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

GapMind for Amino acid biosynthesis

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

Align gamma-glutamylphosphate reductase (EC 1.2.1.41) (characterized)
to candidate Echvi_2633 Echvi_2633 gamma-glutamyl phosphate reductase

Query= reanno::Cola:Echvi_2633
         (399 letters)



>FitnessBrowser__Cola:Echvi_2633
          Length = 399

 Score =  780 bits (2014), Expect = 0.0
 Identities = 399/399 (100%), Positives = 399/399 (100%)

Query: 1   MKILSTQKKNDVLASMIKIIDKNREKILTANKADLDAFQRDDQALYDRLVVNDAKIDGMI 60
           MKILSTQKKNDVLASMIKIIDKNREKILTANKADLDAFQRDDQALYDRLVVNDAKIDGMI
Sbjct: 1   MKILSTQKKNDVLASMIKIIDKNREKILTANKADLDAFQRDDQALYDRLVVNDAKIDGMI 60

Query: 61  QAVQEVKDQDDPVGKEISKRTLANGLDITNKTAPFGTIMIIYESRPDVTIEAAVLAFKAN 120
           QAVQEVKDQDDPVGKEISKRTLANGLDITNKTAPFGTIMIIYESRPDVTIEAAVLAFKAN
Sbjct: 61  QAVQEVKDQDDPVGKEISKRTLANGLDITNKTAPFGTIMIIYESRPDVTIEAAVLAFKAN 120

Query: 121 SKILLKGGKEAVNSNKVLVECWHEALEENGLSKDWIELFTLNREQTQAFLKNPSEKLDLI 180
           SKILLKGGKEAVNSNKVLVECWHEALEENGLSKDWIELFTLNREQTQAFLKNPSEKLDLI
Sbjct: 121 SKILLKGGKEAVNSNKVLVECWHEALEENGLSKDWIELFTLNREQTQAFLKNPSEKLDLI 180

Query: 181 VPRGGERLIAFVKEHAQCAVLVSGRGNNFAYVAEDADWELAKKVIINAKTNKISGCNALD 240
           VPRGGERLIAFVKEHAQCAVLVSGRGNNFAYVAEDADWELAKKVIINAKTNKISGCNALD
Sbjct: 181 VPRGGERLIAFVKEHAQCAVLVSGRGNNFAYVAEDADWELAKKVIINAKTNKISGCNALD 240

Query: 241 KILVDEKLPDFESKLADLAKSLASYKVELVAEKELVPAIEGAKEVPSEDTWYEEFLALKA 300
           KILVDEKLPDFESKLADLAKSLASYKVELVAEKELVPAIEGAKEVPSEDTWYEEFLALKA
Sbjct: 241 KILVDEKLPDFESKLADLAKSLASYKVELVAEKELVPAIEGAKEVPSEDTWYEEFLALKA 300

Query: 301 LIGKVNGLDEAIAKINKYSGGHSATILTTDKDKAATFMEQVDSAAVYHNASTRFTDGGQM 360
           LIGKVNGLDEAIAKINKYSGGHSATILTTDKDKAATFMEQVDSAAVYHNASTRFTDGGQM
Sbjct: 301 LIGKVNGLDEAIAKINKYSGGHSATILTTDKDKAATFMEQVDSAAVYHNASTRFTDGGQM 360

Query: 361 GVGAELAISTDKLHHRGPLGLEQLVTNKYYVFGSGQIRD 399
           GVGAELAISTDKLHHRGPLGLEQLVTNKYYVFGSGQIRD
Sbjct: 361 GVGAELAISTDKLHHRGPLGLEQLVTNKYYVFGSGQIRD 399


Lambda     K      H
   0.314    0.132    0.367 

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: 767
Number of extensions: 33
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: 399
Length of database: 399
Length adjustment: 31
Effective length of query: 368
Effective length of database: 368
Effective search space:   135424
Effective search space used:   135424
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate Echvi_2633 Echvi_2633 (gamma-glutamyl phosphate reductase)
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))

