Alignments for a candidate for lysA in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Azohydromonas australica DSM 1124

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_029000552.1 H537_RS0128300 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>NCBI__GCF_000430725.1:WP_029000552.1
          Length = 427

 Score =  479 bits (1233), Expect = e-140
 Identities = 233/418 (55%), Positives = 320/418 (76%), Gaps = 5/418 (1%)

Query: 3   YFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAVKA 62
           +   + DG+L+ E   L  LA ++GTPLYVYSR  +     A++K++    HL+CYA+KA
Sbjct: 9   FLQRRADGRLYFEDCALDALAREHGTPLYVYSRGAMRAALAAYEKALAGRAHLLCYAMKA 68

Query: 63  NSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKC 122
           NS+L VL   A+ G GFDIVS GEL+RVLAAG D  KVVFSGVGKT AEM++ALQ  ++C
Sbjct: 69  NSSLAVLQLFAQAGCGFDIVSGGELQRVLAAGADAGKVVFSGVGKTPAEMRQALQAGVRC 128

Query: 123 FNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQV 182
           FNVESE EL RL++VA  +G +AP+SLR+NPDVDAKTHPYISTGL+ NKFGI+  RA  V
Sbjct: 129 FNVESEAELDRLSQVAQGMGRRAPVSLRVNPDVDAKTHPYISTGLKGNKFGISHQRALDV 188

Query: 183 YRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGLG 242
           Y+ A +LP L+V GIDCHIGSQ+T + P++DA +R+L L+++++A+GI + HLD+GGGLG
Sbjct: 189 YKHAAALPGLEVVGIDCHIGSQITEIGPYLDALERVLDLVEAVEAQGITLHHLDLGGGLG 248

Query: 243 VVYRDELPPQPSEYAKALLDRLER--HRDLELIFEPGRAIAANAGVLVTKVEFLK--HTE 298
           + Y DE PP P     ALL+R++   H   E++ EPGR++  NAGVL+T+V++LK    E
Sbjct: 249 ITYTDEAPPTPDALVTALLERIDARGHGHREILMEPGRSLVGNAGVLLTEVQYLKPSEVE 308

Query: 299 HKNFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGE-AQTYDLVGPVCETSDFLGKDRDLV 357
            K+F I+DAAMNDL+RPA+Y+AW  I+P   R GE A+T+D+VGPVCE+ D+LG++R L 
Sbjct: 309 GKHFCIVDAAMNDLMRPAMYEAWMGIVPCVERAGEAAETWDVVGPVCESGDWLGRERTLA 368

Query: 358 LQEGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVL 415
           ++EGD+LAV S+GAYG +M+SNYNTRPR AEVMV+G++ + +R+RE++  L+A E ++
Sbjct: 369 VREGDVLAVLSAGAYGMSMASNYNTRPRAAEVMVEGSQAWCIREREKVEDLFAHERLI 426


Lambda     K      H
   0.319    0.137    0.405 

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: 497
Number of extensions: 15
Number of successful extensions: 4
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: 417
Length of database: 427
Length adjustment: 32
Effective length of query: 385
Effective length of database: 395
Effective search space:   152075
Effective search space used:   152075
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_029000552.1 H537_RS0128300 (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.18168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-162  526.5   0.0   2.1e-162  526.3   0.0    1.0  1  lcl|NCBI__GCF_000430725.1:WP_029000552.1  H537_RS0128300 diaminopimelate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000430725.1:WP_029000552.1  H537_RS0128300 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  526.3   0.0  2.1e-162  2.1e-162       3     416 ..      12     423 ..      10     424 .. 0.98

  Alignments for each domain:
  == domain 1  score: 526.3 bits;  conditional E-value: 2.1e-162
                                 TIGR01048   3 ekkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllae 71 
                                               ++ dg+l+ e+++l +la+e+gtPlYvy++ ++r++l+a+++a +++ +l++YA+KAns+lavl+l+a+
  lcl|NCBI__GCF_000430725.1:WP_029000552.1  12 RRADGRLYFEDCALDALAREHGTPLYVYSRGAMRAALAAYEKALAGRAHLLCYAMKANSSLAVLQLFAQ 80 
                                               56799******************************************9********************* PP

                                 TIGR01048  72 eGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgk 140
                                               +G+g+d+vsgGEl+r+laAg++a k+vfsg+gk+ +e+++al+++++++nv+s++el++l+++a+++g 
  lcl|NCBI__GCF_000430725.1:WP_029000552.1  81 AGCGFDIVSGGELQRVLAAGADAGKVVFSGVGKTPAEMRQALQAGVRCFNVESEAELDRLSQVAQGMGR 149
                                               ********************************************************************* PP

                                 TIGR01048 141 karvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfv 209
                                               +a+v+lRvnpdvdakth+yisTGlk +KFGi++++a+++y+ a++l+ le+vGi++HIGSqi+++ p+ 
  lcl|NCBI__GCF_000430725.1:WP_029000552.1 150 RAPVSLRVNPDVDAKTHPYISTGLKGNKFGISHQRALDVYKHAAALPGLEVVGIDCHIGSQITEIGPYL 218
                                               ********************************************************************* PP

                                 TIGR01048 210 eaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelgl.klklilE 277
                                               +a+e+v++l+e ++++gi+l++ldlGGGlgi+y++e  +p+++ ++ +lle++  +   g+ + ++++E
  lcl|NCBI__GCF_000430725.1:WP_029000552.1 219 DALERVLDLVEAVEAQGITLHHLDLGGGLGITYTDEA-PPTPDALVTALLERIDAR---GHgHREILME 283
                                               ***********************************99.**********99988884...77699***** PP

                                 TIGR01048 278 pGRslvanagvlltrVesvKeves..rkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvG 344
                                               pGRslv+nagvllt+V+++K +e+  ++f++vDa+mndl+Rpa+Yea++ i+++ +   e++et+dvvG
  lcl|NCBI__GCF_000430725.1:WP_029000552.1 284 PGRSLVGNAGVLLTEVQYLKPSEVegKHFCIVDAAMNDLMRPAMYEAWMGIVPCVERAGEAAETWDVVG 352
                                               ********************888777****************************999999********* PP

                                 TIGR01048 345 plCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledll 413
                                               p+CEsgD l+++r+l   e Gd+lav saGAYg+sm+snYn+rpr+aev+ve+ +a  ir+re++edl+
  lcl|NCBI__GCF_000430725.1:WP_029000552.1 353 PVCESGDWLGRERTLAVRE-GDVLAVLSAGAYGMSMASNYNTRPRAAEVMVEGSQAWCIREREKVEDLF 420
                                               ***************8665.************************************************* PP

                                 TIGR01048 414 ale 416
                                               a+e
  lcl|NCBI__GCF_000430725.1:WP_029000552.1 421 AHE 423
                                               987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (427 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: 6.99
//
[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