Alignments for a candidate for argE in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Klebsiella michiganensis M5al

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate BWI76_RS12865 BWI76_RS12865 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>FitnessBrowser__Koxy:BWI76_RS12865
          Length = 389

 Score =  276 bits (707), Expect = 5e-79
 Identities = 150/378 (39%), Positives = 211/378 (55%), Gaps = 18/378 (4%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           EILG+L+ F +     N  +++WI  +L + G+   +    EG ++N++A +GP    G 
Sbjct: 7   EILGQLLAFDTTSRESNLALIAWIGDFLRARGVTSQLFYDDEGRKANLYARLGPSGPGGV 66

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           ++SGH DVVP     WT  PF L     R YGRG+ DMKGF+A VLA++    A PLR P
Sbjct: 67  MLSGHTDVVPVDGQAWTVPPFALTERDGRYYGRGSADMKGFIACVLASLEAFLAAPLRMP 126

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           LHLA SYDEE GC GV  ++  L     +P   IIGEPT MR +  HKGK A R  V G 
Sbjct: 127 LHLAFSYDEEVGCLGVRSLVDFLRASAEKPALCIIGEPTDMRPVYGHKGKLAVRCRVEGH 186

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHVFEPPYSSLQIGTVKGGQAVNI 244
           + HS+   QG+NAI   A ++ +  A  +       +  F PP  +LQ+GT++GG+A+NI
Sbjct: 187 ACHSAYAPQGVNAISYAAKLIYRLDALGESF-SQHLDRRFSPPSGTLQVGTIRGGEALNI 245

Query: 245 IPDSCEVEFEARAISGVDP------------AELLAPVRKTAEALTTLGFEVEWQELSAY 292
           +P SC  +FE R + G  P             +LL  +RK A+       ++ +Q LS Y
Sbjct: 246 VPQSCWFDFEIRYLPGTRPQAVTDALGDYAREQLLPAMRKVAQC-----SDIHFQTLSHY 300

Query: 293 PALSLEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEY 352
           P L  +P +  A  L +  G +    V+YGTE GLF  AG+  +ICGPG + + H+ DEY
Sbjct: 301 PGLLSDPQSAFARWLAQWCGSDDFTTVAYGTEGGLFDEAGVATLICGPGSMAQGHRADEY 360

Query: 353 ILIDELMACRAMVEALGA 370
           I I +   C AM++ L A
Sbjct: 361 ISIPQTERCLAMLDNLCA 378


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: 373
Number of extensions: 13
Number of successful extensions: 3
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: 389
Length adjustment: 30
Effective length of query: 344
Effective length of database: 359
Effective search space:   123496
Effective search space used:   123496
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 BWI76_RS12865 BWI76_RS12865 (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.29573.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.1e-117  379.1   0.0   1.2e-117  378.9   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS12865  BWI76_RS12865 acetylornithine de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS12865  BWI76_RS12865 acetylornithine deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.9   0.0  1.2e-117  1.2e-117       1     364 [.       7     376 ..       7     377 .. 0.96

  Alignments for each domain:
  == domain 1  score: 378.9 bits;  conditional E-value: 1.2e-117
                               TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvv 71 
                                             eil++L+afd++s+ sn++li ++ d+l++ gv+ +     +g  k nl a  Gp+ g gg++lsGhtDvv
  lcl|FitnessBrowser__Koxy:BWI76_RS12865   7 EILGQLLAFDTTSRESNLALIAWIGDFLRARGVTSQLFYDDEG-RKANLYARLGPS-GPGGVMLSGHTDVV 75 
                                             79*******************************9999888888.9*********87.59************ PP

                               TIGR01892  72 PvdeaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakkli 142
                                             Pvd++aWt  pf Lte+dgr YgrG+aDmkGF+a+vLa +    aa+L+ Plhl++s+Deevg++G+++l+
  lcl|FitnessBrowser__Koxy:BWI76_RS12865  76 PVDGQAWTVPPFALTERDGRYYGRGSADMKGFIACVLASLEAFLAAPLRMPLHLAFSYDEEVGCLGVRSLV 146
                                             *********************************************************************** PP

                               TIGR01892 143 eala...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladkl 210
                                             + l    ++pal i+GePt++++v  hkGk + + +v+G+  hs+++ +Gv+ai  aakl+ rl al +  
  lcl|FitnessBrowser__Koxy:BWI76_RS12865 147 DFLRasaEKPALCIIGEPTDMRPVYGHKGKLAVRCRVEGHACHSAYAPQGVNAISYAAKLIYRLDALGESF 217
                                             98766679*************************************************************98 PP

                               TIGR01892 211 kredleeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkeka 276
                                               ++l+  F pp  tl++Gt++GG+a ni++++C + +e+R +pG  p++++  l + a e     +++ a
  lcl|FitnessBrowser__Koxy:BWI76_RS12865 218 S-QHLDRRFSPPSGTLQVGTIRGGEALNIVPQSCWFDFEIRYLPGTRPQAVTDALGDYAREqllpaMRKVA 287
                                             7.5799*************************************************9999887887565666 PP

                               TIGR01892 277 pgfevkveelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpd 346
                                                +++ ++ls +p+l  ++++  ++ l++  G+    +v+ygte gl+ e+G+ ++++GPG++ q h++d
  lcl|FitnessBrowser__Koxy:BWI76_RS12865 288 QCSDIHFQTLSHYPGLLSDPQSAFARWLAQWCGSdDFTTVAYGTEGGLFDEAGVATLICGPGSMAQGHRAD 358
                                             778999***************************9899********************************** PP

                               TIGR01892 347 eYveieelkrcrallerl 364
                                             eY+ i + +rc a+l +l
  lcl|FitnessBrowser__Koxy:BWI76_RS12865 359 EYISIPQTERCLAMLDNL 376
                                             **************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (389 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.64
//
[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