Alignments for a candidate for argE in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Acidovorax sp. GW101-3H11

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate Ac3H11_4519 Acetylornithine deacetylase (EC 3.5.1.16)

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4519
          Length = 372

 Score =  217 bits (552), Expect = 5e-61
 Identities = 124/356 (34%), Positives = 192/356 (53%), Gaps = 9/356 (2%)

Query: 21  NNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGYIISGHMDVVPAAETGW 80
           N +++ +IR +L   G+   +    +  ++N+FAT+G  +  G I+SGH D VP     W
Sbjct: 11  NLELIHFIRDHLAKLGVKSRLTFNEDKTKANLFATLGEGKPAGIILSGHTDTVPWDGQDW 70

Query: 81  TSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRPLHLALSYDEEAGCRGV 140
           T DP    V+   LYGRG+ DMK F+   ++   +         +HLA SY+EE GC GV
Sbjct: 71  TMDPLSALVKDGNLYGRGSADMKAFIGIAVSHAEQFLHSDAPFAIHLAFSYEEEIGCFGV 130

Query: 141 PHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGRSGHSSRPDQGLNAIHG 200
             +IA L +   +PL  I+GEPT M    AHKG    +  VRG+  HSS     +NAI  
Sbjct: 131 KELIADLRDANIKPLACIVGEPTSMVPAIAHKGVYRYKCCVRGKEAHSSLTPHSVNAIEM 190

Query: 201 VAGVL--TQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQAVNIIPDSCEVEFEARAI 258
            A V+   + +AE        FE  F+ P+S+  +G   GG A N++P   E  +E R +
Sbjct: 191 AARVVGRVRDMAEGFEKNEPRFEG-FDVPFSTSSVGQFHGGIADNVVPRDAEFRYEFRDL 249

Query: 259 SGVDPAELLAPVRKTAEALTTLGFEV------EWQELSAYPALSLEPDAPLAALLEELTG 312
              + A++ A V   A++L     +V       ++ +   P+     D P+  L +EL+G
Sbjct: 250 PTANAAQMQAEVVAYAKSLEPAMKKVAPAAGFAFETICEIPSFLGSKDDPVTRLAQELSG 309

Query: 313 REALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILIDELMACRAMVEAL 368
            ++   V++GTEAGLF+ AGI  ++CGPG I +AH+PDEY+ +++L  C A ++ L
Sbjct: 310 EKSTTLVAFGTEAGLFKNAGISTVVCGPGSIQQAHQPDEYVSLEQLARCEAFMQGL 365


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: 308
Number of extensions: 11
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: 372
Length adjustment: 30
Effective length of query: 344
Effective length of database: 342
Effective search space:   117648
Effective search space used:   117648
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 Ac3H11_4519 (Acetylornithine deacetylase (EC 3.5.1.16))
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.31685.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   7.5e-107  343.5   0.0   8.5e-107  343.3   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4519  Acetylornithine deacetylase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4519  Acetylornithine deacetylase (EC 3.5.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.3   0.0  8.5e-107  8.5e-107       7     363 ..       1     364 [.       1     366 [. 0.95

  Alignments for each domain:
  == domain 1  score: 343.3 bits;  conditional E-value: 8.5e-107
                                        TIGR01892   7 vafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGht 68 
                                                      v +++vs +sn++li++++d+l++lgv+ +   + ++++k nl+a+ G  +  +g++lsGht
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4519   1 VRMNTVSHHSNLELIHFIRDHLAKLGVKSRL-TFNEDKTKANLFATLGEGK-PAGIILSGHT 60 
                                                      6799***********************9765.566666**********777.89******** PP

                                        TIGR01892  69 DvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaD 130
                                                      D+vP d++ Wt Dp+   +kdg LYgrG+aDmk F+ +++  + +    +    +hl++s++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4519  61 DTVPWDGQDWTMDPLSALVKDGNLYGRGSADMKAFIGIAVSHAEQFLHSDAPFAIHLAFSYE 122
                                                      ****************************************99999999999999******** PP

                                        TIGR01892 131 eevglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrG 189
                                                      ee+g+ G+k+li+ l     +p   ivGePts+v+  ahkG    k  vrG+e+hss + + 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4519 123 EEIGCFGVKELIADLRdanIKPLACIVGEPTSMVPAIAHKGVYRYKCCVRGKEAHSSLTPHS 184
                                                      *************9988889****************************************** PP

                                        TIGR01892 190 vsaielaakllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlel 250
                                                      v+aie+aa++++r+ ++a+  ++ e+  e+F++p++t  +G+ +GG a n++++  e+  e+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4519 185 VNAIEMAARVVGRVRDMAEGFEKnEPRFEGFDVPFSTSSVGQFHGGIADNVVPRDAEFRYEF 246
                                                      *********************9967788********************************** PP

                                        TIGR01892 251 RpipGmdpeellallekiaee....vkekapgfevkveelsatpaleleedaelvallekla 308
                                                      R +p  + ++++a++ + a++    +k+ ap+ +   e+   +p++   +d ++ +l+++l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4519 247 RDLPTANAAQMQAEVVAYAKSlepaMKKVAPAAGFAFETICEIPSFLGSKDDPVTRLAQELS 308
                                                      *************99998887667788999******************************** PP

                                        TIGR01892 309 Ga.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelkrcraller 363
                                                      G+ ++  v++gteagl++++Gi++vv+GPG+i+qahqpdeYv +e+l rc+a+++ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4519 309 GEkSTTLVAFGTEAGLFKNAGISTVVCGPGSIQQAHQPDEYVSLEQLARCEAFMQG 364
                                                      **78899**********************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (372 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: 00:00:00.01
# Mc/sec: 9.90
//
[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