GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Marivita geojedonensis DPG-138

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_085637148.1 MGEO_RS10755 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_002115805.1:WP_085637148.1
          Length = 383

 Score =  252 bits (643), Expect = 1e-71
 Identities = 142/382 (37%), Positives = 200/382 (52%), Gaps = 16/382 (4%)

Query: 2   QAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEA 61
           ++ EIL  L+ F ++    N +++ ++ G LE  G   +V+    G ++N+FAT+GP   
Sbjct: 4   RSTEILRDLIAFPTISADSNFEMILYMAGLLEEAGARCEVMSSACGTKANLFATLGPDRN 63

Query: 62  RGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPL 121
            G ++SGH DVVP A+  WT DPF +      LYGRGT DMKGF+AA LA  P  A    
Sbjct: 64  GGILLSGHSDVVPVADQAWTHDPFEMIERDGLLYGRGTCDMKGFIAAALAMAPHFAKRIA 123

Query: 122 RRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTV 181
            RP+H A +YDEE GC G   +   L      P  AIIGEPT MR I  HKG        
Sbjct: 124 ERPMHFAFTYDEEVGCLGARQLADDLSARGLVPGIAIIGEPTEMRIIDGHKGCNEYSTHF 183

Query: 182 RGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQ 240
            G +GH S PD G+NA+      L   +   D L    P    F+PP++++ +G + GG 
Sbjct: 184 NGLAGHGSLPDHGVNAVEYAVRYLNHLLGLKDALRARAPKNSPFDPPWTTVNVGALTGGV 243

Query: 241 AVNIIPDSCEVEFEARAISGVDP-----------AELLAPVRKTAEALTTLGFEVEWQEL 289
           A N+I  S +V++E R +   D              +L P  K       +  EV  + +
Sbjct: 244 AHNVIAPSAQVDWEMRPVQTGDAEFVKESLQTYCETVLLPKMKEVHPGAMITTEVIGEVV 303

Query: 290 SAYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKP 349
              P      D     ++ ELTG  +   V++GTEAGLFQ  G D ++CGPG I +AHK 
Sbjct: 304 GLMPT----EDNEARRIVSELTGANSCDVVAFGTEAGLFQALGTDVVVCGPGSIEQAHKA 359

Query: 350 DEYILIDELMACRAMVEALGAR 371
           DE++ +++L  C  M+E LGAR
Sbjct: 360 DEFLALEQLSQCLTMLERLGAR 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: 390
Number of extensions: 15
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: 383
Length adjustment: 30
Effective length of query: 344
Effective length of database: 353
Effective search space:   121432
Effective search space used:   121432
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_085637148.1 MGEO_RS10755 (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.980624.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.5e-116  372.7   0.0   1.1e-115  372.6   0.0    1.0  1  NCBI__GCF_002115805.1:WP_085637148.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085637148.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.6   0.0  1.1e-115  1.1e-115       1     364 [.       7     378 ..       7     379 .. 0.97

  Alignments for each domain:
  == domain 1  score: 372.6 bits;  conditional E-value: 1.1e-115
                             TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPv 73 
                                           eil++L+af+++sa sn ++i y+++ lee+g   ev+  a g +k nl+a+ Gp + +gg++lsGh+DvvPv
  NCBI__GCF_002115805.1:WP_085637148.1   7 EILRDLIAFPTISADSNFEMILYMAGLLEEAGARCEVMSSACG-TKANLFATLGPDR-NGGILLSGHSDVVPV 77 
                                           79****************************************9.************9.9************** PP

                             TIGR01892  74 deaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala 146
                                           +++aWt+Dpf + e+dg LYgrGt+DmkGF+a++La +p+ a+    +P+h ++++Deevg++Ga++l++ l 
  NCBI__GCF_002115805.1:WP_085637148.1  78 ADQAWTHDPFEMIERDGLLYGRGTCDMKGFIAAALAMAPHFAKRIAERPMHFAFTYDEEVGCLGARQLADDLS 150
                                           **********************************************************************999 PP

                             TIGR01892 147 ...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edl 215
                                                p  ai+GePt+++ +  hkG      + +G  gh s pd+Gv+a+e a + l++l++l+d l+  ++ 
  NCBI__GCF_002115805.1:WP_085637148.1 151 argLVPGIAIIGEPTEMRIIDGHKGCNEYSTHFNGLAGHGSLPDHGVNAVEYAVRYLNHLLGLKDALRArAPK 223
                                           55566999***********************************************************975899 PP

                             TIGR01892 216 eeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkv 283
                                           +++F+pp++t+n+G + GG a n+ia + ++  e+Rp+   d e +++ l++  e+     +ke +pg  + +
  NCBI__GCF_002115805.1:WP_085637148.1 224 NSPFDPPWTTVNVGALTGGVAHNVIAPSAQVDWEMRPVQTGDAEFVKESLQTYCETvllpkMKEVHPGAMITT 296
                                           9*************************************************9999987777789999******* PP

                             TIGR01892 284 eelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelk 355
                                           e+     +l + ed+e+ +++ +l+Ga + +vv++gteagl+q lG++ vv+GPG+i+qah++de++ +e+l 
  NCBI__GCF_002115805.1:WP_085637148.1 297 EVIGEVVGLMPTEDNEARRIVSELTGAnSCDVVAFGTEAGLFQALGTDVVVCGPGSIEQAHKADEFLALEQLS 369
                                           **************************9899******************************************* PP

                             TIGR01892 356 rcrallerl 364
                                           +c  +lerl
  NCBI__GCF_002115805.1:WP_085637148.1 370 QCLTMLERL 378
                                           ******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (383 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.80
//
[ok]

This GapMind analysis is from Jul 26 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