GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Shewanella amazonensis SB2B

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 6939152 Sama_3250 diaminopimelate decarboxylase (RefSeq)

Query= BRENDA::P56129
         (405 letters)



>lcl|FitnessBrowser__SB2B:6939152 Sama_3250 diaminopimelate
           decarboxylase (RefSeq)
          Length = 414

 Score =  320 bits (821), Expect = 4e-92
 Identities = 179/389 (46%), Positives = 239/389 (61%), Gaps = 2/389 (0%)

Query: 11  HKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIG 70
           H TP Y+Y    +++ +  +  A      LICYA+KANSNL++L++LA L SG D VS G
Sbjct: 25  HGTPLYVYSRATLERHWHAFDGAVASHPHLICYAVKANSNLAVLNVLARLGSGFDIVSGG 84

Query: 71  EIYRALKAGIKPYRIVFSGVGKSGFEIEQALKLNILFLNVESFMELTTIETIAQSLGIKA 130
           E+ R L+AG  P ++VFSGVGK+  E+E AL   I+  N+ES  EL  +  +A  LG  A
Sbjct: 85  ELSRVLEAGGDPAKVVFSGVGKTVAEMELALNTGIMCFNLESGAELELLNEVAGRLGKVA 144

Query: 131 RISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQL 190
            +S+R+NP++DA THPYISTGLKENKFG+  +EA  +F  A     L    V  HIGSQL
Sbjct: 145 PVSLRVNPDVDAGTHPYISTGLKENKFGIPMEEAEALFARAAALPNLAVKGVDCHIGSQL 204

Query: 191 SDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNSLQ 250
           ++L+P ++A  ++  +   L   GI +  FDVGGG+GV+Y  E       YA  IL  L 
Sbjct: 205 TELKPFLDAMDRMLALIDRLAEQGIVIEHFDVGGGLGVTYNGETPPHPDVYAAAILEKLN 264

Query: 251 GLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVVVDAGMNDFLRPSLYHAKHAIRV 310
           G  L +I EPGR+I A +G  +TQVLY K   +KRFV+VD  MND +RPSLY A   I +
Sbjct: 265 GRPLKLIFEPGRAIAANAGIFVTQVLYTKDNGDKRFVIVDGAMNDLIRPSLYGAWQNI-I 323

Query: 311 ITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKLVIEKVGAYGSSMASQYNSRP 370
                    + CDVVGPVCE+ D   KD  L     GD LV+   GAYG +MAS YN+RP
Sbjct: 324 PAVKTNEPTTRCDVVGPVCETGDFLGKDREL-AAGSGDLLVVRSAGAYGFTMASNYNTRP 382

Query: 371 KLLELALEDHKIRVIRKREALEDLWRLEE 399
           +  EL ++  K  V+R+RE L  LW+ E+
Sbjct: 383 RAAELMVDGDKAYVVREREKLSQLWQGEQ 411


Lambda     K      H
   0.319    0.137    0.390 

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: 383
Number of extensions: 16
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: 414
Length adjustment: 31
Effective length of query: 374
Effective length of database: 383
Effective search space:   143242
Effective search space used:   143242
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 6939152 Sama_3250 (diaminopimelate decarboxylase (RefSeq))
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.18331.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.8e-162  525.5   0.0   4.7e-162  525.2   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6939152  Sama_3250 diaminopimelate decarb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939152  Sama_3250 diaminopimelate decarboxylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.2   0.0  4.7e-162  4.7e-162       6     416 ..       8     410 ..       5     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 525.2 bits;  conditional E-value: 4.7e-162
                         TIGR01048   6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgG 82 
                                       + +l++e++d++ la+e+gtPlYvy+++tl+++++a++ a++++ +l++YAvKAnsnlavl++la++G+g+d+vsgG
  lcl|FitnessBrowser__SB2B:6939152   8 EERLFAEECDVAGLAAEHGTPLYVYSRATLERHWHAFDGAVASHPHLICYAVKANSNLAVLNVLARLGSGFDIVSGG 84 
                                       56899************************************************************************ PP

                         TIGR01048  83 EleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakthey 159
                                       El r+l+Ag ++ k+vfsg+gk+ +e+e al+++i ++n++s +elell+e+a++lgk a+v+lRvnpdvda th+y
  lcl|FitnessBrowser__SB2B:6939152  85 ELSRVLEAGGDPAKVVFSGVGKTVAEMELALNTGIMCFNLESGAELELLNEVAGRLGKVAPVSLRVNPDVDAGTHPY 161
                                       ***************************************************************************** PP

                         TIGR01048 160 isTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGG 236
                                       isTGlke+KFGi +eeae+ + +a++l++l + G+++HIGSq+++l+pf +a+++++ l+++l+e+gi +e++d+GG
  lcl|FitnessBrowser__SB2B:6939152 162 ISTGLKENKFGIPMEEAEALFARAAALPNLAVKGVDCHIGSQLTELKPFLDAMDRMLALIDRLAEQGIVIEHFDVGG 238
                                       ***************************************************************************** PP

                         TIGR01048 237 GlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmnd 313
                                       Glg++y+ e+ +p+++ ya+++lekl++     + lkli+EpGR+++anag+++t+V ++K+++ ++fv+vD++mnd
  lcl|FitnessBrowser__SB2B:6939152 239 GLGVTYNGET-PPHPDVYAAAILEKLNG-----RPLKLIFEPGRAIAANAGIFVTQVLYTKDNGDKRFVIVDGAMND 309
                                       ********99.***************99.....6******************************************* PP

                         TIGR01048 314 liRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprp 390
                                       liRp+lY+a+++i+++ + ++e+t+++dvvGp+CE+gD+l+kdrel +   Gdll+v+saGAYg++m+snYn+rpr+
  lcl|FitnessBrowser__SB2B:6939152 310 LIRPSLYGAWQNIIPAVK-TNEPTTRCDVVGPVCETGDFLGKDRELAAGS-GDLLVVRSAGAYGFTMASNYNTRPRA 384
                                       ****************66.6677***********************9887.************************** PP

                         TIGR01048 391 aevlveegkarlirrretledllale 416
                                       ae++v+++ka+++r+re+l++l++ e
  lcl|FitnessBrowser__SB2B:6939152 385 AELMVDGDKAYVVREREKLSQLWQGE 410
                                       ***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (414 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: 9.74
//
[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