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_RS30425 AZOBR_RS30425 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__azobra:AZOBR_RS30425
          Length = 385

 Score =  292 bits (747), Expect = 1e-83
 Identities = 159/376 (42%), Positives = 228/376 (60%), Gaps = 10/376 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           +IL +LV F +V    N D++ W +  LE+ G    ++P  +G ++N+FA++GP +  G 
Sbjct: 9   DILERLVAFPTVSRDSNLDLILWAKERLEAAGATTRLVPSEDGRKANLFASVGPADRPGV 68

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           ++SGH DVVP     WTSDPFRL   A  LYGRGT DMKGF+AA +A   + +   L +P
Sbjct: 69  LLSGHTDVVPVDGQAWTSDPFRLTRRAGNLYGRGTADMKGFVAAAMALAQRASGRTLSQP 128

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           LHLALSYDEE GC GV  +I  +  L  +P   I+GEPT M+ + AHKGK A R+  RG 
Sbjct: 129 LHLALSYDEEVGCLGVRRLIDMMAALPVRPRFCIVGEPTLMQVVTAHKGKTALRIDCRGV 188

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQAVN 243
             HSS   QG+NAIH    +LT      +R+   G  +  ++ P++++  G ++GG A+N
Sbjct: 189 ECHSSLAPQGMNAIHMACDMLTGLRRLQERVQTEGSRDADYDVPWTTIHAGVIQGGSALN 248

Query: 244 IIPDSCEVEFEARAISGVDPAE-LLAPVRKTAEALTTL------GFEVEWQELSAYPALS 296
           I+P+ C ++ E R +   DP E LL  VR  A A+ T          VE  ELS+YP+L 
Sbjct: 249 IVPNHCRLDMEIRHLP-QDPVEPLLDAVRAEAAAIETRARSAFPAAAVEIAELSSYPSLD 307

Query: 297 LEPDAPLAALLEELTGREALPAVSYGTEAGLF-QRAGIDAIICGPGDIGRAHKPDEYILI 355
            + D+ + + ++ LTG  +L  +S+GTE GLF QR  +  ++CGPG IG AHKPDE+I  
Sbjct: 308 TDGDSEVVSFVKALTGGNSLGKISFGTEGGLFQQRLSLPTVVCGPGSIGEAHKPDEFIAE 367

Query: 356 DELMACRAMVEALGAR 371
           ++L AC  M++ L  R
Sbjct: 368 EQLAACDRMLDLLLTR 383


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: 367
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 AZOBR_RS30425 AZOBR_RS30425 (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.9820.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-122  394.6   0.0   2.5e-122  394.4   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS30425  AZOBR_RS30425 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS30425  AZOBR_RS30425 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.4   0.0  2.5e-122  2.5e-122       1     362 [.       9     378 ..       9     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 394.4 bits;  conditional E-value: 2.5e-122
                                 TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtD 69 
                                               +il++Lvaf++vs+ sn+dli +++++le++g +++ +p  dg  k nl+a++Gp++ + g++lsGhtD
  lcl|FitnessBrowser__azobra:AZOBR_RS30425   9 DILERLVAFPTVSRDSNLDLILWAKERLEAAGATTRLVPSEDG-RKANLFASVGPAD-RPGVLLSGHTD 75 
                                               79*****************************************.9***********9.*********** PP

                                 TIGR01892  70 vvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGa 138
                                               vvPvd++aWtsDpfrLt ++g LYgrGtaDmkGF+a+++a ++      L +Plhl+ls+Deevg++G+
  lcl|FitnessBrowser__azobra:AZOBR_RS30425  76 VVPVDGQAWTSDPFRLTRRAGNLYGRGTADMKGFVAAAMALAQRASGRTLSQPLHLALSYDEEVGCLGV 144
                                               ********************************************************************* PP

                                 TIGR01892 139 kklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlv 204
                                               ++li+++a    rp+  ivGePt ++ v ahkGk + ++  rG e hss + +G++ai++a ++l+ l 
  lcl|FitnessBrowser__azobra:AZOBR_RS30425 145 RRLIDMMAalpVRPRFCIVGEPTLMQVVTAHKGKTALRIDCRGVECHSSLAPQGMNAIHMACDMLTGLR 213
                                               *****9998889********************************************************* PP

                                 TIGR01892 205 aladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee. 271
                                               +l+++++  +  +  +++p++t++ G+++GG+a ni+++ C+l +e+R +p  + e ll  +++ a++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS30425 214 RLQERVQTeGSRDADYDVPWTTIHAGVIQGGSALNIVPNHCRLDMEIRHLPQDPVEPLLDAVRAEAAAi 282
                                               ******985788999************************************999999*****9999983 PP

                                 TIGR01892 272 ...vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllq.elGieavvlG 335
                                                  ++   p+  v++ els +p+l+++ d+e+v +++ l+G  ++  +s+gte gl+q +l +++vv+G
  lcl|FitnessBrowser__azobra:AZOBR_RS30425 283 etrARSAFPAAAVEIAELSSYPSLDTDGDSEVVSFVKALTGGnSLGKISFGTEGGLFQqRLSLPTVVCG 351
                                               33344557999*****************************87699***********963699******* PP

                                 TIGR01892 336 PGdidqahqpdeYveieelkrcralle 362
                                               PG+i++ah+pde++  e+l +c+ +l 
  lcl|FitnessBrowser__azobra:AZOBR_RS30425 352 PGSIGEAHKPDEFIAEEQLAACDRMLD 378
                                               ***********************9986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.25
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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