Alignments for a candidate for argH in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Echinicola vietnamensis KMM 6221, DSM 17526

Align arginosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate Echvi_3852 Echvi_3852 argininosuccinate lyase

Query= reanno::Cola:Echvi_3852
         (444 letters)



>FitnessBrowser__Cola:Echvi_3852
          Length = 444

 Score =  887 bits (2293), Expect = 0.0
 Identities = 444/444 (100%), Positives = 444/444 (100%)

Query: 1   MKLWQKNTTSTKEVEQFTIGRDPEFDIVLAPFDVLGSLAHATMLESIDLLTKEELAILKK 60
           MKLWQKNTTSTKEVEQFTIGRDPEFDIVLAPFDVLGSLAHATMLESIDLLTKEELAILKK
Sbjct: 1   MKLWQKNTTSTKEVEQFTIGRDPEFDIVLAPFDVLGSLAHATMLESIDLLTKEELAILKK 60

Query: 61  GLKDIYQEIQEGTFTIDPGVEDVHSQVEFLLTERYGDVGKKLHSGRSRNDQVAVDLKLYY 120
           GLKDIYQEIQEGTFTIDPGVEDVHSQVEFLLTERYGDVGKKLHSGRSRNDQVAVDLKLYY
Sbjct: 61  GLKDIYQEIQEGTFTIDPGVEDVHSQVEFLLTERYGDVGKKLHSGRSRNDQVAVDLKLYY 120

Query: 121 RAVIQEVLDDAKALFDLLLTLAEKHQNDLMPGYTHTQLAMPSSFGLWFGAMAESLAEDME 180
           RAVIQEVLDDAKALFDLLLTLAEKHQNDLMPGYTHTQLAMPSSFGLWFGAMAESLAEDME
Sbjct: 121 RAVIQEVLDDAKALFDLLLTLAEKHQNDLMPGYTHTQLAMPSSFGLWFGAMAESLAEDME 180

Query: 181 LWLAAYNLADRNPLGSAAGYGSSFPLNRTMTTRLLGFKDMHYNVINAQNNRGKTEKAIAF 240
           LWLAAYNLADRNPLGSAAGYGSSFPLNRTMTTRLLGFKDMHYNVINAQNNRGKTEKAIAF
Sbjct: 181 LWLAAYNLADRNPLGSAAGYGSSFPLNRTMTTRLLGFKDMHYNVINAQNNRGKTEKAIAF 240

Query: 241 AMAGMAGTLNRLSADIIIFMNQHFGFVKFPDNLTTGSSIMPHKKNPDVFELIRAKANQIQ 300
           AMAGMAGTLNRLSADIIIFMNQHFGFVKFPDNLTTGSSIMPHKKNPDVFELIRAKANQIQ
Sbjct: 241 AMAGMAGTLNRLSADIIIFMNQHFGFVKFPDNLTTGSSIMPHKKNPDVFELIRAKANQIQ 300

Query: 301 SGPQNLMMQMTNTTTGYHRDLQLLKETTFPDFEKLKDCLQITKFMLEHIEIKPDILEDKF 360
           SGPQNLMMQMTNTTTGYHRDLQLLKETTFPDFEKLKDCLQITKFMLEHIEIKPDILEDKF
Sbjct: 301 SGPQNLMMQMTNTTTGYHRDLQLLKETTFPDFEKLKDCLQITKFMLEHIEIKPDILEDKF 360

Query: 361 YKHLFSVEVVNDLVLQGMPFRDAYKKVGLDIESDDFAPDHTVNHSHEGSIGQLCLDEIRT 420
           YKHLFSVEVVNDLVLQGMPFRDAYKKVGLDIESDDFAPDHTVNHSHEGSIGQLCLDEIRT
Sbjct: 361 YKHLFSVEVVNDLVLQGMPFRDAYKKVGLDIESDDFAPDHTVNHSHEGSIGQLCLDEIRT 420

Query: 421 KMETALAKFDFSAIETSYQKLLEA 444
           KMETALAKFDFSAIETSYQKLLEA
Sbjct: 421 KMETALAKFDFSAIETSYQKLLEA 444


Lambda     K      H
   0.319    0.135    0.389 

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: 826
Number of extensions: 14
Number of successful extensions: 1
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: 444
Length of database: 444
Length adjustment: 32
Effective length of query: 412
Effective length of database: 412
Effective search space:   169744
Effective search space used:   169744
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate Echvi_3852 Echvi_3852 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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/TIGR00838.hmm
# target sequence database:        /tmp/gapView.16867.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.8e-104  336.2   0.1   2.3e-104  335.8   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3852  Echvi_3852 argininosuccinate lya


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3852  Echvi_3852 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.8   0.1  2.3e-104  2.3e-104      11     387 ..      11     388 ..       3     396 .. 0.94

  Alignments for each domain:
  == domain 1  score: 335.8 bits;  conditional E-value: 2.3e-104
                            TIGR00838  11 dkavaefn..aslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklelevdaeDiH 82 
                                           k+v++f+  +  +fD  la  D+ gs+ah+++L+   +lt+ee + l+++L+++++e++eg++++++ +eD+H
  lcl|FitnessBrowser__Cola:Echvi_3852  11 TKEVEQFTigRDPEFDIVLAPFDVLGSLAHATMLESIDLLTKEELAILKKGLKDIYQEIQEGTFTIDPGVEDVH 84 
                                          45666665225679************************************************************ PP

                            TIGR00838  83 lavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmpgytHLq 156
                                          ++vE  l+++ g dvgkklh+grsRnDqva+dl+ly r+ ++e+++  k+l + l+ +Aek+++ lmpgytH q
  lcl|FitnessBrowser__Cola:Echvi_3852  85 SQVEFLLTERYG-DVGKKLHSGRSRNDQVAVDLKLYYRAVIQEVLDDAKALFDLLLTLAEKHQNDLMPGYTHTQ 157
                                          ************.************************************************************* PP

                            TIGR00838 157 rAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensldavsdR 230
                                           A P +++ ++ a ae+l++D+e  l a++ ++++PlGs+A  g+sf+++r+++++lLgF+++  n ++a  +R
  lcl|FitnessBrowser__Cola:Echvi_3852 158 LAMPSSFGLWFGAMAESLAEDMELWLAAYNLADRNPLGSAAGYGSSFPLNRTMTTRLLGFKDMHYNVINAQNNR 231
                                          ************************************************************************** PP

                            TIGR00838 231 DfiiEll.saaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGnltg 303
                                               ++ +a+a ++  l rl+ ++i+f  + fgfv+++d++++gssimP KKnpDv EliR+k+ +++   + 
  lcl|FitnessBrowser__Cola:Echvi_3852 232 GKTEKAIaFAMAGMAGTLNRLSADIIIFMNQHFGFVKFPDNLTTGSSIMPHKKNPDVFELIRAKANQIQSGPQN 305
                                          98766542556667789********************************************************* PP

                            TIGR00838 304 lltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrkGv 377
                                          l++ +  + + Y +Dlq  ke+ f   ++++++l++ +++l++++++ + le++  k+     ++ + lv +G+
  lcl|FitnessBrowser__Cola:Echvi_3852 306 LMMQMTNTTTGYHRDLQLLKETTFPDFEKLKDCLQITKFMLEHIEIKPDILEDKFYKH-LFSVEVVNDLVLQGM 378
                                          **************************************************88777665.567899999****** PP

                            TIGR00838 378 PFReaheivG 387
                                          PFR+a++ vG
  lcl|FitnessBrowser__Cola:Echvi_3852 379 PFRDAYKKVG 388
                                          *******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (444 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: 11.18
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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