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.2420238.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  FitnessBrowser__HerbieS:HSERO_RS13940  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS13940  
   #    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..egagglvlsGht 68 
                                            l+ Lvafd++s+ sn++li+ v+d l+++gva     + d+ +k nl+a+     Gp+  + +gg+vlsGht
  FitnessBrowser__HerbieS:HSERO_RS13940   7 LETLVAFDTTSRNSNLELITTVRDSLQQQGVASWLAHNKDK-TKANLFATlpatAGPHagSTEGGIVLSGHT 77 
                                            789******************************99999999.*****98522226998445589******** PP

                              TIGR01892  69 DvvPvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakk 140
                                            DvvPvd+++W +Dpf+Ltekdg LY+rG++DmkGF+a++La vp+  a++  kP+hl++s+Dee+g+ Ga+ 
  FitnessBrowser__HerbieS:HSERO_RS13940  78 DVVPVDGQKWDTDPFKLTEKDGALYARGSCDMKGFIATALALVPEYLAMPRVKPIHLAFSFDEEIGCIGAPV 149
                                            ************************************************************************ PP

                              TIGR01892 141 lieala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladk 209
                                            ++e +     + +  +vGePts+  v ahkG+  ++ +v+G+++hss + +G +aie aa+l+  + + ad 
  FitnessBrowser__HerbieS:HSERO_RS13940 150 MLEEIVkrgIKVDGCVVGEPTSMNVVVAHKGINVFACKVHGKSAHSSLTPQGCNAIEHAARLICAIRDFADG 221
                                            *****9555567899********************************************************* PP

                              TIGR01892 210 lkr.edleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkek 275
                                             k  +++++ F++p++t++  +++GG avn i++ Ce++ e+R +pGm  ++++a++ k  +e     ++++
  FitnessBrowser__HerbieS:HSERO_RS13940 222 YKAnGPYDQFFDVPFSTMTTNQIRGGIAVNTIPELCEFTYEFRNLPGMSVADIQAQIDKYIAEvllpkMRTE 293
                                            9986889999*************************************************9998777777889 PP

                              TIGR01892 276 apgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpd 346
                                             p+  v++++    pale+ e+a + +l++ l+G+ +++ v+ygteagl+q++Gi+++v+GPGdi++ah+p+
  FitnessBrowser__HerbieS:HSERO_RS13940 294 FPDARVEIDNFAGSPALEAVEQAAITELVRALTGDrQTRKVAYGTEAGLFQQIGIPTIVCGPGDIGNAHKPN 365
                                            9**********************************99*********************************** PP

                              TIGR01892 347 eYveieelkrcrallerl 364
                                            e+v + ++++c+++l++l
  FitnessBrowser__HerbieS:HSERO_RS13940 366 EFVTLAQMEHCEQFLRKL 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.94
//
[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