Alignments for a candidate for dapE in Beijerinckia mobilis UQM 1969

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapE in Beijerinckia mobilis UQM 1969

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate WP_034991565.1 DL88_RS03205 succinyl-diaminopimelate desuccinylase

Query= BRENDA::P44514
         (377 letters)



>NCBI__GCF_000745425.1:WP_034991565.1
          Length = 388

 Score =  290 bits (742), Expect = 5e-83
 Identities = 161/385 (41%), Positives = 237/385 (61%), Gaps = 11/385 (2%)

Query: 1   MKEKVVSLAQDLIRRPSISPNDEGCQQIIAERLEKLGFQIEWMPFNDTL-----NLWAKH 55
           M++  + LA+ LI  PS++P D G   I+  RL++ GF+   + F D       NL+A+ 
Sbjct: 4   MQDNALDLARALIACPSVTPQDGGALGILENRLKQAGFRTHRLTFQDEGTPDIDNLYARF 63

Query: 56  GTSEPVIAFAGHTDVVPTGDENQWSSPPFSAEIIDGMLYGRGAADMKGSLAAMIVAAEEY 115
           GT  P +AFAGHTDVVP G  + W   PF+ +I DG ++GRGAADMKG++AA  +AA ++
Sbjct: 64  GTKGPCLAFAGHTDVVPVGSASDWRFDPFAGKIEDGQIWGRGAADMKGAIAAFAIAAMDF 123

Query: 116 VKANPNHKGTIALLITSDEEATAKDGTIHVVETLMARDEKITYCMVGEPSSAKNLGDVVK 175
           V  + + +G+IA LIT DEE  + +GTI ++     + E   +C+VGEP++ + LGD++K
Sbjct: 124 VTTH-SFEGSIAFLITGDEEGPSINGTIKLLHWATEQGEHFDHCIVGEPTNPQQLGDMIK 182

Query: 176 NGRRGSITGNLYIQGIQGHVAYPHLAENPIHKAALFLQELTTYQWDKGNEFFPPTSLQIA 235
            GRRGS+ G L +QG QGHVAYP  A+NPI      +  L     D+G   F  ++L++ 
Sbjct: 183 IGRRGSLNGTLRVQGKQGHVAYPQRADNPIPTLIRLIAALKV-PLDEGTAHFDASNLEVV 241

Query: 236 NIHAGTGSNNVIPAELYIQFNLRYCTEVTDEIIKQKVAEMLEK--HNLKYRIEWNLSGKP 293
            + +GTG+ NVIPA+   +FN+R+    T E ++Q++A  +EK   N  Y + +     P
Sbjct: 242 ALTSGTGAYNVIPAQAEAKFNIRFNDLWTAETLRQELATRIEKVAENAAYTLTFEPCNAP 301

Query: 294 -FLTKPGKLLDSITSAIEETIGITPKAETGGGTSDGRFIALMGAEVVEFGPLNSTIHKVN 352
            FLTKP    + + SAIE+  G  P+  T GGTSD RFI+     VVEFG +  T+H V+
Sbjct: 302 AFLTKPDPFTELVASAIEKGTGRRPELSTTGGTSDARFISAY-CPVVEFGLVGQTMHMVD 360

Query: 353 ECVSVEDLGKCGEIYHKMLVNLLDS 377
           E VSV+D+ +  EIY  +LV+  DS
Sbjct: 361 ERVSVDDITRLKEIYESILVDYFDS 385


Lambda     K      H
   0.316    0.134    0.394 

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: 408
Number of extensions: 20
Number of successful extensions: 6
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: 388
Length adjustment: 30
Effective length of query: 347
Effective length of database: 358
Effective search space:   124226
Effective search space used:   124226
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_034991565.1 DL88_RS03205 (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.29956.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-129  417.7   0.0   2.4e-129  417.5   0.0    1.0  1  lcl|NCBI__GCF_000745425.1:WP_034991565.1  DL88_RS03205 succinyl-diaminopim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745425.1:WP_034991565.1  DL88_RS03205 succinyl-diaminopimelate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.5   0.0  2.4e-129  2.4e-129       2     368 ..       9     380 ..       8     382 .. 0.96

  Alignments for each domain:
  == domain 1  score: 417.5 bits;  conditional E-value: 2.4e-129
                                 TIGR01246   2 lelakeLisrksvtPndagaqeliaerLkklgfeieilefed.....tknlwatrgteepvlvfaGhtD 65 
                                               l+la+ Li  +svtP+d ga+ ++++rLk+ gf++++l+f+d     + nl+a+ gt+ p l+faGhtD
  lcl|NCBI__GCF_000745425.1:WP_034991565.1   9 LDLARALIACPSVTPQDGGALGILENRLKQAGFRTHRLTFQDegtpdIDNLYARFGTKGPCLAFAGHTD 77 
                                               6899**********************************99853333379******************** PP

                                 TIGR01246  66 vvPaGelekWssdpfepeerdGklygrGaaDmkgslaafvvaaerfvkknadhkGslsllitsDeegea 134
                                               vvP+G+ ++W+ dpf+ +++dG+++grGaaDmkg++aaf +aa +fv+ +  ++Gs+++lit Deeg +
  lcl|NCBI__GCF_000745425.1:WP_034991565.1  78 VVPVGSASDWRFDPFAGKIEDGQIWGRGAADMKGAIAAFAIAAMDFVTTH-SFEGSIAFLITGDEEGPS 145
                                               ***********************************************998.5***************** PP

                                 TIGR01246 135 idGtkkvvetlkerdelidyavvgePssvkklGDvikiGrrGsitgklkikGiqGhvaYPhkaenPvhk 203
                                               i+Gt+k++++ +e+ e+ d+++vgeP+  ++lGD+ikiGrrGs++g+l+++G+qGhvaYP++a+nP+++
  lcl|NCBI__GCF_000745425.1:WP_034991565.1 146 INGTIKLLHWATEQGEHFDHCIVGEPTNPQQLGDMIKIGRRGSLNGTLRVQGKQGHVAYPQRADNPIPT 214
                                               ********************************************************************* PP

                                 TIGR01246 204 avpvlkeliaiklDeGneffppsslqianieagtgasnviPgelkvkfnlrfssevseeelkskvekil 272
                                               +++++++l ++ lDeG+++f +s+l++  +++gtga nviP+++++kfn+rf+  +++e+l++++++ +
  lcl|NCBI__GCF_000745425.1:WP_034991565.1 215 LIRLIAAL-KVPLDEGTAHFDASNLEVVALTSGTGAYNVIPAQAEAKFNIRFNDLWTAETLRQELATRI 282
                                               ****9998.689****************************************************99999 PP

                                 TIGR01246 273 dkh..kldYelewk.lsgepfltkegklikkvaeaieevlkkkpelstsGGtsDarfiaklgaevvelG 338
                                               +k   +  Y+l ++ + + +fltk +  ++ va+aie+ ++++pelst+GGtsDarfi ++ + vve+G
  lcl|NCBI__GCF_000745425.1:WP_034991565.1 283 EKVaeNAAYTLTFEpCNAPAFLTKPDPFTELVASAIEKGTGRRPELSTTGGTSDARFISAY-CPVVEFG 350
                                               98656899*****8456788*****************************************.******* PP

                                 TIGR01246 339 lvndtihkvneavkiedleklsevyeklle 368
                                               lv +t+h v+e+v+++d+ +l+e+ye++l 
  lcl|NCBI__GCF_000745425.1:WP_034991565.1 351 LVGQTMHMVDERVSVDDITRLKEIYESILV 380
                                               ***************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (388 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: 9.55
//
[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