkkkvtvhleggeLeievkedg.kvyltGpavlvle 265
                                         CG+ a+A+av ++++g+t++ vtv+++gg L+ie++e++ +v++tGpa+   +
  lcl|FitnessBrowser__Smeli:SMc03856 229 CGSAACAAAVNGARTGRTERMVTVNVPGGPLKIEWRERDdHVIMTGPAEWEWS 281
                                         *************************************999*******987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (306 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.97
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis