Alignments for a candidate for lysA in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Nitratiruptor tergarcus DSM 16512

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_084275312.1 B8779_RS04255 diaminopimelate decarboxylase

Query= BRENDA::P56129
         (405 letters)



>NCBI__GCF_900176045.1:WP_084275312.1
          Length = 400

 Score =  441 bits (1135), Expect = e-128
 Identities = 224/392 (57%), Positives = 292/392 (74%), Gaps = 2/392 (0%)

Query: 3   NYEELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLES 62
           +Y+ L Q + TP Y+YDFD+I + +   K AFK RKS+I YA+KANSNLS+L  LA+L S
Sbjct: 2   DYKALAQKYGTPLYVYDFDEISRNYNKIKTAFKARKSIIAYAVKANSNLSLLKHLANLGS 61

Query: 63  GADCVSIGEIYRALKAGIKPYRIVFSGVGKSGFEIEQALKLNILFLNVESFMELTTIETI 122
           GADCVSIGEI RAL AGI  Y+I+FSGVGK   EI +AL+ +ILF+N+ES  EL  +E I
Sbjct: 62  GADCVSIGEIKRALLAGIPNYKIIFSGVGKRDDEIAEALEKDILFINIESEAELFRVEEI 121

Query: 123 AQSLGIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSV 182
           A  LG +ARIS+R+NPNID  THPYISTGL ENKFGV    A +++L AK S +L PV +
Sbjct: 122 AAKLGKQARISVRVNPNIDPLTHPYISTGLSENKFGVAIDTAKKLYLKAKSSPYLNPVGI 181

Query: 183 HFHIGSQLSDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYA 242
           HFHIGSQL++L PI EAS  VA++ ++L  + ID++FFDVGGG+G+ Y++E+TI+ YDYA
Sbjct: 182 HFHIGSQLTELAPIKEASAIVAELTRALQKIDIDIKFFDVGGGLGIRYKDEKTIEPYDYA 241

Query: 243 QGILNSLQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVVVDAGMNDFLRPSLY 302
           Q IL++L G D+TIICEPGR IV  +G  +T VLYEK+  +KRF++VD GMND LRPSLY
Sbjct: 242 QAILSTLSGTDMTIICEPGRFIVGNAGVFLTSVLYEKETGSKRFIIVDGGMNDLLRPSLY 301

Query: 303 HAKHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKLVIEKVGAYGSSM 362
           +A H + V+   K  + S  DVVGPVCES D F KD  LP+ E GD +V++  GAYG  M
Sbjct: 302 NAYHEVEVV--GKSEDASLADVVGPVCESGDFFAKDRLLPKTEHGDIVVVKSAGAYGFVM 359

Query: 363 ASQYNSRPKLLELALEDHKIRVIRKREALEDL 394
           +S YN+RP+  E+A+E  + R+IR+RE+ E L
Sbjct: 360 SSNYNTRPRPAEVAIEGGEDRLIRERESFEYL 391


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: 452
Number of extensions: 15
Number of successful extensions: 2
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: 400
Length adjustment: 31
Effective length of query: 374
Effective length of database: 369
Effective search space:   138006
Effective search space used:   138006
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_084275312.1 B8779_RS04255 (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.298076.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-166  538.1   0.0   6.2e-166  537.9   0.0    1.0  1  NCBI__GCF_900176045.1:WP_084275312.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176045.1:WP_084275312.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.9   0.0  6.2e-166  6.2e-166      14     417 .]       1     396 [.       1     396 [. 0.99

  Alignments for each domain:
  == domain 1  score: 537.9 bits;  conditional E-value: 6.2e-166
                             TIGR01048  14 vdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGEler 86 
                                           +d+k+la+++gtPlYvyd +++ ++++++k+afka++s ++YAvKAnsnl++l++la++G+g+d+vs GE++r
  NCBI__GCF_900176045.1:WP_084275312.1   1 MDYKALAQKYGTPLYVYDFDEISRNYNKIKTAFKARKSIIAYAVKANSNLSLLKHLANLGSGADCVSIGEIKR 73 
                                           5799********************************************************************* PP

                             TIGR01048  87 alaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakthey 159
                                           al Ag++++ki+fsg+gk+++e+++ale +i +in++s++el ++eeia++lgk+ar+++Rvnp++d+ th+y
  NCBI__GCF_900176045.1:WP_084275312.1  74 ALLAGIPNYKIIFSGVGKRDDEIAEALEKDILFINIESEAELFRVEEIAAKLGKQARISVRVNPNIDPLTHPY 146
                                           ************************************************************************* PP

                             TIGR01048 160 isTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleel 232
                                           isTGl e+KFG+++++a++ y  a+++++l++vGih+HIGSq+++l+p++ea + v++l++ l++  i+++++
  NCBI__GCF_900176045.1:WP_084275312.1 147 ISTGLSENKFGVAIDTAKKLYLKAKSSPYLNPVGIHFHIGSQLTELAPIKEASAIVAELTRALQKIDIDIKFF 219
                                           ************************************************************************* PP

                             TIGR01048 233 dlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfv 305
                                           d+GGGlgi+y++e+ ++++++ya+++l++l++     +++++i+EpGR++v+nagv+lt+V ++Ke++s++f+
  NCBI__GCF_900176045.1:WP_084275312.1 220 DVGGGLGIRYKDEK-TIEPYDYAQAILSTLSG-----TDMTIICEPGRFIVGNAGVFLTSVLYEKETGSKRFI 286
                                           ************99.***************99.....6*********************************** PP

                             TIGR01048 306 lvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYga 378
                                           +vD+gmndl+Rp+lY+ayhe+ ++ + e++  + +dvvGp+CEsgD++akdr lp++e+Gd+++v+saGAYg+
  NCBI__GCF_900176045.1:WP_084275312.1 287 IVDGGMNDLLRPSLYNAYHEVEVVGKSEDA--SLADVVGPVCESGDFFAKDRLLPKTEHGDIVVVKSAGAYGF 357
                                           ************************886666..9**************************************** PP

                             TIGR01048 379 smssnYnsrprpaevlveegkarlirrretledllalel 417
                                            mssnYn+rprpaev++e+g+ rlir+re++e l+++e+
  NCBI__GCF_900176045.1:WP_084275312.1 358 VMSSNYNTRPRPAEVAIEGGEDRLIRERESFEYLIEKEV 396
                                           ***********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (400 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 25.83
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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