Alignments for a candidate for lysA in Phyllobacterium endophyticum PEPV15

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Phyllobacterium endophyticum PEPV15

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_106719045.1 CU100_RS23350 diaminopimelate decarboxylase

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



>NCBI__GCF_003010935.1:WP_106719045.1
          Length = 421

 Score =  416 bits (1069), Expect = e-121
 Identities = 221/422 (52%), Positives = 284/422 (67%), Gaps = 5/422 (1%)

Query: 1   MDHFNRKNGVLHAENVSIPAIAAEVGTPVYVYSTATLERHASALKNALAGLPSVHLAFAI 60
           M+HF  ++GVLHAE VSIP IA  VGTP Y YSTAT+ERH      A A + ++ +A+A+
Sbjct: 1   MNHFGYRDGVLHAEGVSIPDIAKAVGTPFYCYSTATIERHFKVFSAAFADMDTL-VAYAL 59

Query: 61  KANPNLAVLGVLARQGYGADVVSGGELKRALAAGMPAEDVVFSGVGKTRAELQLGLDEGI 120
           KAN N AVL  LAR G GADVVS GE++RALAAG+PA  +VFSGVGK + E+   L  GI
Sbjct: 60  KANSNQAVLKTLARLGSGADVVSEGEMRRALAAGIPAGKIVFSGVGKKQGEMDFALAAGI 119

Query: 121 GQFNLELEEEGEVLADLAHAQGKTAPAVLRVNPDVDAGTHAKISTGKAENKFGVAIDRAL 180
             FN+E E E E+L+  A A GK AP  LR+NPDVDA TH KISTGK+ENKFG+ + +A 
Sbjct: 120 HCFNVESEPELEMLSARAVAAGKIAPVSLRINPDVDAKTHKKISTGKSENKFGIPLAKAS 179

Query: 181 EIFDRLAKRPGLNLRGVAIHIGSQLTELAPLEAAYKRVGELVAQLRAAGHTITHVDLGGG 240
            I+ R +  PGL + GV +HIGSQ+T+L P + A++ + ELVAQL+A GH I HVDLGGG
Sbjct: 180 AIYARASLLPGLKVTGVDMHIGSQITDLEPFDNAFRLLAELVAQLQADGHDIKHVDLGGG 239

Query: 241 LGVPYH-AGQTVSTAEEFGAMVARVTQGWNVTLMFEPGRFICGNAGVLVTEVIWVKPAAG 299
           LG+PYH         + +  +V +  +   +  +FEPGR I GNAG+LVTEVI++K    
Sbjct: 240 LGIPYHFDNNPPPLPDAYAQIVQKHIKPLGLKTIFEPGRLIVGNAGILVTEVIYLKEGDA 299

Query: 300 NPYVIVDAAMNDLARPALYDAYHEFEAVEPTG---EKFVANIAGPVCETGDTFAMGREID 356
             +VIVDAAMNDL RP LYDA+H    V+  G    +   ++ GPVCETGD   + R++ 
Sbjct: 300 RNFVIVDAAMNDLIRPTLYDAFHIMHPVKEPGANAPRIRGDVVGPVCETGDYLGLDRDLP 359

Query: 357 VVKSGDLAVFRTAGAYGATMASTYNSRALVPEVLVSGDRFAVVADRIQPETIMGAERVPE 416
               GDL    TAGAYGA  A TYN+R LVPEVLV+GD F VV  R   + ++G + +PE
Sbjct: 360 RPAPGDLIAIGTAGAYGAVQAGTYNTRLLVPEVLVNGDLFHVVRPRTTYDELIGLDSIPE 419

Query: 417 WV 418
           W+
Sbjct: 420 WL 421


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: 547
Number of extensions: 24
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: 419
Length of database: 421
Length adjustment: 32
Effective length of query: 387
Effective length of database: 389
Effective search space:   150543
Effective search space used:   150543
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 WP_106719045.1 CU100_RS23350 (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.1436292.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-142  460.5   0.0   2.5e-142  460.2   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106719045.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106719045.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.2   0.0  2.5e-142  2.5e-142       5     415 ..       7     414 ..       5     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 460.2 bits;  conditional E-value: 2.5e-142
                             TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgld 77 
                                           +dg l +egv++ ++a+  gtP+Y y+++t++++++ +++af++ ++lv+YA+KAnsn avl++la++G+g+d
  NCBI__GCF_003010935.1:WP_106719045.1   7 RDGVLHAEGVSIPDIAKAVGTPFYCYSTATIERHFKVFSAAFADMDTLVAYALKANSNQAVLKTLARLGSGAD 79 
                                           68999****************************************9*************************** PP

                             TIGR01048  78 vvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnp 150
                                           vvs+GE+ ralaAg++a kivfsg+gk++ e+  al+++i+++nv+s+ ele+l++ a  +gk a+v+lR+np
  NCBI__GCF_003010935.1:WP_106719045.1  80 VVSEGEMRRALAAGIPAGKIVFSGVGKKQGEMDFALAAGIHCFNVESEPELEMLSARAVAAGKIAPVSLRINP 152
                                           ************************************************************************* PP

                             TIGR01048 151 dvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelk 223
                                           dvdakth++isTG+ e+KFGi +++a ++y +a+ l+ l+++G+++HIGSqi+dlepf +a++ +++l+++l+
  NCBI__GCF_003010935.1:WP_106719045.1 153 DVDAKTHKKISTGKSENKFGIPLAKASAIYARASLLPGLKVTGVDMHIGSQITDLEPFDNAFRLLAELVAQLQ 225
                                           ************************************************************************* PP

                             TIGR01048 224 eegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesv 296
                                           ++g +++++dlGGGlgi+y+ ++++p l + ++++++k  k     l lk i+EpGR +v+nag+l+t+V ++
  NCBI__GCF_003010935.1:WP_106719045.1 226 ADGHDIKHVDLGGGLGIPYHFDNNPPPLPDAYAQIVQKHIK----PLGLKTIFEPGRLIVGNAGILVTEVIYL 294
                                           **********************9999998887777766666....37999*********************** PP

                             TIGR01048 297 KevesrkfvlvDagmndliRpalYeayheiaalkrlee.eetetvdvvGplCEsgDvlakdrelpeveeGdll 368
                                           Ke + r+fv+vDa+mndliRp lY+a h + ++k+  + +++ + dvvGp+CE+gD l+ dr+lp+  +Gdl+
  NCBI__GCF_003010935.1:WP_106719045.1 295 KEGDARNFVIVDAAMNDLIRPTLYDAFHIMHPVKEPGAnAPRIRGDVVGPVCETGDYLGLDRDLPRPAPGDLI 367
                                           *********************************997651677889**************************** PP

                             TIGR01048 369 avasaGAYgasmssnYnsrprpaevlveegkarlirrretledllal 415
                                           a+  aGAYga  + +Yn+r  + evlv+++  +++r r t+++l+ l
  NCBI__GCF_003010935.1:WP_106719045.1 368 AIGTAGAYGAVQAGTYNTRLLVPEVLVNGDLFHVVRPRTTYDELIGL 414
                                           ********************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (421 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: 00:00:00.01
# Mc/sec: 14.39
//
[ok]

This GapMind analysis is from Jul 26 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