Alignments for a candidate for dapE in Alicycliphilus denitrificans K601

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Alicycliphilus denitrificans K601

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate WP_013519098.1 ALIDE2_RS12280 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>NCBI__GCF_000204645.1:WP_013519098.1
          Length = 392

 Score =  452 bits (1163), Expect = e-132
 Identities = 227/384 (59%), Positives = 275/384 (71%), Gaps = 12/384 (3%)

Query: 6   SLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTK----NIWLRRGTKAP 61
           +L L ++LI+RPSVTP+D  C  LLAERL  +GFA E L  G +     N+W +R     
Sbjct: 5   TLLLTEQLIARPSVTPEDAGCLDLLAERLAPLGFACERLDSGPSSFRVCNLWAKRAATPT 64

Query: 62  --------VVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTAC 113
                    V FAGHTDVVPTGPVE+W S PF P +RDGRLYGRGA+DMKTSIA FV A 
Sbjct: 65  SQSQAAIKTVVFAGHTDVVPTGPVEQWSSAPFTPTQRDGRLYGRGASDMKTSIAAFVVAV 124

Query: 114 ERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGD 173
           E F+A  P    +IA L+TSDEEG ++DGT  VV+ L+AR E +D+CIVGEPT+V   GD
Sbjct: 125 EEFLAATPAPAIAIAFLLTSDEEGPSVDGTKVVVEQLRARGERLDWCIVGEPTSVQSTGD 184

Query: 174 MIKNGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSF 233
           MIKNGRRG+LSG LTV+G QGHIAYPHLA NP+H   PAL EL   VWD GN++FPPTS+
Sbjct: 185 MIKNGRRGTLSGRLTVRGVQGHIAYPHLARNPIHQAVPALAELAATVWDRGNDFFPPTSW 244

Query: 234 QISNINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQ 293
           Q+SNI+GGTGATNVIPGE+ + FNFRF TEST   LK+RVHA+LD HG++YDL W+  GQ
Sbjct: 245 QMSNIHGGTGATNVIPGEVAIDFNFRFCTESTAESLKERVHAVLDHHGLEYDLAWTLGGQ 304

Query: 294 PFLTQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQIN 353
           PFLT  G+L    + AI    G+  ELSTTGGTSDGRFI  I  +++ELGP N +IH+I+
Sbjct: 305 PFLTTPGELVGAVQQAIHAETGLTTELSTTGGTSDGRFIAQICPQVVELGPPNDSIHKID 364

Query: 354 ENVRLNDIPKLSAVYEGILARLLA 377
           EN+RL DI  L  +Y   L  L A
Sbjct: 365 ENIRLTDIEPLKNIYRRTLENLNA 388


Lambda     K      H
   0.317    0.135    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: 495
Number of extensions: 16
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: 381
Length of database: 392
Length adjustment: 30
Effective length of query: 351
Effective length of database: 362
Effective search space:   127062
Effective search space used:   127062
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_013519098.1 ALIDE2_RS12280 (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.14864.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-155  503.2   0.0   2.5e-155  503.0   0.0    1.0  1  lcl|NCBI__GCF_000204645.1:WP_013519098.1  ALIDE2_RS12280 succinyl-diaminop


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013519098.1  ALIDE2_RS12280 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  503.0   0.0  2.5e-155  2.5e-155       4     370 .]       8     386 ..       5     386 .. 0.97

  Alignments for each domain:
  == domain 1  score: 503.0 bits;  conditional E-value: 2.5e-155
                                 TIGR01246   4 lakeLisrksvtPndagaqeliaerLkklgfeieilefe....dtknlwatrgt........eepvlvf 60 
                                               l+++Li r+svtP+dag+++l+aerL  lgf++e+l  +     + nlwa+r            +++vf
  lcl|NCBI__GCF_000204645.1:WP_013519098.1   8 LTEQLIARPSVTPEDAGCLDLLAERLAPLGFACERLDSGpssfRVCNLWAKRAAtptsqsqaAIKTVVF 76 
                                               7889********************************9983322467*****9988988876656799** PP

                                 TIGR01246  61 aGhtDvvPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsD 129
                                               aGhtDvvP+G++e+Wss pf+p++rdG+lygrGa Dmk+s+aafvva+e+f+++ +     +++l+tsD
  lcl|NCBI__GCF_000204645.1:WP_013519098.1  77 AGHTDVVPTGPVEQWSSAPFTPTQRDGRLYGRGASDMKTSIAAFVVAVEEFLAATPAPAIAIAFLLTSD 145
                                               ********************************************************************* PP

                                 TIGR01246 130 eegeaidGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkae 198
                                               eeg ++dGtk vve l++r e +d+++vgeP+sv++ GD+ik+GrrG ++g+l+++G+qGh+aYPh+a+
  lcl|NCBI__GCF_000204645.1:WP_013519098.1 146 EEGPSVDGTKVVVEQLRARGERLDWCIVGEPTSVQSTGDMIKNGRRGTLSGRLTVRGVQGHIAYPHLAR 214
                                               ********************************************************************* PP

                                 TIGR01246 199 nPvhkavpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelksk 267
                                               nP+h+avp+l+el+a+ +D Gn+ffpp+s q++ni++gtga+nviPge+++ fn+rf++e+++e+lk++
  lcl|NCBI__GCF_000204645.1:WP_013519098.1 215 NPIHQAVPALAELAATVWDRGNDFFPPTSWQMSNIHGGTGATNVIPGEVAIDFNFRFCTESTAESLKER 283
                                               ********************************************************************* PP

                                 TIGR01246 268 vekildkhkldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevve 336
                                               v+++ld+h+l+Y+l w+l g+pflt  g+l+ +v++ai+  ++ ++elst+GGtsD+rfia++  +vve
  lcl|NCBI__GCF_000204645.1:WP_013519098.1 284 VHAVLDHHGLEYDLAWTLGGQPFLTTPGELVGAVQQAIHAETGLTTELSTTGGTSDGRFIAQICPQVVE 352
                                               ********************************************************************* PP

                                 TIGR01246 337 lGlvndtihkvneavkiedleklsevyeklleel 370
                                               lG+ nd+ihk++e++++ d+e l+++y+++le+l
  lcl|NCBI__GCF_000204645.1:WP_013519098.1 353 LGPPNDSIHKIDENIRLTDIEPLKNIYRRTLENL 386
                                               *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (392 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: 11.65
//
[ok]

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

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