Alignments for a candidate for lysA in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Escherichia coli BW25113

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate 16919 b2838 diaminopimelate decarboxylase, PLP-binding (NCBI)

Query= SwissProt::E0IWI3
         (420 letters)



>FitnessBrowser__Keio:16919
          Length = 420

 Score =  845 bits (2182), Expect = 0.0
 Identities = 420/420 (100%), Positives = 420/420 (100%)

Query: 1   MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIH 60
           MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIH
Sbjct: 1   MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIH 60

Query: 61  ILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVN 120
           ILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVN
Sbjct: 61  ILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVN 120

Query: 121 AGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQR 180
           AGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQR
Sbjct: 121 AGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQR 180

Query: 181 HHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVD 240
           HHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVD
Sbjct: 181 HHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVD 240

Query: 241 TEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDA 300
           TEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDA
Sbjct: 241 TEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDA 300

Query: 301 GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA 360
           GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA
Sbjct: 301 GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA 360

Query: 361 LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL 420
           LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL
Sbjct: 361 LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL 420


Lambda     K      H
   0.320    0.136    0.405 

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: 792
Number of extensions: 23
Number of successful extensions: 1
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: 420
Length of database: 420
Length adjustment: 32
Effective length of query: 388
Effective length of database: 388
Effective search space:   150544
Effective search space used:   150544
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: 50 (23.9 bits)

Align candidate 16919 b2838 (diaminopimelate decarboxylase, PLP-binding (NCBI))
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# 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/TIGR01048.hmm
# target sequence database:        /tmp/gapView.20868.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.1e-150  487.7   0.0   1.3e-150  487.5   0.0    1.0  1  lcl|FitnessBrowser__Keio:16919  b2838 diaminopimelate decarboxyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16919  b2838 diaminopimelate decarboxylase, PLP-binding (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.5   0.0  1.3e-150  1.3e-150       5     416 ..       6     418 ..       2     419 .. 0.98

  Alignments for each domain:
  == domain 1  score: 487.5 bits;  conditional E-value: 1.3e-150
                       TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGE 83 
                                      ++++++++ +l +l +efg+P++vyd++ +r++++alk+++     +v +A+KA+sn+++lrl++e+G+++d+vs GE
  lcl|FitnessBrowser__Keio:16919   6 FSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFD-----VVRFAQKACSNIHILRLMREQGVKVDSVSLGE 79 
                                     57889999********************************98.....79****************************** PP

                       TIGR01048  84 leralaAgvk....aekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakthe 158
                                     +eralaAg++    +++ivf+++++++++le++ el+i  +n++sv++l++l ++++++    rv+lRvnp++++ +++
  lcl|FitnessBrowser__Keio:16919  80 IERALAAGYNpqthPDDIVFTADVIDQATLERVSELQIP-VNAGSVDMLDQLGQVSPGH----RVWLRVNPGFGHGHSQ 153
                                     *********9899999**********************9.*******************....**************** PP

                       TIGR01048 159 yisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGG 237
                                     +++TG ++sK+Gi+++ +++a+  ++++++l+lvGih+HIGS++++++  + + ++v +++e     g++l+++++GGG
  lcl|FitnessBrowser__Keio:16919 154 KTNTGGENSKHGIWYT-DLPAALDVIQRHHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEF----GQDLQAISAGGG 227
                                     ****************.999*******************************************....9*********** PP

                       TIGR01048 238 lgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndli 315
                                     l+++y++ eea+d+e+y+  ++++ e+ a +lg+ +kl +EpGR+lva++gvl+t+V+svK+++sr+fvlvDag+ndl+
  lcl|FitnessBrowser__Keio:16919 228 LSVPYQQGEEAVDTEHYYGLWNAAREQIArHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLM 306
                                     *****************************9************************************************* PP

                       TIGR01048 316 RpalYeayheiaalkr....leeeetetvdvvGplCEsgDvlakd.......relpeveeGdllavasaGAYgasmssn 383
                                     Rpa+Y++yh+i+al++    le+++t+++ v+GplCEsgDv++++       r+lpev++Gd+l+++++GAYgasmssn
  lcl|FitnessBrowser__Keio:16919 307 RPAMYGSYHHISALAAdgrsLEHAPTVETVVAGPLCESGDVFTQQeggnvetRALPEVKAGDYLVLHDTGAYGASMSSN 385
                                     *************987788899********************************************************* PP

                       TIGR01048 384 Ynsrprpaevlveegkarlirrretledllale 416
                                     Ynsrp + evl+++g+arlirrr+t+e+llale
  lcl|FitnessBrowser__Keio:16919 386 YNSRPLLPEVLFDNGQARLIRRRQTIEELLALE 418
                                     ******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (420 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.01
//
[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