Alignments for a candidate for lysA in Caminibacter mediatlanticus TB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Caminibacter mediatlanticus TB-2

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate WP_007474124.1 CMTB2_RS03820 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>NCBI__GCF_000170735.1:WP_007474124.1
          Length = 402

 Score =  456 bits (1173), Expect = e-133
 Identities = 225/392 (57%), Positives = 293/392 (74%)

Query: 3   NYEELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLES 62
           N+ E  + + TP Y+YDF+  ++ +   K+AFK RKS+I YA+KANSNLS++   A L S
Sbjct: 2   NFLEFAKKYDTPLYVYDFNHFEKQYNELKQAFKARKSIIAYAIKANSNLSVIKKFASLGS 61

Query: 63  GADCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETI 122
           GADCVSIGE++RAL AG+  Y+I+FSGVGK   EI++AL  +IL LNVES  ELK I+ I
Sbjct: 62  GADCVSIGEVKRALLAGVDKYKIIFSGVGKRDDEIKEALDKDILMLNVESEAELKRIDEI 121

Query: 123 AQSLGIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSV 182
           A+S+  +ARISIR+NP+ID KTHPYISTGL ENKFGV  + A +M++ AKKS  L P+ +
Sbjct: 122 AKSMNKEARISIRVNPDIDPKTHPYISTGLSENKFGVDIESAKKMYINAKKSKNLNPIGI 181

Query: 183 HFHIGSQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYA 242
           HFHIGSQL +L PI EAS+ VA + +SL A+ +D++FFD+GGG+G+ Y++EETIK YDYA
Sbjct: 182 HFHIGSQLTELNPIKEASEIVANLVRSLKAINVDIKFFDIGGGLGIKYKDEETIKPYDYA 241

Query: 243 QGILNALQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLY 302
           Q IL+ L GLD+TIICEPGR +V   G  +T+VLYEK   +KRFVIVD  MND +RPSLY
Sbjct: 242 QAILSTLSGLDVTIICEPGRFLVGNGGWFLTKVLYEKVNGDKRFVIVDGAMNDLIRPSLY 301

Query: 303 HAKHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSM 362
           +A H + VI+  K  +IS  ++VGPVCES D F KD  +P+  PGD I I   GAYG +M
Sbjct: 302 NAYHKVEVISSVKNPQISKANIVGPVCESGDFFAKDIEVPQTNPGDLIVIHSAGAYGFTM 361

Query: 363 ASQYNSRPKLLELALEDHKIRVIRKREALEDL 394
           +S YN+RP+  E+A+ED K RVIR+RE  EDL
Sbjct: 362 SSNYNTRPRPCEIAIEDGKDRVIRRRETFEDL 393


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: 475
Number of extensions: 12
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: 405
Length of database: 402
Length adjustment: 31
Effective length of query: 374
Effective length of database: 371
Effective search space:   138754
Effective search space used:   138754
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_007474124.1 CMTB2_RS03820 (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.14397.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-167  541.2   0.0   6.9e-167  541.1   0.0    1.0  1  lcl|NCBI__GCF_000170735.1:WP_007474124.1  CMTB2_RS03820 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000170735.1:WP_007474124.1  CMTB2_RS03820 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  541.1   0.0  6.9e-167  6.9e-167      15     416 ..       2     397 ..       1     398 [. 0.99

  Alignments for each domain:
  == domain 1  score: 541.1 bits;  conditional E-value: 6.9e-167
                                 TIGR01048  15 dlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGE 83 
                                               +  e a++++tPlYvyd +++++++++lk+afka++s ++YA+KAnsnl+v++ +a++G+g+d+vs GE
  lcl|NCBI__GCF_000170735.1:WP_007474124.1   2 NFLEFAKKYDTPLYVYDFNHFEKQYNELKQAFKARKSIIAYAIKANSNLSVIKKFASLGSGADCVSIGE 70 
                                               567899*************************************************************** PP

                                 TIGR01048  84 leralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdv 152
                                               ++ral Agv+++ki+fsg+gk+++e+++al+ +i ++nv+s++el++++eiak+++k+ar+++Rvnpd+
  lcl|NCBI__GCF_000170735.1:WP_007474124.1  71 VKRALLAGVDKYKIIFSGVGKRDDEIKEALDKDILMLNVESEAELKRIDEIAKSMNKEARISIRVNPDI 139
                                               ********************************************************************* PP

                                 TIGR01048 153 daktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvkllee 221
                                               d+kth+yisTGl e+KFG+++e+a+++y  a+k+++l+++Gih+HIGSq+++l+p++ea e v++l+++
  lcl|NCBI__GCF_000170735.1:WP_007474124.1 140 DPKTHPYISTGLSENKFGVDIESAKKMYINAKKSKNLNPIGIHFHIGSQLTELNPIKEASEIVANLVRS 208
                                               ********************************************************************* PP

                                 TIGR01048 222 lkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvll 290
                                               lk+  ++++++d+GGGlgi+y++ee ++++++ya+++l++l++     l++++i+EpGR+lv+n+g++l
  lcl|NCBI__GCF_000170735.1:WP_007474124.1 209 LKAINVDIKFFDIGGGLGIKYKDEE-TIKPYDYAQAILSTLSG-----LDVTIICEPGRFLVGNGGWFL 271
                                               ************************9.************99999.....8******************** PP

                                 TIGR01048 291 trVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrel 359
                                               t+V ++K ++ ++fv+vD++mndliRp+lY+ayh++ +++++++ + +++++vGp+CEsgD++akd+e+
  lcl|NCBI__GCF_000170735.1:WP_007474124.1 272 TKVLYEKVNGDKRFVIVDGAMNDLIRPSLYNAYHKVEVISSVKNPQISKANIVGPVCESGDFFAKDIEV 340
                                               ********************************************************************* PP

                                 TIGR01048 360 peveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                               p++++Gdl++++saGAYg++mssnYn+rprp+e+++e+gk r+irrret+edl+a e
  lcl|NCBI__GCF_000170735.1:WP_007474124.1 341 PQTNPGDLIVIHSAGAYGFTMSSNYNTRPRPCEIAIEDGKDRVIRRRETFEDLIACE 397
                                               ******************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (402 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: 00:00:00.01
# Mc/sec: 9.15
//
[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