GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Azospirillum brasilense Sp245

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate AZOBR_RS31030 AZOBR_RS31030 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__azobra:AZOBR_RS31030
          Length = 398

 Score =  263 bits (673), Expect = 5e-75
 Identities = 146/374 (39%), Positives = 209/374 (55%), Gaps = 12/374 (3%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           E+L  L+ F +     N D++ +IR +L   G++  ++   E  ++N++ATIGP +  G 
Sbjct: 19  ELLRDLIAFDTTSRNSNLDLIHYIRDHLAELGVSSTLVFNEERTKANLYATIGPMDRGGV 78

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
            +SGH DVVP  +  W+SDPF L     +L+GRGT DMKGF+AA LA  P   A  L  P
Sbjct: 79  CLSGHTDVVPVDDQDWSSDPFTLTERDGKLFGRGTADMKGFIAAALAMAPDFLAANLTTP 138

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           +H A SYDEE GC GVP ++ +L  +  +P   I+GEPT MR I  HKGK A R  V G 
Sbjct: 139 VHYAFSYDEELGCLGVPGLLTQLAGMAVKPRLCIVGEPTRMRVIVGHKGKVALRCRVHGH 198

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLV-GGPFEHVFEPPYSSLQIGTVKGGQAVN 243
           + HSS   QG+NA+   A +++       R    GPF+H ++ PY+++  G ++GG A N
Sbjct: 199 ACHSSLAPQGVNAVEYAAELVSFLRGMGRRFAEQGPFDHDYDIPYTTVHTGVMEGGTARN 258

Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEAL--------TTLGFEVEWQELSAYPAL 295
           I+P     EFE R ++    A +L  +R  A+ L           GF   W+ LS  PAL
Sbjct: 259 IVPSDASFEFEIRHLADHPVAPMLKELRDFAKTLEPEMRAVRPDAGF--SWETLSDSPAL 316

Query: 296 SLEPDAPLAALLEELTGREALPAVSYGTEAGLFQR-AGIDAIICGPGDIGRAHKPDEYIL 354
              P++    L++ L  +     V++GTE  LF   A I A++CGPGDI +AHKPDEY+ 
Sbjct: 317 DTPPESEEVTLVKNLAEQNGHGKVAFGTEGALFTSIANIPAVVCGPGDIEQAHKPDEYVE 376

Query: 355 IDELMACRAMVEAL 368
           + EL      +  L
Sbjct: 377 LSELARAERFLHRL 390


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: 375
Number of extensions: 10
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: 398
Length adjustment: 30
Effective length of query: 344
Effective length of database: 368
Effective search space:   126592
Effective search space used:   126592
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 AZOBR_RS31030 AZOBR_RS31030 (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.8140.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.3e-118  379.7   0.0   8.3e-118  379.5   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS31030  AZOBR_RS31030 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS31030  AZOBR_RS31030 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  379.5   0.0  8.3e-118  8.3e-118       1     364 [.      19     390 ..      19     391 .. 0.96

  Alignments for each domain:
  == domain 1  score: 379.5 bits;  conditional E-value: 8.3e-118
                                 TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                               e+l++L+afd++s+ sn+dli+y++d+l+elgv+   + + + ++k nl a+iGp + +gg+ lsGhtD
  lcl|FitnessBrowser__azobra:AZOBR_RS31030  19 ELLRDLIAFDTTSRNSNLDLIHYIRDHLAELGVSSTLVFNEE-RTKANLYATIGPMD-RGGVCLSGHTD 85 
                                               6799******************************98776655.5************9.*********** PP

                                 TIGR01892  70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138
                                               vvPvd++ W+sDpf+Lte+dg+L+grGtaDmkGF+a++La +pd  aa+L  P+h ++s+Dee g++G+
  lcl|FitnessBrowser__azobra:AZOBR_RS31030  86 VVPVDDQDWSSDPFTLTERDGKLFGRGTADMKGFIAAALAMAPDFLAANLTTPVHYAFSYDEELGCLGV 154
                                               ********************************************************************* PP

                                 TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204
                                               + l+ +la    +p+l ivGePt+++ +  hkGk++ + +v+G+  hss + +Gv+a+e aa+l++ l 
  lcl|FitnessBrowser__azobra:AZOBR_RS31030 155 PGLLTQLAgmaVKPRLCIVGEPTRMRVIVGHKGKVALRCRVHGHACHSSLAPQGVNAVEYAAELVSFLR 223
                                               ****99988889********************************************************* PP

                                 TIGR01892 205 aladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee. 271
                                               ++  +  + +++++ ++ py+t++ G+++GG+a ni+++   +++e+R ++  + + +l++l++ a++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS31030 224 GMGRRFAEqGPFDHDYDIPYTTVHTGVMEGGTARNIVPSDASFEFEIRHLADHPVAPMLKELRDFAKTl 292
                                               *****98879*************************************************9999998875 PP

                                 TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqe.lGieavvlG 335
                                                  +++  p+ +  +e+ls  pal++++++e v l+++la +     v++gte +l+++ + i+avv+G
  lcl|FitnessBrowser__azobra:AZOBR_RS31030 293 epeMRAVRPDAGFSWETLSDSPALDTPPESEEVTLVKNLAEQnGHGKVAFGTEGALFTSiANIPAVVCG 361
                                               566778899*******************************9977889********99983579****** PP

                                 TIGR01892 336 PGdidqahqpdeYveieelkrcrallerl 364
                                               PGdi+qah+pdeYve++el r++ +l+rl
  lcl|FitnessBrowser__azobra:AZOBR_RS31030 362 PGDIEQAHKPDEYVELSELARAERFLHRL 390
                                               *************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (398 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: 10.55
//
[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