Alignments for a candidate for argE in Herbaspirillum seropedicae SmR1

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.2446982.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  FitnessBrowser__HerbieS:HSERO_RS16100  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS16100  
   #    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.egagglvlsGhtDvv 71 
                                            +il+ L++f++vs+ sn+ lie+v+d+le +g  ++    a+   k nl+a+ G +  g+ g v+sGhtDvv
  FitnessBrowser__HerbieS:HSERO_RS16100  18 DILTTLIGFNTVSRESNLGLIEWVRDHLERHGAVTRLTYDAER-RKANLFATLGDAgPGRFGTVFSGHTDVV 88 
                                            79******************************77766666665.9*********9989************** PP

                              TIGR01892  72 PvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklie 143
                                            Pv +++W +Dpf   + dg+L+grG++DmkGF+a+ +a +p ++ a+L+ Plh  +s+Deevg++G+++l++
  FitnessBrowser__HerbieS:HSERO_RS16100  89 PVTGQKWDTDPFVAHVADGKLFGRGACDMKGFIAICMARLPAIDLARLHTPLHFSFSYDEEVGCLGVRELLA 160
                                            **********************************************************************99 PP

                              TIGR01892 144 ala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr 212
                                             l     rp+ +i+GePt +++v ahkGk s +  v+G+ +hss p+ G++ i  aa +  ++ + a ++++
  FitnessBrowser__HerbieS:HSERO_RS16100 161 DLQqndIRPTGVIIGEPTMMQPVIAHKGKRSYRCSVHGHAAHSSCPHLGINSIDFAAMMQLKIREIALRVRH 232
                                            9887889**************************************************9999*********99 PP

                              TIGR01892 213 .edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapg 278
                                             + +++ F++py+++      GG+a nii+++ e+v+e R +pG+dp+e+ +++++ ae+     ++ +  +
  FitnessBrowser__HerbieS:HSERO_RS16100 233 sGVQDDDFDVPYSSIATTLTSGGNAPNIIPDKAEFVFEHRFLPGIDPAEVFEEVKAYAEQeilpqMRIDGVQ 304
                                            788999**************************************************9988887777778889 PP

                              TIGR01892 279 fevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYv 349
                                            + ++ e+l+ +p++ +++d +lv  + +++G+ +a+ v +gte gl+ ++G++av++GPGdi +ah+p+e+v
  FitnessBrowser__HerbieS:HSERO_RS16100 305 GRIEFETLTSYPGMCTPADDPLVTSALRILGSeRARKVGFGTEGGLFGQAGMPAVICGPGDIAHAHKPNEFV 376
                                            9999***************************989************************************** PP

                              TIGR01892 350 eieelkrcralle 362
                                             +e+l rc+ +  
  FitnessBrowser__HerbieS:HSERO_RS16100 377 TLEQLARCERFFD 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 20.06
//
[ok]

This GapMind analysis is from Jul 25 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:

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 2024 update 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 original 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