Alignments for a candidate for dapE in Thiomicrorhabdus chilensis DSM 12352

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Thiomicrorhabdus chilensis DSM 12352

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_028486542.1 B076_RS0106155 succinyl-diaminopimelate desuccinylase

Query= BRENDA::Q9KQ52
         (377 letters)



>NCBI__GCF_000483485.1:WP_028486542.1
          Length = 377

 Score =  459 bits (1182), Expect = e-134
 Identities = 224/374 (59%), Positives = 277/374 (74%), Gaps = 1/374 (0%)

Query: 4   SPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLF 63
           S  +ALA++LI   SVTP D GCQ+L+ + L+ LGF IE+M F + +N WAR+G Q P  
Sbjct: 2   SETIALAQQLIQIDSVTPDDKGCQNLIADYLRPLGFNIEAMPFGEVSNLWARKGDQGPFI 61

Query: 64  VFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDH 123
           VFAGHTDVVP GP S W  PPF   +    ++GRG ADMK S+AC +VA +RFI + P H
Sbjct: 62  VFAGHTDVVPTGPESAWSHPPFSAHIEGDMMYGRGTADMKSSIACFMVACKRFIGDFPQH 121

Query: 124 QGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGSI 183
            GSIG+LITSDEEGP I+GTV+V+ETL ARNE  D C+VGEPSS+  +GD +KNGRRGS+
Sbjct: 122 AGSIGYLITSDEEGPAIDGTVKVIETLEARNEKFDYCLVGEPSSSKKLGDSIKNGRRGSL 181

Query: 184 TGDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAGTG 243
           +G L +KG QGH+AYP LA NP+H   PAL +L   QWD GN YFPPTSFQI N+ AGTG
Sbjct: 182 SGHLTIKGIQGHIAYPELAENPIHTLAPALEQLVHLQWDHGNEYFPPTSFQISNINAGTG 241

Query: 244 ASNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDT-GEL 302
           A+NVIPG  +V FNFRFSTE T E +K  VH+VLD H L+YD+ W+LSG PF+T   GEL
Sbjct: 242 ATNVIPGSVEVLFNFRFSTEHTPETLKEGVHAVLDHHNLNYDLDWSLSGLPFITPAQGEL 301

Query: 303 LAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLE 362
           + AV  A + V    P L T GGTSDGRFIA  GAQV+ELGP+NATIH+++E V I+DLE
Sbjct: 302 IQAVTQATKTVMGYEPELSTGGGTSDGRFIAPTGAQVIELGPLNATIHQIDERVSISDLE 361

Query: 363 KLTDMYQKTLNHLL 376
            LT++Y +TL +LL
Sbjct: 362 HLTEIYYQTLVNLL 375


Lambda     K      H
   0.318    0.135    0.403 

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: 494
Number of extensions: 15
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: 377
Length of database: 377
Length adjustment: 30
Effective length of query: 347
Effective length of database: 347
Effective search space:   120409
Effective search space used:   120409
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_028486542.1 B076_RS0106155 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

# 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/TIGR01246.hmm
# target sequence database:        /tmp/gapView.29602.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01246  [M=370]
Accession:   TIGR01246
Description: dapE_proteo: succinyl-diaminopimelate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.5e-171  553.7   0.0   1.1e-170  553.5   0.0    1.0  1  lcl|NCBI__GCF_000483485.1:WP_028486542.1  B076_RS0106155 succinyl-diaminop


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000483485.1:WP_028486542.1  B076_RS0106155 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.5   0.0  1.1e-170  1.1e-170       3     370 .]       6     374 ..       4     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 553.5 bits;  conditional E-value: 1.1e-170
                                 TIGR01246   3 elakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaGe 71 
                                               +la++Li++ svtP+d+g+q+lia+ L+ lgf+ie + f+++ nlwa++g + p +vfaGhtDvvP+G+
  lcl|NCBI__GCF_000483485.1:WP_028486542.1   6 ALAQQLIQIDSVTPDDKGCQNLIADYLRPLGFNIEAMPFGEVSNLWARKGDQGPFIVFAGHTDVVPTGP 74 
                                               799****************************************************************** PP

                                 TIGR01246  72 lekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtkk 140
                                               +++Ws +pf+++++  ++ygrG+aDmk+s+a+f+va++rf+ ++++h Gs++ litsDeeg aidGt+k
  lcl|NCBI__GCF_000483485.1:WP_028486542.1  75 ESAWSHPPFSAHIEGDMMYGRGTADMKSSIACFMVACKRFIGDFPQHAGSIGYLITSDEEGPAIDGTVK 143
                                               ********************************************************************* PP

                                 TIGR01246 141 vvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvlk 209
                                               v+etl++r+e+ dy++vgePss+kklGD+ik+GrrGs++g+l+ikGiqGh+aYP++aenP+h+++p+l+
  lcl|NCBI__GCF_000483485.1:WP_028486542.1 144 VIETLEARNEKFDYCLVGEPSSSKKLGDSIKNGRRGSLSGHLTIKGIQGHIAYPELAENPIHTLAPALE 212
                                               ********************************************************************* PP

                                 TIGR01246 210 eliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkld 278
                                               +l++ ++D+Gne+fpp+s+qi+ni+agtga+nviPg+++v fn+rfs+e++ e+lk+ v+++ld+h+l+
  lcl|NCBI__GCF_000483485.1:WP_028486542.1 213 QLVHLQWDHGNEYFPPTSFQISNINAGTGATNVIPGSVEVLFNFRFSTEHTPETLKEGVHAVLDHHNLN 281
                                               ********************************************************************* PP

                                 TIGR01246 279 Yelewklsgepfltk.egklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihk 346
                                               Y+l+w+lsg pf+t  +g+li++v++a + v++ +pelst+GGtsD+rfia  ga+v+elG++n+tih+
  lcl|NCBI__GCF_000483485.1:WP_028486542.1 282 YDLDWSLSGLPFITPaQGELIQAVTQATKTVMGYEPELSTGGGTSDGRFIAPTGAQVIELGPLNATIHQ 350
                                               **************999**************************************************** PP

                                 TIGR01246 347 vneavkiedleklsevyeklleel 370
                                               ++e+v+i+dle+l+e+y+++l +l
  lcl|NCBI__GCF_000483485.1:WP_028486542.1 351 IDERVSISDLEHLTEIYYQTLVNL 374
                                               ********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (377 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.56
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
the source code
instructions for running GapMind on your computer
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