Alignments for a candidate for dapC in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Pseudarthrobacter sulfonivorans Ar51

Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_058931843.1 AU252_RS17705 succinyldiaminopimelate transaminase

Query= BRENDA::Q82IK5
         (364 letters)



>NCBI__GCF_001484605.1:WP_058931843.1
          Length = 382

 Score =  402 bits (1034), Expect = e-117
 Identities = 207/368 (56%), Positives = 255/368 (69%), Gaps = 11/368 (2%)

Query: 8   LPTFPWDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSPGYPTVWGTPE 67
           LP +PW+ + PY A+A+ HP G V+LS+GTPVDP P LIQ AL AAAD+PGYPTV GT  
Sbjct: 12  LPDYPWEAMTPYLAKASEHPGGAVNLSIGTPVDPTPALIQDALRAAADAPGYPTVHGTVP 71

Query: 68  LRDALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPTQLGLGPGDKVAHPRLAYPTYEV 127
           LR+A+  W ERR G  G+   +++P VGSKELVAWLP  LGL PGD V  P++AYPTY++
Sbjct: 72  LREAIAAWFERRRGVPGLDPKNIMPTVGSKELVAWLPLLLGLKPGDVVVRPKVAYPTYDI 131

Query: 128 GARLARADHVVYDDPTELDPTG---LKLLWLNSPSNPTGKVLSKAELTRIVAWAREHGIL 184
           GA  A    V  D   ELD      ++L+W+NSP NPTG V     L  +VA ARE G +
Sbjct: 132 GATFAGVTSVATDHLDELDNATRARVRLIWVNSPGNPTGSVRDVESLKALVAQARELGAV 191

Query: 185 VFSDECYLELGWEA-------DPV-SVLHPDVCGGSYEGIVSVHSLSKRSNLAGYRAAFL 236
           V SDECY ELGW A       +PV S+L P V GGS+EG+++V+SLSK+SN+AGYRAAF+
Sbjct: 192 VASDECYAELGWGAWDAQRGGEPVPSILDPRVSGGSHEGLLAVYSLSKQSNVAGYRAAFV 251

Query: 237 AGDPAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERYAARRTALRDALLSH 296
           AGDPA++  L+  RKH GM+   P Q A+  ALGDD HV+ Q++ Y  RR  L  AL   
Sbjct: 252 AGDPAIMANLVNSRKHAGMIVPYPVQEAMRVALGDDTHVQAQKDLYRGRRERLVPALQGF 311

Query: 297 GFRIEHSEASLYLWATRGESCWDTVAHLADLGILVAPGDFYGSAGEQFVRVALTATDERV 356
           G  I+ S+A LYLW+T GES WDTVA LA+ GI+V PG FYG AG  FVRVALT TDER+
Sbjct: 312 GLEIKDSDAGLYLWSTAGESTWDTVARLAERGIVVGPGVFYGEAGNGFVRVALTGTDERI 371

Query: 357 AAAVRRLA 364
            AAV RLA
Sbjct: 372 DAAVARLA 379


Lambda     K      H
   0.319    0.135    0.420 

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: 550
Number of extensions: 23
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: 364
Length of database: 382
Length adjustment: 30
Effective length of query: 334
Effective length of database: 352
Effective search space:   117568
Effective search space used:   117568
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_058931843.1 AU252_RS17705 (succinyldiaminopimelate transaminase)
to HMM TIGR03539 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

# 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/TIGR03539.hmm
# target sequence database:        /tmp/gapView.15772.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03539  [M=357]
Accession:   TIGR03539
Description: DapC_actino: succinyldiaminopimelate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-177  574.2   0.8   5.7e-177  574.0   0.8    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058931843.1  AU252_RS17705 succinyldiaminopim


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058931843.1  AU252_RS17705 succinyldiaminopimelate transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  574.0   0.8  5.7e-177  5.7e-177       1     356 [.      12     378 ..      12     379 .. 0.98

  Alignments for each domain:
  == domain 1  score: 574.0 bits;  conditional E-value: 5.7e-177
                                 TIGR03539   1 lPdfPWdklaeakakaashpdGivdlsvGtPvdpvpalirealaeaadapgyPqtaGteelreaivdal 69 
                                               lPd+PW++++++ aka++hp+G v+ls+GtPvdp+pali++al +aadapgyP+++Gt  lreai++++
  lcl|NCBI__GCF_001484605.1:WP_058931843.1  12 LPDYPWEAMTPYLAKASEHPGGAVNLSIGTPVDPTPALIQDALRAAADAPGYPTVHGTVPLREAIAAWF 80 
                                               8******************************************************************** PP

                                 TIGR03539  70 errlgvkgldeeavlPviGtkelvallPtllGlgagdtvviPevayPtyevgarlagaeavaaddltel 138
                                               err+gv+gld+++++P++G+kelva+lP llGl++gd+vv+P+vayPty++ga++ag + va+d+l+el
  lcl|NCBI__GCF_001484605.1:WP_058931843.1  81 ERRRGVPGLDPKNIMPTVGSKELVAWLPLLLGLKPGDVVVRPKVAYPTYDIGATFAGVTSVATDHLDEL 149
                                               ********************************************************************* PP

                                 TIGR03539 139 dp...ekvkliwlnsPanPtGrvlsveelrkvvalarergvvvasdecylelgWege........avsv 196
                                               d+   ++v+liw+nsP+nPtG+v++ve+l+++va+are g+vvasdecy+elgW +         ++s+
  lcl|NCBI__GCF_001484605.1:WP_058931843.1 150 DNatrARVRLIWVNSPGNPTGSVRDVESLKALVAQARELGAVVASDECYAELGWGAWdaqrggepVPSI 218
                                               99776789*********************************************97766779999999** PP

                                 TIGR03539 197 ldpevcggdlegllavhslskrsnlagyragfvaGdealvaellevrkhaGlmvpaPvqaamvaaladd 265
                                               ldp+v+gg++egllav+slsk+sn+agyra+fvaGd+a++a+l+++rkhaG++vp+Pvq+am++al+dd
  lcl|NCBI__GCF_001484605.1:WP_058931843.1 219 LDPRVSGGSHEGLLAVYSLSKQSNVAGYRAAFVAGDPAIMANLVNSRKHAGMIVPYPVQEAMRVALGDD 287
                                               ********************************************************************* PP

                                 TIGR03539 266 ehvaeqkeryaarrellkaalekaGfriehseaglylWatrgedaretvdrlaelGilvaPGdfygeag 334
                                               +hv++qk++y+ rre+l +al+ +G++i+ s+aglylW+t+ge++++tv+rlae+Gi+v+PG fygeag
  lcl|NCBI__GCF_001484605.1:WP_058931843.1 288 THVQAQKDLYRGRRERLVPALQGFGLEIKDSDAGLYLWSTAGESTWDTVARLAERGIVVGPGVFYGEAG 356
                                               ********************************************************************* PP

                                 TIGR03539 335 kefvrvaltatderiaaaverl 356
                                               + fvrvalt+tderi+aav+rl
  lcl|NCBI__GCF_001484605.1:WP_058931843.1 357 NGFVRVALTGTDERIDAAVARL 378
                                               *********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (357 nodes)
Target sequences:                          1  (382 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: 10.54
//
[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