Alignments for a candidate for lysA in Amycolatopsis halophila YIM 93223

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Amycolatopsis halophila YIM 93223

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_034274259.1 AMYHA_RS22275 diaminopimelate decarboxylase

Query= BRENDA::P9WIU7
         (447 letters)



>NCBI__GCF_000504245.1:WP_034274259.1
          Length = 478

 Score =  564 bits (1454), Expect = e-165
 Identities = 287/448 (64%), Positives = 344/448 (76%), Gaps = 5/448 (1%)

Query: 3   ELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFG 62
           EL  L P VWPRNT R   GVV IAG+ + +LA+ YGTPLFVIDE DF+SRC E A AF 
Sbjct: 29  ELDRLYPKVWPRNTYRAPDGVVRIAGVDVRELAETYGTPLFVIDEVDFKSRCSEYAEAFE 88

Query: 63  SGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSE 122
             A VHYA+KAFL +E+ARW++++GL LDVC+GGELA+A HA FP ER+T HGNNKSV E
Sbjct: 89  DPALVHYASKAFLSAEIARWVADKGLSLDVCSGGELAIAKHADFPMERVTFHGNNKSVDE 148

Query: 123 LTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQK 182
           L  AV AGVG +V+DS  EI RL  IA + G+ Q+VLVR+TVGVEAHTHEFI+TAHEDQK
Sbjct: 149 LETAVDAGVGTVVLDSYLEIARLAKIAEDRGVTQNVLVRVTVGVEAHTHEFIATAHEDQK 208

Query: 183 FGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEF 242
           FG S+ASG A  AVRRV + + LRLVGLHSHIGSQIFD DGFE+AA RVIGL+ D+  E 
Sbjct: 209 FGFSLASGDAAEAVRRVVSANGLRLVGLHSHIGSQIFDTDGFEVAARRVIGLIADLREEH 268

Query: 243 GPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPG 302
           GP+ + Q+  VDLGGG G++Y   D+PPP A++  ++  IV  E    GLP PK+  EPG
Sbjct: 269 GPQISEQLEIVDLGGGFGVAYTDRDNPPPPAQMVTQIRAIVRKECEFAGLPVPKIACEPG 328

Query: 303 RAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVS- 361
           RAIA PGT+TLYEVGT+KDV +     RRYVSVDGGMSDNIRTALY A YD RLVSR S 
Sbjct: 329 RAIAAPGTVTLYEVGTIKDVALGDGLSRRYVSVDGGMSDNIRTALYDAVYDCRLVSRSSD 388

Query: 362 ----DAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVG 417
               D   V +R+VGKHCESGDI+VRD W+PD++ PGDL+AVAATGAYCYS++S YN + 
Sbjct: 389 DGAVDVESVLSRVVGKHCESGDIVVRDCWLPDNLGPGDLLAVAATGAYCYSMASGYNKLL 448

Query: 418 RPAVVAVHAGNARLVLRRETVDDLLSLE 445
           +PAVVAV  G++RL+LRRET +DL  LE
Sbjct: 449 KPAVVAVRNGSSRLLLRRETEEDLTRLE 476


Lambda     K      H
   0.319    0.136    0.400 

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: 695
Number of extensions: 32
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: 447
Length of database: 478
Length adjustment: 33
Effective length of query: 414
Effective length of database: 445
Effective search space:   184230
Effective search space used:   184230
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_034274259.1 AMYHA_RS22275 (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.725490.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-142  458.8   0.0   7.4e-142  458.6   0.0    1.0  1  NCBI__GCF_000504245.1:WP_034274259.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034274259.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  458.6   0.0  7.4e-142  7.4e-142       6     416 ..      47     476 ..      42     477 .. 0.96

  Alignments for each domain:
  == domain 1  score: 458.6 bits;  conditional E-value: 7.4e-142
                             TIGR01048   6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldv 78 
                                           dg + i+gvd++elae++gtPl+v+de ++++r+++++eaf++  +lv+YA+KA+ + +++r++a++Gl+ldv
  NCBI__GCF_000504245.1:WP_034274259.1  47 DGVVRIAGVDVRELAETYGTPLFVIDEVDFKSRCSEYAEAFED-PALVHYASKAFLSAEIARWVADKGLSLDV 118
                                           78999************************************97.58*************************** PP

                             TIGR01048  79 vsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpd 151
                                           +sgGEl++a++A ++ e+++f+gn+ks +ele+a+++++ ++++ds  e+++l +ia++ g +++vl+Rv+++
  NCBI__GCF_000504245.1:WP_034274259.1 119 CSGGELAIAKHADFPMERVTFHGNNKSVDELETAVDAGVGTVVLDSYLEIARLAKIAEDRGVTQNVLVRVTVG 191
                                           ************************************************************************* PP

                             TIGR01048 152 vdaktheyisTGlkesKFGieve..eaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleel 222
                                           v+a+the+i+T+++++KFG++++  +a+ea++++++ + l+lvG+h HIGSqi+d+++f+ aa++v+ l+++l
  NCBI__GCF_000504245.1:WP_034274259.1 192 VEAHTHEFIATAHEDQKFGFSLAsgDAAEAVRRVVSANGLRLVGLHSHIGSQIFDTDGFEVAARRVIGLIADL 264
                                           **********************98899********************************************** PP

                             TIGR01048 223 kee.....gieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elgl.klklilEpGRslvanagv 288
                                           +ee     + +le +dlGGG+g++y++ +++p +++++ ++ + ++ke+   gl  +k+ +EpGR+++a+++v
  NCBI__GCF_000504245.1:WP_034274259.1 265 REEhgpqiSEQLEIVDLGGGFGVAYTDRDNPPPPAQMVTQIRAIVRKECeFAGLpVPKIACEPGRAIAAPGTV 337
                                           *99988777899*************************************7778889***************** PP

                             TIGR01048 289 lltrVesvKeves.....rkfvlvDagmndliRpalYeayheiaalkr.....leeeetetvdvvGplCEsgD 351
                                           +l++V+++K+v       r++v+vD+gm+d+iR+alY+a+++ ++++r       + e++  +vvG++CEsgD
  NCBI__GCF_000504245.1:WP_034274259.1 338 TLYEVGTIKDVALgdglsRRYVSVDGGMSDNIRTALYDAVYDCRLVSRssddgAVDVESVLSRVVGKHCESGD 410
                                           **********98778888*****************************9554444455777889********** PP

                             TIGR01048 352 vlakdrelp.eveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                           ++++d +lp +  +Gdllava++GAY++sm+s Yn+  +pa+v+v++g+ rl++rret edl +le
  NCBI__GCF_000504245.1:WP_034274259.1 411 IVVRDCWLPdNLGPGDLLAVAATGAYCYSMASGYNKLLKPAVVAVRNGSSRLLLRRETEEDLTRLE 476
                                           *********7789*************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (478 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: 31.00
//
[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