Aligments for a candidate for dapE in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapE in Magnetospirillum magneticum AMB-1

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate WP_011386228.1 AMB_RS19600 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386228.1 AMB_RS19600
           succinyl-diaminopimelate desuccinylase
          Length = 379

 Score =  298 bits (764), Expect = 1e-85
 Identities = 170/381 (44%), Positives = 232/381 (60%), Gaps = 8/381 (2%)

Query: 1   MTETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFG----DTKNIWLRR 56
           M+    + LA+ LI  PSVTP+D     +LA  L ++GFA   +       + +N++ R 
Sbjct: 1   MSFRDPVPLAQALIRCPSVTPEDAGALDVLAGALEELGFACHHIRSATGGPEIRNLYARL 60

Query: 57  GTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERF 116
           GT+AP +CFAGHTDVVP G  + W   PF      GRL+GRG+ADMK +IACFV A  R 
Sbjct: 61  GTEAPNLCFAGHTDVVPPG--KGWTVEPFAAGIDQGRLFGRGSADMKGAIACFVAAVARL 118

Query: 117 VAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIK 176
           + +    +GS++LLIT DEEG A+DGT KV+D L AR E ID CIVGEPT   KLGDM+K
Sbjct: 119 L-EDGAPKGSLSLLITGDEEGPAVDGTVKVLDWLAARGERIDCCIVGEPTNPRKLGDMMK 177

Query: 177 NGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQIS 236
            GRRGSL+  LTV G QGH AYPHLA NP+      L  LT+   DEG  +F  ++  ++
Sbjct: 178 IGRRGSLNCRLTVFGTQGHSAYPHLADNPIPRLLDILRRLTEAPLDEGTPHFQASTLALT 237

Query: 237 NINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFL 296
            ++ G  ATNVIP E    FN RF+   + A L++ +   + + G + +++   SG+ FL
Sbjct: 238 TVDVGNPATNVIPAEARAGFNIRFNDLHSGASLERWIRDTVAQAGGEVEIKVEVSGESFL 297

Query: 297 TQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENV 356
           T  G L+D    A  E  G+  ELST+GGTSD RFIK     ++E G    T+H+ +E+V
Sbjct: 298 TPPGALSDALAEAAFEVTGLRPELSTSGGTSDARFIKNHC-PVVEFGLVGQTMHKSDEHV 356

Query: 357 RLNDIPKLSAVYEGILARLLA 377
            + D+  L+ +Y  +L RL A
Sbjct: 357 SVADMEALTEIYRRVLVRLAA 377


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: 426
Number of extensions: 25
Number of successful extensions: 5
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: 379
Length adjustment: 30
Effective length of query: 351
Effective length of database: 349
Effective search space:   122499
Effective search space used:   122499
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_011386228.1 AMB_RS19600 (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.19309.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-130  419.3   0.0     8e-130  419.0   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386228.1  AMB_RS19600 succinyl-diaminopime


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386228.1  AMB_RS19600 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  419.0   0.0    8e-130    8e-130       4     370 .]       9     375 ..       7     375 .. 0.97

  Alignments for each domain:
  == domain 1  score: 419.0 bits;  conditional E-value: 8e-130
                                 TIGR01246   4 lakeLisrksvtPndagaqeliaerLkklgfeieilefe....dtknlwatrgteepvlvfaGhtDvvP 68 
                                               la+ Li+ +svtP+daga++++a  L++lgf++++++      +++nl+a+ gte+p+l+faGhtDvvP
  lcl|NCBI__GCF_000009985.1:WP_011386228.1   9 LAQALIRCPSVTPEDAGALDVLAGALEELGFACHHIRSAtggpEIRNLYARLGTEAPNLCFAGHTDVVP 77 
                                               7999******************************99864333479************************ PP

                                 TIGR01246  69 aGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegeaidG 137
                                                G  + W+ +pf++ + +G+l+grG+aDmkg++a+fv+a+ r +++ a  kGslsllit Deeg a+dG
  lcl|NCBI__GCF_000009985.1:WP_011386228.1  78 PG--KGWTVEPFAAGIDQGRLFGRGSADMKGAIACFVAAVARLLEDGA-PKGSLSLLITGDEEGPAVDG 143
                                               **..9************************************9998765.69****************** PP

                                 TIGR01246 138 tkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhkavp 206
                                               t+kv+++l +r e id ++vgeP+  +klGD++kiGrrGs++ +l++ G+qGh aYPh+a+nP+++++ 
  lcl|NCBI__GCF_000009985.1:WP_011386228.1 144 TVKVLDWLAARGERIDCCIVGEPTNPRKLGDMMKIGRRGSLNCRLTVFGTQGHSAYPHLADNPIPRLLD 212
                                               ********************************************************************* PP

                                 TIGR01246 207 vlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekildkh 275
                                               +l++l++  lDeG+ +f++s l ++ +++g+ a+nviP+e+++ fn+rf+  +s ++l++ +++ + + 
  lcl|NCBI__GCF_000009985.1:WP_011386228.1 213 ILRRLTEAPLDEGTPHFQASTLALTTVDVGNPATNVIPAEARAGFNIRFNDLHSGASLERWIRDTVAQA 281
                                               ********************************************************************* PP

                                 TIGR01246 276 kldYelewklsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelGlvndti 344
                                               + + e++ ++sge+flt  g l +++aea  ev++ +pelstsGGtsDarfi++  + vve+Glv +t+
  lcl|NCBI__GCF_000009985.1:WP_011386228.1 282 GGEVEIKVEVSGESFLTPPGALSDALAEAAFEVTGLRPELSTSGGTSDARFIKNH-CPVVEFGLVGQTM 349
                                               ******************************************************9.************* PP

                                 TIGR01246 345 hkvneavkiedleklsevyeklleel 370
                                               hk +e+v+++d+e+l+e+y+++l +l
  lcl|NCBI__GCF_000009985.1:WP_011386228.1 350 HKSDEHVSVADMEALTEIYRRVLVRL 375
                                               **********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (379 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: 7.73
//
[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