Alignments for a candidate for lysA in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Sphingomonas koreensis DSMZ 15582

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate Ga0059261_2051 Ga0059261_2051 diaminopimelate decarboxylase

Query= reanno::Korea:Ga0059261_2051
         (419 letters)



>FitnessBrowser__Korea:Ga0059261_2051
          Length = 419

 Score =  824 bits (2128), Expect = 0.0
 Identities = 419/419 (100%), Positives = 419/419 (100%)

Query: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60
           MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI
Sbjct: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60

Query: 61  KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120
           KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI
Sbjct: 61  KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120

Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180
           GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL
Sbjct: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180

Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240
           EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG
Sbjct: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240

Query: 241 LGVPYHAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAGN 300
           LGVPYHAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAGN
Sbjct: 241 LGVPYHAGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAGN 300

Query: 301 PYVIVDAAMNDLARPALYDAYHEFEAVEPTGEKFVANIAGPVCETGDTFAMGREIDVVKS 360
           PYVIVDAAMNDLARPALYDAYHEFEAVEPTGEKFVANIAGPVCETGDTFAMGREIDVVKS
Sbjct: 301 PYVIVDAAMNDLARPALYDAYHEFEAVEPTGEKFVANIAGPVCETGDTFAMGREIDVVKS 360

Query: 361 GDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPEWVR 419
           GDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPEWVR
Sbjct: 361 GDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPEWVR 419


Lambda     K      H
   0.318    0.135    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: 815
Number of extensions: 21
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: 419
Length of database: 419
Length adjustment: 32
Effective length of query: 387
Effective length of database: 387
Effective search space:   149769
Effective search space used:   149769
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate Ga0059261_2051 Ga0059261_2051 (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.2675.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-132  427.0   0.0   3.3e-132  426.9   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2051  Ga0059261_2051 diaminopimelate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2051  Ga0059261_2051 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.9   0.0  3.3e-132  3.3e-132       4     414 ..       6     410 ..       3     413 .. 0.96

  Alignments for each domain:
  == domain 1  score: 426.9 bits;  conditional E-value: 3.3e-132
                                 TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaees.lvlYAvKAnsnlavlrllae 71 
                                               +k+g l +e+v++ ++a+e gtP+Yvy+++tl+++++alk+a ++  s  +++A+KAn nlavl +la+
  lcl|FitnessBrowser__Korea:Ga0059261_2051   6 RKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSvHLAFAIKANPNLAVLGVLAR 74 
                                               68999***************************************966669******************* PP

                                 TIGR01048  72 eGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgk 140
                                               +G g+dvvsgGEl+ralaAg++ae++vfsg+gk+++el+  l+ +i  +n++ +ee e l ++a+ +gk
  lcl|FitnessBrowser__Korea:Ga0059261_2051  75 QGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGIGQFNLELEEEGEVLADLAHAQGK 143
                                               ********************************************************************* PP

                                 TIGR01048 141 karvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfv 209
                                               +a+ +lRvnpdvda th +isTG++e+KFG+++++a+e++ + +k++ l+l G+ +HIGSq+++l+p++
  lcl|FitnessBrowser__Korea:Ga0059261_2051 144 TAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRALEIFDRLAKRPGLNLRGVAIHIGSQLTELAPLE 212
                                               ********************************************************************* PP

                                 TIGR01048 210 eaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEp 278
                                               +a ++v +l+++l+++g +++++dlGGGlg++y+  ++  ++ee+  ++++++++    g +++l++Ep
  lcl|FitnessBrowser__Korea:Ga0059261_2051 213 AAYKRVGELVAQLRAAGHTITHVDLGGGLGVPYHAGQTVSTAEEFG-AMVARVTQ----GWNVTLMFEP 276
                                               ************************************9666666655.55556666....79******** PP

                                 TIGR01048 279 GRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplC 347
                                               GR++ +nagvl+t+V  vK +    +v+vDa+mndl RpalY+ayhe  a++ + e+   +++++Gp+C
  lcl|FitnessBrowser__Korea:Ga0059261_2051 277 GRFICGNAGVLVTEVIWVKPAAGNPYVIVDAAMNDLARPALYDAYHEFEAVEPTGEK--FVANIAGPVC 343
                                               ***************************************************886666..9********* PP

                                 TIGR01048 348 EsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledlla 414
                                               E+gD++a  re++ v++Gdl + + aGAYga+m+s+Ynsr+ + evlv++++  ++  r + e ++ 
  lcl|FitnessBrowser__Korea:Ga0059261_2051 344 ETGDTFAMGREIDVVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMG 410
                                               *********************************************************9988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (419 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.98
//
[ok]

This GapMind analysis is from Apr 09 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