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_085638538.1 MGEO_RS13260 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_002115805.1:WP_085638538.1
          Length = 386

 Score =  248 bits (633), Expect = 2e-70
 Identities = 145/380 (38%), Positives = 204/380 (53%), Gaps = 14/380 (3%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKE 60
           + A ++L +LV F +V    N ++V+++  YL+SH I    +  PEGD++ ++A IGP+ 
Sbjct: 3   LTARQLLERLVAFPTVSDQSNLELVNFVETYLQSHEITPTKVMNPEGDKAALYANIGPET 62

Query: 61  ARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMP 120
           A G ++SGH DVVP     W SDPF L     RLYGRGT DMKG  A  LAAVP     P
Sbjct: 63  AGGVVLSGHTDVVPVKRQDWRSDPFTLTERDGRLYGRGTCDMKGSDALALAAVPLALRKP 122

Query: 121 LRRPLHLALSYDEEAGCRGVPHMIAR-LPELCRQPLGAIIGEPTGMRAIRAHKGKAAARL 179
           L+RPL +ALSYDEE G  G P MI   L     +P   I+GEP+ M+ +  HKG    ++
Sbjct: 123 LKRPLQIALSYDEETGMTGAPPMIDHMLSHGLPRPGAVIVGEPSMMKVVTGHKGGFGYQV 182

Query: 180 TVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADR----LVGGPFEHVFEPPYSSLQIGT 235
            VRG   HSS   +G++A+  +AG L       +R       G     F PPY+++ +GT
Sbjct: 183 HVRGHEVHSSMMHEGVSAVM-MAGELVSWANRMNRQCAQATPGALAGDFVPPYTTIHVGT 241

Query: 236 VKGGQAVNIIPDSCEVEFEARAISGVDPAEL-------LAPVRKTAEALTTLGFEVEWQE 288
           + GG A NI    C  E + R + G D +E        +A +++  +A+         Q+
Sbjct: 242 ISGGTAHNITARDCRFEIDFRVVPGEDHSEWQQKFLGEVAALQRQMQAIHPDARITADQD 301

Query: 289 LSAYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHK 348
                 L+ E       L   LTG  A   VSY TE GLFQ  G+  +ICGPGDI +AH+
Sbjct: 302 FGV-AGLAPETQGEAEKLARRLTGDNATHVVSYATEGGLFQERGLSTVICGPGDIAQAHQ 360

Query: 349 PDEYILIDELMACRAMVEAL 368
           PDE++ +D+       +E L
Sbjct: 361 PDEFMSLDQFQKGEIFMERL 380


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: 361
Number of extensions: 16
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: 386
Length adjustment: 30
Effective length of query: 344
Effective length of database: 356
Effective search space:   122464
Effective search space used:   122464
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_085638538.1 MGEO_RS13260 (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.941965.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-119  385.6   0.1   1.3e-119  385.4   0.1    1.0  1  NCBI__GCF_002115805.1:WP_085638538.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085638538.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.4   0.1  1.3e-119  1.3e-119       2     365 .]       8     381 ..       7     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 385.4 bits;  conditional E-value: 1.3e-119
                             TIGR01892   2 ilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPvd 74 
                                           +l++Lvaf++vs +sn++l+++ve yl++++++  ++ +++g +k  l a iGp++ agg+vlsGhtDvvPv 
  NCBI__GCF_002115805.1:WP_085638538.1   8 LLERLVAFPTVSDQSNLELVNFVETYLQSHEITPTKVMNPEG-DKAALYANIGPET-AGGVVLSGHTDVVPVK 78 
                                           6899**************************************.***********99.**************** PP

                             TIGR01892  75 eaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala. 146
                                            + W sDpf+Lte+dgrLYgrGt+DmkG  al+Laavp    ++Lk+Pl ++ls+Dee+g++Ga+ +i+ ++ 
  NCBI__GCF_002115805.1:WP_085638538.1  79 RQDWRSDPFTLTERDGRLYGRGTCDMKGSDALALAAVPLALRKPLKRPLQIALSYDEETGMTGAPPMIDHMLs 151
                                           *************************************999999**************************9999 PP

                             TIGR01892 147 ...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr...e 213
                                              +rp  +ivGeP  ++ v  hkG    +v+vrG+e hss  ++Gvsa+++a++l++ + +++ +  +   +
  NCBI__GCF_002115805.1:WP_085638538.1 152 hglPRPGAVIVGEPSMMKVVTGHKGGFGYQVHVRGHEVHSSMMHEGVSAVMMAGELVSWANRMNRQCAQatpG 224
                                           9999*****************************************************9998888887773235 PP

                             TIGR01892 214 dleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee....vkekapgfevk 282
                                            l   F ppy+t+++Gt+ GG+a ni a+ C++++++R +pG d +e ++++    ++    +++ +p+  + 
  NCBI__GCF_002115805.1:WP_085638538.1 225 ALAGDFVPPYTTIHVGTISGGTAHNITARDCRFEIDFRVVPGEDHSEWQQKFLGEVAAlqrqMQAIHPDARIT 297
                                           67789***************************************99887776544444122267777888888 PP

                             TIGR01892 283 veelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieel 354
                                            ++     +l++e ++e+++l+++l+G+ a++vvsy+te gl+qe G+++v++GPGdi qahqpde++ ++++
  NCBI__GCF_002115805.1:WP_085638538.1 298 ADQDFGVAGLAPETQGEAEKLARRLTGDnATHVVSYATEGGLFQERGLSTVICGPGDIAQAHQPDEFMSLDQF 370
                                           88889999********************99******************************************* PP

                             TIGR01892 355 krcrallerlv 365
                                           ++++ ++erlv
  NCBI__GCF_002115805.1:WP_085638538.1 371 QKGEIFMERLV 381
                                           ********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (386 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: 00:00:00.00
# Mc/sec: 23.01
//
[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