GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Pseudomonas fluorescens FW300-N2C3

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AO356_26745 AO356_26745 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26745
          Length = 385

 Score =  238 bits (607), Expect = 2e-67
 Identities = 134/373 (35%), Positives = 205/373 (54%), Gaps = 9/373 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           +IL +L+ F +V    N  ++ ++R  L + GI   ++    G ++N+FA+ GP++  G 
Sbjct: 7   DILKRLMAFDTVSSESNMALIEYVRDLLLTKGIESLIVQDESGKKANLFASTGPRDVPGI 66

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           ++SGH DVVPAA   WT   F   V+  R+YGRG+ DMKGF+A  + A+ +    PL RP
Sbjct: 67  LLSGHTDVVPAAGQAWTFPAFEATVQDGRIYGRGSCDMKGFIALAVDAMLEATEQPLSRP 126

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           L LALS+DEE GC GV  ++  L     +P   +IGEPT M+ +  HKGK + R   RG 
Sbjct: 127 LQLALSHDEEIGCVGVRRLLDVLHLAPVRPFLCVIGEPTNMQFVLGHKGKGSYRTYCRGL 186

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVN 243
             HSS   + +NAIH     +        +L   G  +  ++ PYS++ +G + GG+A+N
Sbjct: 187 EAHSSLAPRSVNAIHVACDFIAALRLSQQQLQEQGARDTDYDVPYSTVHVGQIVGGKALN 246

Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEALT------TLGFEVEWQELSAYPALSL 297
           I+P+ C ++FE R +   D    L  +R+ AE +       +    +E + L+ YP L  
Sbjct: 247 IVPNLCTLDFEVRNLPADDLDGFLEQMRERAELIVGEARKLSSVAAIEIETLNVYPGLDT 306

Query: 298 EPDAPLAALLEELTGREALPA-VSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYILI 355
            P       L+     +   A VS+GTE GLF QR  +  ++CGPG I +AHKPDE+I I
Sbjct: 307 HPSVEAVRFLKNFAAPDTGTAKVSFGTEGGLFKQRLDVPVVVCGPGSIEQAHKPDEFIEI 366

Query: 356 DELMACRAMVEAL 368
            ++ A    ++ L
Sbjct: 367 SQMDAGERFLQGL 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: 348
Number of extensions: 15
Number of successful extensions: 4
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: 385
Length adjustment: 30
Effective length of query: 344
Effective length of database: 355
Effective search space:   122120
Effective search space used:   122120
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 AO356_26745 AO356_26745 (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.9686.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.7e-108  348.9   0.0   1.9e-108  348.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26745  AO356_26745 acetylornithine deac


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26745  AO356_26745 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.7   0.0  1.9e-108  1.9e-108       1     364 [.       7     379 ..       7     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 348.7 bits;  conditional E-value: 1.9e-108
                                       TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglv 63 
                                                     +il++L+afd+vs  sn++lieyv+d l  +g++   ++   g +k nl+a+ Gp++   g++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26745   7 DILKRLMAFDTVSSESNMALIEYVRDLLLTKGIESLIVQDESG-KKANLFASTGPRD-VPGIL 67 
                                                     79*******************************9999988888.9***********9.9**** PP

                                       TIGR01892  64 lsGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlv 126
                                                     lsGhtDvvP++++aWt  +f  t++dgr+YgrG++DmkGF+al+++a+ +   ++L +Pl l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26745  68 LSGHTDVVPAAGQAWTFPAFEATVQDGRIYGRGSCDMKGFIALAVDAMLEATEQPLSRPLQLA 130
                                                     ************************************************9999*********** PP

                                       TIGR01892 127 lsaDeevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrp 186
                                                     ls Dee+g+ G+++l+++l     rp l ++GePt+++ v  hkGk s +   rG e+hss +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26745 131 LSHDEEIGCVGVRRLLDVLHlapVRPFLCVIGEPTNMQFVLGHKGKGSYRTYCRGLEAHSSLA 193
                                                     *****************9987889*************************************** PP

                                       TIGR01892 187 drGvsaielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvl 248
                                                      r v+ai++a +++a l   +++l++ +  +  +++py+t+++G++ GGka ni+++ C l +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26745 194 PRSVNAIHVACDFIAALRLSQQQLQEqGARDTDYDVPYSTVHVGQIVGGKALNIVPNLCTLDF 256
                                                     ************************996788999****************************** PP

                                       TIGR01892 249 elRpipGmdpeellallekiaeevkeka....pgfevkveelsatpaleleedaelvallekl 307
                                                     e+R +p  d++  l+++++ ae ++ +a        +++e+l+ +p+l++++  e+v++l++ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26745 257 EVRNLPADDLDGFLEQMRERAELIVGEArklsSVAAIEIETLNVYPGLDTHPSVEAVRFLKNF 319
                                                     *****************9999986544311103456789999********************9 PP

                                       TIGR01892 308 aGa..aaevvsygteagll.qelGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                     a     +  vs+gte gl+ q+l ++ vv+GPG+i+qah+pde++ei+++ +++ +l+ l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_26745 320 AAPdtGTAKVSFGTEGGLFkQRLDVPVVVCGPGSIEQAHKPDEFIEISQMDAGERFLQGL 379
                                                     887567889********996789*******************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (385 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.50
//
[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:

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