Aligments for a candidate for lysA in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Aligments for a candidate for lysA in Pseudomonas simiae WCS417

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate GFF5387 PS417_27580 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|FitnessBrowser__WCS417:GFF5387 PS417_27580 diaminopimelate
           decarboxylase
          Length = 415

 Score =  321 bits (822), Expect = 3e-92
 Identities = 167/387 (43%), Positives = 249/387 (64%), Gaps = 2/387 (0%)

Query: 9   QTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVS 68
           Q   TP Y+Y    I+  + ++ +A  G   L+CYA+KANSNL +L++LA L +G D VS
Sbjct: 23  QRFGTPTYVYSRAHIEAQYRSFTDALDGVSHLVCYAVKANSNLGVLNVLARLGAGFDIVS 82

Query: 69  IGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGI 128
            GE++R L AG K  +IVFSGVGK+  ++ +AL++ +   N+ES  EL+ ++ +A  +G+
Sbjct: 83  RGELERVLAAGGKAEKIVFSGVGKTREDMRRALEVGVHCFNIESTDELERLQVVAAEMGV 142

Query: 129 KARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGS 188
           +A IS+R+NP++DA THPYISTGLKENKFG+   +A ++++ A +   LE + V  HIGS
Sbjct: 143 RAPISLRVNPDVDAGTHPYISTGLKENKFGIAIADAEDVYIRAAQLPNLEVLGVDCHIGS 202

Query: 189 QLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNA 248
           QL  L P ++A  ++  +   L   GI L   D+GGG+GV Y +EE   + DY + +   
Sbjct: 203 QLTTLPPFLDALDRLLALIDRLGECGIYLHHIDLGGGVGVRYRDEEPPLIADYIKAVRER 262

Query: 249 LQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAI 308
           ++G DLT++ EPGR IVA +G L+TQV Y K  ++K F IVDA MND +RP+LY A   +
Sbjct: 263 IEGRDLTLMFEPGRYIVANAGVLLTQVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMNV 322

Query: 309 RVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNS 368
             +TP +  E    D+VGP+CE+ D   KD  L  LE GD +AI   GAYG  M+S YN+
Sbjct: 323 TAVTP-RASEARAYDIVGPICETGDFLAKDRQL-ALEEGDLLAIHSAGAYGFVMSSNYNT 380

Query: 369 RPKLLELALEDHKIRVIRKREALEDLW 395
           R +  E+ ++  +   +R+RE + +L+
Sbjct: 381 RGRTAEVLVDGDQAFEVRRRETVAELY 407


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: 383
Number of extensions: 10
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: 415
Length adjustment: 31
Effective length of query: 374
Effective length of database: 384
Effective search space:   143616
Effective search space used:   143616
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 GFF5387 PS417_27580 (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.7954.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.1e-163  529.0   0.0   3.9e-163  528.7   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF5387  PS417_27580 diaminopimelate deca


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF5387  PS417_27580 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.7   0.0  3.9e-163  3.9e-163       5     416 ..       7     410 ..       4     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 528.7 bits;  conditional E-value: 3.9e-163
                           TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvv 79 
                                         +dgel++egv+l ++a++fgtP+Yvy+++++++++++++ a  + ++lv+YAvKAnsnl vl++la++G+g+d+v
  lcl|FitnessBrowser__WCS417:GFF5387   7 RDGELFAEGVALSAIAQRFGTPTYVYSRAHIEAQYRSFTDALDGVSHLVCYAVKANSNLGVLNVLARLGAGFDIV 81 
                                         799*****************************************999**************************** PP

                           TIGR01048  80 sgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvda 154
                                         s GEler+laAg kaekivfsg+gk++e++++ale++++++n++s++ele+l+ +a+e+g +a+++lRvnpdvda
  lcl|FitnessBrowser__WCS417:GFF5387  82 SRGELERVLAAGGKAEKIVFSGVGKTREDMRRALEVGVHCFNIESTDELERLQVVAAEMGVRAPISLRVNPDVDA 156
                                         *************************************************************************** PP

                           TIGR01048 155 ktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegiel 229
                                          th+yisTGlke+KFGi++++ae++y +a++l++le++G+++HIGSq++ l pf +a+++++ l+++l e gi l
  lcl|FitnessBrowser__WCS417:GFF5387 157 GTHPYISTGLKENKFGIAIADAEDVYIRAAQLPNLEVLGVDCHIGSQLTTLPPFLDALDRLLALIDRLGECGIYL 231
                                         *************************************************************************** PP

                           TIGR01048 230 eeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkf 304
                                         +++dlGGG+g++y++ee +p +++y +++ e++e+     ++l+l++EpGR++vanagvllt+Ve++K++e++ f
  lcl|FitnessBrowser__WCS417:GFF5387 232 HHIDLGGGVGVRYRDEE-PPLIADYIKAVRERIEG-----RDLTLMFEPGRYIVANAGVLLTQVEYLKHTEHKDF 300
                                         ****************9.************99999.....6********************************** PP

                           TIGR01048 305 vlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgas 379
                                         ++vDa+mndliRpalY+a+++++a+ + ++ e+  +d+vGp+CE+gD+lakdr+l   e Gdlla++saGAYg+ 
  lcl|FitnessBrowser__WCS417:GFF5387 301 AIVDAAMNDLIRPALYQAWMNVTAV-TPRASEARAYDIVGPICETGDFLAKDRQLALEE-GDLLAIHSAGAYGFV 373
                                         *************************.5688889**********************8776.*************** PP

                           TIGR01048 380 mssnYnsrprpaevlveegkarlirrretledllale 416
                                         mssnYn+r+r+aevlv++++a  +rrret+++l a e
  lcl|FitnessBrowser__WCS417:GFF5387 374 MSSNYNTRGRTAEVLVDGDQAFEVRRRETVAELYAGE 410
                                         ********************************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (415 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: 00:00:00.02
# Mc/sec: 7.95
//
[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:

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, 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

GapMind for Amino acid biosynthesis