Alignments for a candidate for argE in Tistlia consotensis USBA 355

GapMind for Amino acid biosynthesis

Alignments for a candidate for argE in Tistlia consotensis USBA 355

Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_085121734.1 B9O00_RS06895 acetylornithine deacetylase

Query= BRENDA::Q92Y75
         (374 letters)



>NCBI__GCF_900177295.1:WP_085121734.1
          Length = 391

 Score =  280 bits (715), Expect = 6e-80
 Identities = 149/365 (40%), Positives = 206/365 (56%), Gaps = 8/365 (2%)

Query: 5   EILGKLVGFRSVVGLPNNDVVSWIRGYLESHGIAVDVLPGPEGDRSNIFATIGPKEARGY 64
           E+L  LVGF +     N  ++ W+  YL  +G+A        G ++N+ ATIGP    G 
Sbjct: 10  EMLAILVGFDTTSRESNLKLIDWVEAYLADYGVACRRSYDDAGGKANLLATIGPSVEGGI 69

Query: 65  IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLAAMPLRRP 124
           ++SGH DVVP     WTSDPFR+     RLYGRGT DMK F A  LA VP     PL RP
Sbjct: 70  VLSGHTDVVPVDGQSWTSDPFRMVARNGRLYGRGTADMKAFSAVALALVPDFLERPLARP 129

Query: 125 LHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVRGR 184
           +HLALSYDEE GC GV  ++A L     +P   ++GEPT MR + AHKG +     + G+
Sbjct: 130 IHLALSYDEEVGCIGVHRLVADLSANLPRPGLVMVGEPTEMRVVNAHKGVSGFVTRIHGK 189

Query: 185 SGHSSRPDQGLNAIHGVAGVLTQAVAEADRLVGGPFEHV-FEPPYSSLQIGTVKGGQAVN 243
           S HSS+P +G NAI   A ++      A+    GP     FEPP+++  IG ++GG A+N
Sbjct: 190 SAHSSQPHRGGNAIVAAARLIAFLHEMAEEKKTGPQSSAGFEPPHTTFGIGVIQGGSALN 249

Query: 244 IIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGF-------EVEWQELSAYPALS 296
           I+ + C+ ++E R +   DPAE+L    + A  +            E+  + L+A P L+
Sbjct: 250 IVAEHCQFQWEFRRVPADDPAEILGRFERYAREVVLPDLRRHAPDAEIVTETLAAVPPLA 309

Query: 297 LEPDAPLAALLEELTGREALPAVSYGTEAGLFQRAGIDAIICGPGDIGRAHKPDEYILID 356
            E D     LL+ LT       VSYGTE G+FQ+AG+  ++CGPG I +AH+PDE+I   
Sbjct: 310 PEDDGLAETLLKRLTDANQAHVVSYGTEGGVFQQAGLSTVVCGPGSIDQAHQPDEFIEAK 369

Query: 357 ELMAC 361
           +L  C
Sbjct: 370 QLELC 374


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: 429
Number of extensions: 19
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: 391
Length adjustment: 30
Effective length of query: 344
Effective length of database: 361
Effective search space:   124184
Effective search space used:   124184
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 WP_085121734.1 B9O00_RS06895 (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.1955639.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-127  409.9   0.0   5.5e-127  409.7   0.0    1.0  1  NCBI__GCF_900177295.1:WP_085121734.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177295.1:WP_085121734.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.7   0.0  5.5e-127  5.5e-127       1     364 [.      10     381 ..      10     382 .. 0.96

  Alignments for each domain:
  == domain 1  score: 409.7 bits;  conditional E-value: 5.5e-127
                             TIGR01892   1 eilakLvafdsvsarsnvdlieyvedyleelgvavevlpvadgaeksnllaviGpkegagglvlsGhtDvvPv 73 
                                           e+la Lv+fd++s+ sn++li++ve+yl++ gva ++     g  k nlla+iGp++ +gg+vlsGhtDvvPv
  NCBI__GCF_900177295.1:WP_085121734.1  10 EMLAILVGFDTTSRESNLKLIDWVEAYLADYGVACRRSYDDAG-GKANLLATIGPSV-EGGIVLSGHTDVVPV 80 
                                           57899******************************99876666.8***********9.*************** PP

                             TIGR01892  74 deaaWtsDpfrLtekdgrLYgrGtaDmkGFlalvLaavpdlaaakLkkPlhlvlsaDeevglaGakklieala 146
                                           d+++WtsDpfr+  ++grLYgrGtaDmk F a++La vpd    +L +P+hl+ls+Deevg+ G+++l++ l 
  NCBI__GCF_900177295.1:WP_085121734.1  81 DGQSWTSDPFRMVARNGRLYGRGTADMKAFSAVALALVPDFLERPLARPIHLALSYDEEVGCIGVHRLVADLS 153
                                           *********************************************************************9887 PP

                             TIGR01892 147 ...rrpalaivGePtslvavRahkGkasakvtvrGreghssrpdrGvsaielaakllarlvaladklkr.edl 215
                                              +rp l++vGePt+++ v ahkG   +  +++G+++hss+p+rG +ai  aa+l+a l ++a++ k   + 
  NCBI__GCF_900177295.1:WP_085121734.1 154 anlPRPGLVMVGEPTEMRVVNAHKGVSGFVTRIHGKSAHSSQPHRGGNAIVAAARLIAFLHEMAEEKKTgPQS 226
                                           7889************************************************************999983556 PP

                             TIGR01892 216 eeaFtppyatlniGtvkGGkavniiaaaCelvlelRpipGmdpeellallekiaee.....vkekapgfevkv 283
                                             +F+pp++t  iG+++GG+a ni+a+ C+++ e+R +p  dp+e+l+ +e  a e     ++++ap+ e+++
  NCBI__GCF_900177295.1:WP_085121734.1 227 SAGFEPPHTTFGIGVIQGGSALNIVAEHCQFQWEFRRVPADDPAEILGRFERYAREvvlpdLRRHAPDAEIVT 299
                                           678*************************************************9999777778899******** PP

                             TIGR01892 284 eelsatpaleleedaelvalleklaGa.aaevvsygteagllqelGieavvlGPGdidqahqpdeYveieelk 355
                                           e+l a p l++e+d+ ++ ll++l+ a +a+vvsygte g +q++G+++vv+GPG+idqahqpde++e ++l+
  NCBI__GCF_900177295.1:WP_085121734.1 300 ETLAAVPPLAPEDDGLAETLLKRLTDAnQAHVVSYGTEGGVFQQAGLSTVVCGPGSIDQAHQPDEFIEAKQLE 372
                                           *************************9889******************************************** PP

                             TIGR01892 356 rcrallerl 364
                                            c +++ rl
  NCBI__GCF_900177295.1:WP_085121734.1 373 LCAEVMLRL 381
                                           *****9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (391 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: 16.88
//
[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 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