GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Burkholderia phytofirmans PsJN

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate BPHYT_RS11720 BPHYT_RS11720 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__BFirm:BPHYT_RS11720
          Length = 387

 Score =  299 bits (766), Expect = 8e-86
 Identities = 156/372 (41%), Positives = 223/372 (59%), Gaps = 10/372 (2%)

Query: 6   ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65
           +L +L+GF +V    N +++ +IRGYL   G+  ++    E  ++N+FATIGP+E  G +
Sbjct: 9   LLERLIGFATVSRDSNLEMIDFIRGYLGELGVESELFYNAERSKANLFATIGPREGGGIV 68

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     WT D FRL     RLYGRG  DMKG++A+VLAAVP L    L+ P+
Sbjct: 69  LSGHTDVVPVEGQAWTVDAFRLTERDGRLYGRGAADMKGYIASVLAAVPGLRERELKLPV 128

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           HLA SYDEE GC GV  M+A L +   +P   +IGEPT ++ +  HKGK A R  V+G  
Sbjct: 129 HLAFSYDEEVGCLGVRPMLAELAQRAHKPALCLIGEPTELKPVLGHKGKLAMRCQVKGAP 188

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH--VFEPPYSSLQIGTVKGGQAVN 243
            HS+    G+NAI   A ++ + + E   L+  P  H   F+PP+S++Q G + GG+A+N
Sbjct: 189 CHSAYAPYGVNAIQYAARMIGR-LEEIGELLARPEHHDARFDPPFSTVQTGVINGGRALN 247

Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEA-------LTTLGFEVEWQELSAYPALS 296
           I+P  CE +FE RA+ G D   +   ++  AEA             ++ +Q LSAYP L+
Sbjct: 248 IVPAECEFDFEVRALPGFDANRVADELQIYAEAELLPKMRAVKSDTDIRFQSLSAYPGLA 307

Query: 297 LEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILID 356
             PD+  A LL  L+G      V++GTE GLF  AGI  ++CGPG + + HKPDE++ + 
Sbjct: 308 TSPDSEAARLLALLSGSTEYGTVAFGTEGGLFDEAGIPTVVCGPGSMDQGHKPDEFVTVA 367

Query: 357 ELMACRAMVEAL 368
           +L  C AM+  L
Sbjct: 368 QLRECDAMLARL 379


Lambda     K      H
   0.319    0.137    0.410 

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: 413
Number of extensions: 13
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: 374
Length of database: 387
Length adjustment: 30
Effective length of query: 344
Effective length of database: 357
Effective search space:   122808
Effective search space used:   122808
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 BPHYT_RS11720 BPHYT_RS11720 (acetylornithine deacetylase)
to HMM TIGR01892 (argE: acetylornithine deacetylase (ArgE) (EC 3.5.1.16))

# 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/TIGR01892.hmm
# target sequence database:        /tmp/gapView.26813.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01892  [M=365]
Accession:   TIGR01892
Description: AcOrn-deacetyl: acetylornithine deacetylase (ArgE)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   3.3e-129  417.0   0.0   3.8e-129  416.8   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS11720  BPHYT_RS11720 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS11720  BPHYT_RS11720 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.8   0.0  3.8e-129  3.8e-129       2     364 ..       9     379 ..       8     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: 416.8 bits;  conditional E-value: 3.8e-129
                                TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvv 71 
                                              +l++L++f +vs+ sn+++i+++++yl elgv+ e   +a+   k nl+a+iGp+e  gg+vlsGhtDvv
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720   9 LLERLIGFATVSRDSNLEMIDFIRGYLGELGVESELFYNAER-SKANLFATIGPRE-GGGIVLSGHTDVV 76 
                                              6899************************************99.*************.79*********** PP

                                TIGR01892  72 PvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkl 141
                                              Pv+++aWt D+frLte+dgrLYgrG+aDmkG++a vLaavp l   +Lk P+hl++s+Deevg++G++ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720  77 PVEGQAWTVDAFRLTERDGRLYGRGAADMKGYIASVLAAVPGLRERELKLPVHLAFSYDEEVGCLGVRPM 146
                                              ********************************************************************** PP

                                TIGR01892 142 ieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvalad 208
                                              ++ la   ++pal ++GePt+l++v  hkGk +++ +v+G   hs+++  Gv+ai+ aa++++rl++  +
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720 147 LAELAqraHKPALCLIGEPTELKPVLGHKGKLAMRCQVKGAPCHSAYAPYGVNAIQYAARMIGRLEEIGE 216
                                              *99997778899********************************************************** PP

                                TIGR01892 209 klkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....v 272
                                               l r e+++  F+pp++t++ G+++GG+a ni++a+Ce+ +e+R++pG d +++  +l+  ae+     +
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720 217 LLARpEHHDARFDPPFSTVQTGVINGGRALNIVPAECEFDFEVRALPGFDANRVADELQIYAEAellpkM 286
                                              ****999999*************************************************99998888766 PP

                                TIGR01892 273 kekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidq 341
                                              ++ + +++++ + lsa+p+l++ +d+e+++ll+ l+G+ +  +v++gte gl+ e+Gi++vv+GPG++dq
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720 287 RAVKSDTDIRFQSLSAYPGLATSPDSEAARLLALLSGStEYGTVAFGTEGGLFDEAGIPTVVCGPGSMDQ 356
                                              6777788889999*************************8999**************************** PP

                                TIGR01892 342 ahqpdeYveieelkrcrallerl 364
                                               h+pde+v + +l++c+a+l+rl
  lcl|FitnessBrowser__BFirm:BPHYT_RS11720 357 GHKPDEFVTVAQLRECDAMLARL 379
                                              ********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (387 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.63
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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:

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:

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:

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:

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