Alignments for a candidate for dapE in Methylovulum miyakonense HT12

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Methylovulum miyakonense HT12

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate WP_019866822.1 METMI_RS0113510 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>NCBI__GCF_000384075.1:WP_019866822.1
          Length = 377

 Score =  462 bits (1189), Expect = e-135
 Identities = 227/373 (60%), Positives = 273/373 (73%)

Query: 4   TQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAPVV 63
           + +LEL K LISRPSVTP D  CQ+LLAE L  +GF AE L F DT+NIWLRRG   P+ 
Sbjct: 2   SDTLELLKTLISRPSVTPQDAGCQELLAECLAPLGFTAERLDFADTQNIWLRRGQDKPLF 61

Query: 64  CFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNH 123
            F GHTDVVP G +  WDSPPFEP  +DG+LYGRGAADMK  IA FVTA  RF+AKHP+H
Sbjct: 62  TFLGHTDVVPPGSLSAWDSPPFEPTIKDGKLYGRGAADMKGGIAAFVTAVGRFLAKHPDH 121

Query: 124 QGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSL 183
           QGSIA+++TSDEEG A  G  KVVDVL+ R E ID+C+VGEP++  ++GD+I+ GRRGSL
Sbjct: 122 QGSIAVMMTSDEEGIATHGVVKVVDVLEQRGEKIDWCLVGEPSSDKRIGDVIRVGRRGSL 181

Query: 184 SGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTG 243
              LTV G QGH+AYP LA NP+HTFAPAL  LT+EVWD+GNE+FPPT  Q+SNINGGTG
Sbjct: 182 CARLTVIGIQGHVAYPELAENPIHTFAPALKALTEEVWDQGNEFFPPTRLQVSNINGGTG 241

Query: 244 ATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGKLT 303
           A N+IPG L+V+FN RF TE     ++QR HAILD  G +Y L W  SGQPFLT +G+L 
Sbjct: 242 AENIIPGHLDVQFNLRFCTELDAQTIQQRTHAILDPFGFKYQLDWRLSGQPFLTASGELV 301

Query: 304 DVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDIPK 363
               AAI    G      T GGTSDGRFI     ++IELGP N +IH+INE++ L D+  
Sbjct: 302 AATHAAIKSVTGYAPLDDTGGGTSDGRFIAPTGAQVIELGPLNESIHKINEHIGLEDLET 361

Query: 364 LSAVYEGILARLL 376
           LSA+YE +L  LL
Sbjct: 362 LSAIYEQVLVNLL 374


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: 474
Number of extensions: 17
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: 381
Length of database: 377
Length adjustment: 30
Effective length of query: 351
Effective length of database: 347
Effective search space:   121797
Effective search space used:   121797
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_019866822.1 METMI_RS0113510 (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.12482.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-167  542.5   0.0   2.7e-167  542.3   0.0    1.0  1  lcl|NCBI__GCF_000384075.1:WP_019866822.1  METMI_RS0113510 succinyl-diamino


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000384075.1:WP_019866822.1  METMI_RS0113510 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.3   0.0  2.7e-167  2.7e-167       2     370 .]       5     373 ..       4     373 .. 1.00

  Alignments for each domain:
  == domain 1  score: 542.3 bits;  conditional E-value: 2.7e-167
                                 TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefedtknlwatrgteepvlvfaGhtDvvPaG 70 
                                               lel+k Lisr+svtP+dag+qel+ae L  lgf++e+l f dt+n+w++rg+++p ++f GhtDvvP G
  lcl|NCBI__GCF_000384075.1:WP_019866822.1   5 LELLKTLISRPSVTPQDAGCQELLAECLAPLGFTAERLDFADTQNIWLRRGQDKPLFTFLGHTDVVPPG 73 
                                               689****************************************************************** PP

                                 TIGR01246  71 elekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidGtk 139
                                               +l++W+s+pfep+++dGklygrGaaDmkg++aafv+a+ rf++k++dh+Gs+++++tsDeeg a +G++
  lcl|NCBI__GCF_000384075.1:WP_019866822.1  74 SLSAWDSPPFEPTIKDGKLYGRGAADMKGGIAAFVTAVGRFLAKHPDHQGSIAVMMTSDEEGIATHGVV 142
                                               ********************************************************************* PP

                                 TIGR01246 140 kvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavpvl 208
                                               kvv++l++r e+id+++vgePss k++GDvi++GrrGs+ ++l++ GiqGhvaYP++aenP+h+++p+l
  lcl|NCBI__GCF_000384075.1:WP_019866822.1 143 KVVDVLEQRGEKIDWCLVGEPSSDKRIGDVIRVGRRGSLCARLTVIGIQGHVAYPELAENPIHTFAPAL 211
                                               ********************************************************************* PP

                                 TIGR01246 209 keliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkhkl 277
                                               k+l+++ +D+Gneffpp++lq++ni++gtga n+iPg+l+v+fnlrf++e+ +++++++ ++ild ++ 
  lcl|NCBI__GCF_000384075.1:WP_019866822.1 212 KALTEEVWDQGNEFFPPTRLQVSNINGGTGAENIIPGHLDVQFNLRFCTELDAQTIQQRTHAILDPFGF 280
                                               ********************************************************************* PP

                                 TIGR01246 278 dYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndtihk 346
                                               +Y+l+w+lsg+pflt +g+l+++ ++ai+ v++ +p  +t+GGtsD+rfia  ga+v+elG++n++ihk
  lcl|NCBI__GCF_000384075.1:WP_019866822.1 281 KYQLDWRLSGQPFLTASGELVAATHAAIKSVTGYAPLDDTGGGTSDGRFIAPTGAQVIELGPLNESIHK 349
                                               ********************************************************************* PP

                                 TIGR01246 347 vneavkiedleklsevyeklleel 370
                                               +ne++ +edle ls++ye++l +l
  lcl|NCBI__GCF_000384075.1:WP_019866822.1 350 INEHIGLEDLETLSAIYEQVLVNL 373
                                               *********************987 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.98
//
[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