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_RS13940 HSERO_RS13940 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__HerbieS:HSERO_RS13940
          Length = 390

 Score =  252 bits (643), Expect = 1e-71
 Identities = 144/384 (37%), Positives = 208/384 (54%), Gaps = 15/384 (3%)

Query: 1   MQAAEILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATI---- 56
           M   + L  LV F +     N ++++ +R  L+  G+A  +    +  ++N+FAT+    
Sbjct: 1   MNTRQWLETLVAFDTTSRNSNLELITTVRDSLQQQGVASWLAHNKDKTKANLFATLPATA 60

Query: 57  GPKEAR---GYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAV 113
           GP       G ++SGH DVVP     W +DPF+L  +   LY RG+ DMKGF+A  LA V
Sbjct: 61  GPHAGSTEGGIVLSGHTDVVPVDGQKWDTDPFKLTEKDGALYARGSCDMKGFIATALALV 120

Query: 114 PKLAAMPLRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKG 173
           P+  AMP  +P+HLA S+DEE GC G P M+  + +   +  G ++GEPT M  + AHKG
Sbjct: 121 PEYLAMPRVKPIHLAFSFDEEIGCIGAPVMLEEIVKRGIKVDGCVVGEPTSMNVVVAHKG 180

Query: 174 KAAARLTVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQ 232
                  V G+S HSS   QG NAI   A ++      AD     GP++  F+ P+S++ 
Sbjct: 181 INVFACKVHGKSAHSSLTPQGCNAIEHAARLICAIRDFADGYKANGPYDQFFDVPFSTMT 240

Query: 233 IGTVKGGQAVNIIPDSCEVEFEARAISGVDPAELLAPVRK-TAEALTTL------GFEVE 285
              ++GG AVN IP+ CE  +E R + G+  A++ A + K  AE L            VE
Sbjct: 241 TNQIRGGIAVNTIPELCEFTYEFRNLPGMSVADIQAQIDKYIAEVLLPKMRTEFPDARVE 300

Query: 286 WQELSAYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGR 345
               +  PAL     A +  L+  LTG      V+YGTEAGLFQ+ GI  I+CGPGDIG 
Sbjct: 301 IDNFAGSPALEAVEQAAITELVRALTGDRQTRKVAYGTEAGLFQQIGIPTIVCGPGDIGN 360

Query: 346 AHKPDEYILIDELMACRAMVEALG 369
           AHKP+E++ + ++  C   +  LG
Sbjct: 361 AHKPNEFVTLAQMEHCEQFLRKLG 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: 354
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: 390
Length adjustment: 30
Effective length of query: 344
Effective length of database: 360
Effective search space:   123840
Effective search space used:   123840
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_RS13940 HSERO_RS13940 (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.21387.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.1e-120  387.5   0.0   3.6e-120  387.3   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS13940  HSERO_RS13940 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS13940  HSERO_RS13940 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.3   0.0  3.6e-120  3.6e-120       3     364 ..       7     383 ..       5     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 387.3 bits;  conditional E-value: 3.6e-120
                                  TIGR01892   3 lakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllav....iGpk..egagglvl 64 
                                                l+ Lvafd++s+ sn++li+ v+d l+++gva     + d+ +k nl+a+     Gp+  + +gg+vl
  lcl|FitnessBrowser__HerbieS:HSERO_RS13940   7 LETLVAFDTTSRNSNLELITTVRDSLQQQGVASWLAHNKDK-TKANLFATlpatAGPHagSTEGGIVL 73 
                                                789******************************99999999.*****98522226998445589**** PP

                                  TIGR01892  65 sGhtDvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDee 132
                                                sGhtDvvPvd+++W +Dpf+Ltekdg LY+rG++DmkGF+a++La vp+  a++  kP+hl++s+Dee
  lcl|FitnessBrowser__HerbieS:HSERO_RS13940  74 SGHTDVVPVDGQKWDTDPFKLTEKDGALYARGSCDMKGFIATALALVPEYLAMPRVKPIHLAFSFDEE 141
                                                ******************************************************************** PP

                                  TIGR01892 133 vglaGakklieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaa 197
                                                +g+ Ga+ ++e +     + +  +vGePts+  v ahkG+  ++ +v+G+++hss + +G +aie aa
  lcl|FitnessBrowser__HerbieS:HSERO_RS13940 142 IGCIGAPVMLEEIVkrgIKVDGCVVGEPTSMNVVVAHKGINVFACKVHGKSAHSSLTPQGCNAIEHAA 209
                                                *************9555567899********************************************* PP

                                  TIGR01892 198 kllarlvaladklkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellal 264
                                                +l+  + + ad  k  +++++ F++p++t++  +++GG avn i++ Ce++ e+R +pGm  ++++a+
  lcl|FitnessBrowser__HerbieS:HSERO_RS13940 210 RLICAIRDFADGYKAnGPYDQFFDVPFSTMTTNQIRGGIAVNTIPELCEFTYEFRNLPGMSVADIQAQ 277
                                                ************9986889999********************************************** PP

                                  TIGR01892 265 lekiaee.....vkekapgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqe 326
                                                + k  +e     ++++ p+  v++++    pale+ e+a + +l++ l+G+ +++ v+ygteagl+q+
  lcl|FitnessBrowser__HerbieS:HSERO_RS13940 278 IDKYIAEvllpkMRTEFPDARVEIDNFAGSPALEAVEQAAITELVRALTGDrQTRKVAYGTEAGLFQQ 345
                                                ***99987777778899**********************************99*************** PP

                                  TIGR01892 327 lGieavvlGPGdidqahqpdeYveieelkrcrallerl 364
                                                +Gi+++v+GPGdi++ah+p+e+v + ++++c+++l++l
  lcl|FitnessBrowser__HerbieS:HSERO_RS13940 346 IGIPTIVCGPGDIGNAHKPNEFVTLAQMEHCEQFLRKL 383
                                                ***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (390 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.34
//
[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