# 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/TIGR00407.hmm
# target sequence database:        /tmp/gapView.24643.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00407  [M=398]
Accession:   TIGR00407
Description: proA: glutamate-5-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   5.8e-111  357.0   3.2   6.6e-111  356.9   3.2    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2633  Echvi_2633 gamma-glutamyl phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2633  Echvi_2633 gamma-glutamyl phosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.9   3.2  6.6e-111  6.6e-111       8     398 .]       1     388 [.       1     388 [. 0.94

  Alignments for each domain:
  == domain 1  score: 356.9 bits;  conditional E-value: 6.6e-111
                            TIGR00407   8 laqlstaeknealskiadeLkaeaelilaanakdiaaakenGladalldrLlLteeklksiaddvkdvieLadP 81 
                                          ++ lst++kn++l+ + + + ++ e il an+ d+ a +     +al+drL ++++k+ +++++v++v + +dP
  lcl|FitnessBrowser__Cola:Echvi_2633   1 MKILSTQKKNDVLASMIKIIDKNREKILTANKADLDAFQRD--DQALYDRLVVNDAKIDGMIQAVQEVKDQDDP 72 
                                          6789*******************************998887..589**************************** PP

                            TIGR00407  82 vGkvieareldeGLklervrvPlGvlgviyearPevivdvasLclktGnaviLkGgkeavrsnkalveviqdal 155
                                          vGk i++r+l +GL + + ++P G + +iye+rP+v++++a L++k+   ++LkGgkeav+snk+lve  ++al
  lcl|FitnessBrowser__Cola:Echvi_2633  73 VGKEISKRTLANGLDITNKTAPFGTIMIIYESRPDVTIEAAVLAFKANSKILLKGGKEAVNSNKVLVECWHEAL 146
                                          ************************************************************************** PP

                            TIGR00407 156 eqtglpveavqliedpdreevkellkl.deyvdlliPrGgnelvklikeestiPvlehadGvChiyldesadla 228
                                          e+ gl++  ++l +  +re+ + +lk   e +dl++PrGg++l+  +ke+++  vl+++ G+   y+ e+ad +
  lcl|FitnessBrowser__Cola:Echvi_2633 147 EENGLSKDWIELFTL-NREQTQAFLKNpSEKLDLIVPRGGERLIAFVKEHAQCAVLVSGRGNNFAYVAEDADWE 219
                                          *************98.9*****999863689******************************************* PP

                            TIGR00407 229 kakkvivdaktqrPstCnaietLLvnkaiae..efleeLekqleekgvelradalvlkllelekateaevsked 300
                                           akkvi++akt++ s+Cna++ +Lv++++ +  + l  L+k l+   vel a++     +e  +a+e+    + 
  lcl|FitnessBrowser__Cola:Echvi_2633 220 LAKKVIINAKTNKISGCNALDKILVDEKLPDfeSKLADLAKSLASYKVELVAEKELVPAIE--GAKEVPSE-DT 290
                                          ****************************983114455677788889999999877665554..55776655.55 PP

                            TIGR00407 301 fdkeflsldLsvkivedleeaiehirqygtkhsdailtedkknaekfvkevdsaavyvnastrfadGfrfGfGa 374
                                          + +efl+l+  +  v+ l+eai+ i++y+  hs +ilt dk +a  f+++vdsaavy+nastrf+dG++ G Ga
  lcl|FitnessBrowser__Cola:Echvi_2633 291 WYEEFLALKALIGKVNGLDEAIAKINKYSGGHSATILTTDKDKAATFMEQVDSAAVYHNASTRFTDGGQMGVGA 364
                                          ************************************************************************** PP

                            TIGR00407 375 evgistqklharGPvGLeaLvsyk 398
                                          e++ist+klh rGP+GLe Lv+ k
  lcl|FitnessBrowser__Cola:Echvi_2633 365 ELAISTDKLHHRGPLGLEQLVTNK 388
                                          *********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (398 nodes)
Target sequences:                          1  (399 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: 00:00:00.02
# Mc/sec: 7.12
//
[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