GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Herbaspirillum seropedicae SmR1

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate HSERO_RS16100 HSERO_RS16100 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__HerbieS:HSERO_RS16100
          Length = 400

 Score =  266 bits (680), Expect = 7e-76
 Identities = 146/371 (39%), Positives = 207/371 (55%), Gaps = 12/371 (3%)

Query: 2   QAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEA 61
           Q  +IL  L+GF +V    N  ++ W+R +LE HG    +    E  ++N+FAT+G    
Sbjct: 15  QTLDILTTLIGFNTVSRESNLGLIEWVRDHLERHGAVTRLTYDAERRKANLFATLGDAGP 74

Query: 62  R--GYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAM 119
              G + SGH DVVP     W +DPF   V   +L+GRG  DMKGF+A  +A +P +   
Sbjct: 75  GRFGTVFSGHTDVVPVTGQKWDTDPFVAHVADGKLFGRGACDMKGFIAICMARLPAIDLA 134

Query: 120 PLRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARL 179
            L  PLH + SYDEE GC GV  ++A L +   +P G IIGEPT M+ + AHKGK + R 
Sbjct: 135 RLHTPLHFSFSYDEEVGCLGVRELLADLQQNDIRPTGVIIGEPTMMQPVIAHKGKRSYRC 194

Query: 180 TVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRLV--GGPFEHVFEPPYSSLQIGTVK 237
           +V G + HSS P  G+N+I   A ++   + E    V   G  +  F+ PYSS+      
Sbjct: 195 SVHGHAAHSSCPHLGINSI-DFAAMMQLKIREIALRVRHSGVQDDDFDVPYSSIATTLTS 253

Query: 238 GGQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAE-------ALTTLGFEVEWQELS 290
           GG A NIIPD  E  FE R + G+DPAE+   V+  AE        +  +   +E++ L+
Sbjct: 254 GGNAPNIIPDKAEFVFEHRFLPGIDPAEVFEEVKAYAEQEILPQMRIDGVQGRIEFETLT 313

Query: 291 AYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPD 350
           +YP +    D PL      + G E    V +GTE GLF +AG+ A+ICGPGDI  AHKP+
Sbjct: 314 SYPGMCTPADDPLVTSALRILGSERARKVGFGTEGGLFGQAGMPAVICGPGDIAHAHKPN 373

Query: 351 EYILIDELMAC 361
           E++ +++L  C
Sbjct: 374 EFVTLEQLARC 384


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: 380
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: 400
Length adjustment: 30
Effective length of query: 344
Effective length of database: 370
Effective search space:   127280
Effective search space used:   127280
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 HSERO_RS16100 HSERO_RS16100 (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.15460.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.7e-112  360.6   0.0   5.4e-112  360.4   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS16100  HSERO_RS16100 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS16100  HSERO_RS16100 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.4   0.0  5.4e-112  5.4e-112       1     362 [.      18     389 ..      18     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 360.4 bits;  conditional E-value: 5.4e-112
                                  TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpk.egagglvlsGh 67 
                                                +il+ L++f++vs+ sn+ lie+v+d+le +g  ++    a+   k nl+a+ G +  g+ g v+sGh
  lcl|FitnessBrowser__HerbieS:HSERO_RS16100  18 DILTTLIGFNTVSRESNLGLIEWVRDHLERHGAVTRLTYDAER-RKANLFATLGDAgPGRFGTVFSGH 84 
                                                79******************************77766666665.9*********9989********** PP

                                  TIGR01892  68 tDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevgl 135
                                                tDvvPv +++W +Dpf   + dg+L+grG++DmkGF+a+ +a +p ++ a+L+ Plh  +s+Deevg+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16100  85 TDVVPVTGQKWDTDPFVAHVADGKLFGRGACDMKGFIAICMARLPAIDLARLHTPLHFSFSYDEEVGC 152
                                                ******************************************************************** PP

                                  TIGR01892 136 aGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakll 200
                                                +G+++l++ l     rp+ +i+GePt +++v ahkGk s +  v+G+ +hss p+ G++ i  aa + 
  lcl|FitnessBrowser__HerbieS:HSERO_RS16100 153 LGVRELLADLQqndIRPTGVIIGEPTMMQPVIAHKGKRSYRCSVHGHAAHSSCPHLGINSIDFAAMMQ 220
                                                ******999887889**************************************************999 PP

                                  TIGR01892 201 arlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallek 267
                                                 ++ + a ++++ + +++ F++py+++      GG+a nii+++ e+v+e R +pG+dp+e+ +++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS16100 221 LKIREIALRVRHsGVQDDDFDVPYSSIATTLTSGGNAPNIIPDKAEFVFEHRFLPGIDPAEVFEEVKA 288
                                                9*********99788999************************************************** PP

                                  TIGR01892 268 iaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGi 329
                                                 ae+     ++ +  ++ ++ e+l+ +p++ +++d +lv  + +++G+ +a+ v +gte gl+ ++G+
  lcl|FitnessBrowser__HerbieS:HSERO_RS16100 289 YAEQeilpqMRIDGVQGRIEFETLTSYPGMCTPADDPLVTSALRILGSeRARKVGFGTEGGLFGQAGM 356
                                                99888877777788899999***************************989****************** PP

                                  TIGR01892 330 eavvlGPGdidqahqpdeYveieelkrcralle 362
                                                +av++GPGdi +ah+p+e+v +e+l rc+ +  
  lcl|FitnessBrowser__HerbieS:HSERO_RS16100 357 PAVICGPGDIAHAHKPNEFVTLEQLARCERFFD 389
                                                *****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (400 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.23
//
[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