Alignments for a candidate for argE in Pseudomonas putida KT2440

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.14341.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  lcl|FitnessBrowser__Putida:PP_3571  PP_3571 putative Acetylornithine


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3571  PP_3571 putative Acetylornithine deacetylase
   #    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 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvdea 76 
                                         +la+L++f +vs+ sn++li +++dyl+elgv+ e   +++g +k nl+a++Gp++  gg+vlsGhtDvvPvd++
  lcl|FitnessBrowser__Putida:PP_3571  14 LLARLIGFATVSRDSNLALIGFIRDYLAELGVECELFHNPEG-TKANLFATVGPRD-VGGVVLSGHTDVVPVDGQ 86 
                                         6899**************************************.************9.9***************** PP

                           TIGR01892  77 aWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala...rr 148
                                         aWt +pf L e+dgrLYgrGtaDmkGF+a vLaavp   a++L+ P+hl++s+Deevg++G++++++al     +
  lcl|FitnessBrowser__Putida:PP_3571  87 AWTVEPFALSERDGRLYGRGTADMKGFIASVLAAVPAFLAQPLRMPVHLAFSYDEEVGCLGVRSMLAALQqrpCK 161
                                         *******************************************************************99966667 PP

                           TIGR01892 149 palaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edleeaFtpp 222
                                         p+l ++GePt+l++v  hkGk +++ +v+G   hs+++  Gv+aie aakl+++l +  + l    +++e F+pp
  lcl|FitnessBrowser__Putida:PP_3571 162 PRLCLIGEPTELKPVLGHKGKLAMRCQVQGAACHSAYAPYGVNAIEYAAKLIGKLGEIGEALALpVHHDERFDPP 236
                                         89************************************************************98799******** PP

                           TIGR01892 223 yatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkveelsatpal 292
                                         ++t++ G++kGG+a ni++++Ce+ +e+R++pG + +++  +l++ ae+     +++ + +  ++   lsa+p+l
  lcl|FitnessBrowser__Putida:PP_3571 237 FSTVQAGVIKGGRALNIVPDECEFDFEVRALPGFEAQAVADQLQTYAEAellprMRKVNTASAIRLAPLSAYPGL 311
                                         **********************************************998888766666777788888999***** PP

                           TIGR01892 293 eleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcrallerlv 365
                                         +++ed+e+++l++ l+G+ +  +v++gte gl+ ++Gi++vv+GPG++dq h+pde+v +e+l+ c+a+l rlv
  lcl|FitnessBrowser__Putida:PP_3571 312 ATPEDSEAARLVALLSGSdTFGTVAFGTEGGLFDQAGIPTVVCGPGSMDQGHKPDEFVSVEQLRGCDAMLLRLV 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.97
//
[ok]

This GapMind analysis is from Apr 09 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