GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Pseudomonas putida KT2440

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate PP_3571 PP_3571 putative Acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__Putida:PP_3571
          Length = 391

 Score =  304 bits (779), Expect = 2e-87
 Identities = 159/374 (42%), Positives = 225/374 (60%), Gaps = 20/374 (5%)

Query: 6   ILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYI 65
           +L +L+GF +V    N  ++ +IR YL   G+  ++   PEG ++N+FAT+GP++  G +
Sbjct: 14  LLARLIGFATVSRDSNLALIGFIRDYLAELGVECELFHNPEGTKANLFATVGPRDVGGVV 73

Query: 66  ISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPL 125
           +SGH DVVP     WT +PF L     RLYGRGT DMKGF+A+VLAAVP   A PLR P+
Sbjct: 74  LSGHTDVVPVDGQAWTVEPFALSERDGRLYGRGTADMKGFIASVLAAVPAFLAQPLRMPV 133

Query: 126 HLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRS 185
           HLA SYDEE GC GV  M+A L +   +P   +IGEPT ++ +  HKGK A R  V+G +
Sbjct: 134 HLAFSYDEEVGCLGVRSMLAALQQRPCKPRLCLIGEPTELKPVLGHKGKLAMRCQVQGAA 193

Query: 186 GHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEH--VFEPPYSSLQIGTVKGGQAVN 243
            HS+    G+NAI   A  L   + E    +  P  H   F+PP+S++Q G +KGG+A+N
Sbjct: 194 CHSAYAPYGVNAIE-YAAKLIGKLGEIGEALALPVHHDERFDPPFSTVQAGVIKGGRALN 252

Query: 244 IIPDSCEVEFEARAISGVD------------PAELLAPVRKTAEALTTLGFEVEWQELSA 291
           I+PD CE +FE RA+ G +             AELL  +RK   A       +    LSA
Sbjct: 253 IVPDECEFDFEVRALPGFEAQAVADQLQTYAEAELLPRMRKVNTASA-----IRLAPLSA 307

Query: 292 YPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDE 351
           YP L+   D+  A L+  L+G +    V++GTE GLF +AGI  ++CGPG + + HKPDE
Sbjct: 308 YPGLATPEDSEAARLVALLSGSDTFGTVAFGTEGGLFDQAGIPTVVCGPGSMDQGHKPDE 367

Query: 352 YILIDELMACRAMV 365
           ++ +++L  C AM+
Sbjct: 368 FVSVEQLRGCDAML 381


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: 436
Number of extensions: 14
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: 391
Length adjustment: 30
Effective length of query: 344
Effective length of database: 361
Effective search space:   124184
Effective search space used:   124184
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 PP_3571 PP_3571 (putative 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.3363016.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     1e-128  415.4   0.0   1.2e-128  415.2   0.0    1.0  1  FitnessBrowser__Putida:PP_3571  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Putida:PP_3571  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.2   0.0  1.2e-128  1.2e-128       2     365 .]      14     385 ..      13     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 415.2 bits;  conditional E-value: 1.2e-128
                       TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdeaaWts 80 
                                     +la+L++f +vs+ sn++li +++dyl+elgv+ e   +++g +k nl+a++Gp++  gg+vlsGhtDvvPvd++aWt 
  FitnessBrowser__Putida:PP_3571  14 LLARLIGFATVSRDSNLALIGFIRDYLAELGVECELFHNPEG-TKANLFATVGPRD-VGGVVLSGHTDVVPVDGQAWTV 90 
                                     6899**************************************.************9.9********************* PP

                       TIGR01892  81 DpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...rrpalaivGe 156
                                     +pf L e+dgrLYgrGtaDmkGF+a vLaavp   a++L+ P+hl++s+Deevg++G++++++al     +p+l ++Ge
  FitnessBrowser__Putida:PP_3571  91 EPFALSERDGRLYGRGTADMKGFIASVLAAVPAFLAQPLRMPVHLAFSYDEEVGCLGVRSMLAALQqrpCKPRLCLIGE 169
                                     ***************************************************************9996666789****** PP

                       TIGR01892 157 PtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edleeaFtppyatlniGtvkGG 234
                                     Pt+l++v  hkGk +++ +v+G   hs+++  Gv+aie aakl+++l +  + l    +++e F+pp++t++ G++kGG
  FitnessBrowser__Putida:PP_3571 170 PTELKPVLGHKGKLAMRCQVQGAACHSAYAPYGVNAIEYAAKLIGKLGEIGEALALpVHHDERFDPPFSTVQAGVIKGG 248
                                     ******************************************************98799******************** PP

                       TIGR01892 235 kavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkveelsatpaleleedaelvallekla 308
                                     +a ni++++Ce+ +e+R++pG + +++  +l++ ae+     +++ + +  ++   lsa+p+l+++ed+e+++l++ l+
  FitnessBrowser__Putida:PP_3571 249 RALNIVPDECEFDFEVRALPGFEAQAVADQLQTYAEAellprMRKVNTASAIRLAPLSAYPGLATPEDSEAARLVALLS 327
                                     **********************************998888766666777788888999********************* PP

                       TIGR01892 309 Ga.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                     G+ +  +v++gte gl+ ++Gi++vv+GPG++dq h+pde+v +e+l+ c+a+l rlv
  FitnessBrowser__Putida:PP_3571 328 GSdTFGTVAFGTEGGLFDQAGIPTVVCGPGSMDQGHKPDEFVSVEQLRGCDAMLLRLV 385
                                     *98889************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (391 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 14.73
//
[ok]

This GapMind analysis is from Jul 25 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:

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