GapMind for Amino acid biosynthesis

 

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

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate WP_011386835.1 AMB_RS22725 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|NCBI__GCF_000009985.1:WP_011386835.1 AMB_RS22725
           diaminopimelate decarboxylase
          Length = 424

 Score =  300 bits (768), Expect = 5e-86
 Identities = 168/389 (43%), Positives = 239/389 (61%), Gaps = 3/389 (0%)

Query: 13  TPFYLYDFDKIKQAFLNYKEAFK--GRKSLICYALKANSNLSILSLLAHLESGADCVSIG 70
           TPFY Y    +++ +  + EA K  G  + IC+A KAN N++++   A L +GAD VS G
Sbjct: 27  TPFYCYSTATLQRHYTVFAEALKAAGLDATICFAAKANPNMAVIRTFAQLGAGADVVSEG 86

Query: 71  EIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKA 130
           E+++AL AG+   RIVFSGVGK+  E+E A+   I  +NVES  EL+ +  IA + G   
Sbjct: 87  ELRQALAAGVPAARIVFSGVGKTRHELEFAVAKGIFQINVESEPELEMLSEIAAARGQVM 146

Query: 131 RISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQL 190
            I+IR+NP++DA TH  I+TG KENKFG+    A E++  AK    +EPV++  HIGSQL
Sbjct: 147 PIAIRVNPDVDAGTHAKITTGKKENKFGIEWTRAREVYARAKALPGVEPVAIACHIGSQL 206

Query: 191 LDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQ 250
            +L P  EA  +V  +   L A GID+R  D+GGG+GV Y++E   +   YA+ I   L 
Sbjct: 207 TELTPFREAFLRVRDLVAMLRADGIDIRRLDLGGGLGVPYDDETPPEPAAYAEVIKATLG 266

Query: 251 GLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAI-R 309
            L    + EPGR +V  +G L+++++  K+   + F+IVDA MND  RPSLY A H+I  
Sbjct: 267 DLGCRFVFEPGRLLVGNAGILVSRIIRVKEGSTRTFLIVDAAMNDLARPSLYDAYHSIFP 326

Query: 310 VITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNSR 369
           V  P  G  ++  DVVGPVCE+ DTF K   LP +   D +A    GAYG++M+S YN+R
Sbjct: 327 VAEPKAGAALAEVDVVGPVCETGDTFAKQRRLPPMRTDDLLAFGTAGAYGAAMSSTYNTR 386

Query: 370 PKLLELALEDHKIRVIRKREALEDLWRLE 398
           P + E+ ++     VIR R + ED+  LE
Sbjct: 387 PLIPEVLVKGGDYAVIRVRPSYEDMRSLE 415


Lambda     K      H
   0.319    0.138    0.389 

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: 379
Number of extensions: 14
Number of successful extensions: 3
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: 405
Length of database: 424
Length adjustment: 31
Effective length of query: 374
Effective length of database: 393
Effective search space:   146982
Effective search space used:   146982
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_011386835.1 AMB_RS22725 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# 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/TIGR01048.hmm
# target sequence database:        /tmp/gapView.2923.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-145  470.6   0.0   2.1e-145  470.3   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386835.1  AMB_RS22725 diaminopimelate deca


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386835.1  AMB_RS22725 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.3   0.0  2.1e-145  2.1e-145       4     416 ..       6     415 ..       4     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 470.3 bits;  conditional E-value: 2.1e-145
                                 TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka..eeslvlYAvKAnsnlavlrlla 70 
                                                ++gel++e+v+++++a+e gtP+Y y+++tl+++++ ++ea ka   ++++++A+KAn n+av+r++a
  lcl|NCBI__GCF_000009985.1:WP_011386835.1   6 YQNGELFAEDVAIARIAREVGTPFYCYSTATLQRHYTVFAEALKAagLDATICFAAKANPNMAVIRTFA 74 
                                               589****************************************9965556******************* PP

                                 TIGR01048  71 eeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelg 139
                                               ++G+g+dvvs+GEl +alaAgv+a +ivfsg+gk+++ele a++ +i  inv+s+ ele+l+eia+  g
  lcl|NCBI__GCF_000009985.1:WP_011386835.1  75 QLGAGADVVSEGELRQALAAGVPAARIVFSGVGKTRHELEFAVAKGIFQINVESEPELEMLSEIAAARG 143
                                               ********************************************************************* PP

                                 TIGR01048 140 kkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepf 208
                                               + +++++Rvnpdvda th +i+TG+ke+KFGie ++a+e+y +a++l+ +e+v i +HIGSq+++l pf
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 144 QVMPIAIRVNPDVDAGTHAKITTGKKENKFGIEWTRAREVYARAKALPGVEPVAIACHIGSQLTELTPF 212
                                               ********************************************************************* PP

                                 TIGR01048 209 veaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilE 277
                                               +ea+ +v +l++ l+++gi+++ ldlGGGlg++y++e+ +p+++ yae+++++l +     l  + ++E
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 213 REAFLRVRDLVAMLRADGIDIRRLDLGGGLGVPYDDET-PPEPAAYAEVIKATLGD-----LGCRFVFE 275
                                               ************************************99.************99999.....7999**** PP

                                 TIGR01048 278 pGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrlee.eetetvdvvGp 345
                                               pGR lv+nag+l+ r+  vKe ++r+f +vDa+mndl Rp+lY+ayh+i+++++ ++ ++ ++vdvvGp
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 276 PGRLLVGNAGILVSRIIRVKEGSTRTFLIVDAAMNDLARPSLYDAYHSIFPVAEPKAgAALAEVDVVGP 344
                                               ****************************************************99776155689****** PP

                                 TIGR01048 346 lCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledlla 414
                                               +CE+gD++ak+r+lp ++++dlla   aGAYga+mss+Yn+rp + evlv++g++ +ir r ++ed+ +
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 345 VCETGDTFAKQRRLPPMRTDDLLAFGTAGAYGAAMSSTYNTRPLIPEVLVKGGDYAVIRVRPSYEDMRS 413
                                               ******************************************************************977 PP

                                 TIGR01048 415 le 416
                                               le
  lcl|NCBI__GCF_000009985.1:WP_011386835.1 414 LE 415
                                               65 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (424 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: 00:00:00.02
# Mc/sec: 7.53
//
[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:

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:

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:

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