Alignments for a candidate for pscS in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for pscS in Methanococcus maripaludis C5

Align O-phospho-L-seryl-tRNA:Cys-tRNA synthase (EC 2.5.1.73) (characterized)
to candidate WP_011868122.1 MMARC5_RS01795 O-phospho-L-seryl-tRNA:Cys-tRNA synthase

Query= BRENDA::A4FWT8
         (380 letters)



>NCBI__GCF_000016125.1:WP_011868122.1
          Length = 380

 Score =  765 bits (1976), Expect = 0.0
 Identities = 380/380 (100%), Positives = 380/380 (100%)

Query: 1   MEINTDKYKNITRNLEREMINLNPIQRGGILPTESKKIIYEYWDGYSVCDYCSGRLDRIE 60
           MEINTDKYKNITRNLEREMINLNPIQRGGILPTESKKIIYEYWDGYSVCDYCSGRLDRIE
Sbjct: 1   MEINTDKYKNITRNLEREMINLNPIQRGGILPTESKKIIYEYWDGYSVCDYCSGRLDRIE 60

Query: 61  TPPINEFLEDMSKFLGMDITRPTHGARESKYAVMNSICKEGDYVVLDGNAHYTSYVAIER 120
           TPPINEFLEDMSKFLGMDITRPTHGARESKYAVMNSICKEGDYVVLDGNAHYTSYVAIER
Sbjct: 61  TPPINEFLEDMSKFLGMDITRPTHGARESKYAVMNSICKEGDYVVLDGNAHYTSYVAIER 120

Query: 121 AKLNYEKTDIGEYPTFRVIPESYAEKIDMLEDSKKNIGLILLTHVDGNYGNVADVEKVGK 180
           AKLNYEKTDIGEYPTFRVIPESYAEKIDMLEDSKKNIGLILLTHVDGNYGNVADVEKVGK
Sbjct: 121 AKLNYEKTDIGEYPTFRVIPESYAEKIDMLEDSKKNIGLILLTHVDGNYGNVADVEKVGK 180

Query: 181 IAKSKGYPFLLNCAYSAGRMPIDGKKLNVDFIAASGHKSMAASGPCGLLSINKKYEDEVL 240
           IAKSKGYPFLLNCAYSAGRMPIDGKKLNVDFIAASGHKSMAASGPCGLLSINKKYEDEVL
Sbjct: 181 IAKSKGYPFLLNCAYSAGRMPIDGKKLNVDFIAASGHKSMAASGPCGLLSINKKYEDEVL 240

Query: 241 ETSKVNVVKELQMLGCTSRGIPILSLMASFERLIERVKKWDLELEKTRKVVNELEPLGFK 300
           ETSKVNVVKELQMLGCTSRGIPILSLMASFERLIERVKKWDLELEKTRKVVNELEPLGFK
Sbjct: 241 ETSKVNVVKELQMLGCTSRGIPILSLMASFERLIERVKKWDLELEKTRKVVNELEPLGFK 300

Query: 301 QIGEKPRNHDIIRFETPILDEIAEKDKRRGFFFYEELKRRGLGGIRRGVTKEFKMSVYGL 360
           QIGEKPRNHDIIRFETPILDEIAEKDKRRGFFFYEELKRRGLGGIRRGVTKEFKMSVYGL
Sbjct: 301 QIGEKPRNHDIIRFETPILDEIAEKDKRRGFFFYEELKRRGLGGIRRGVTKEFKMSVYGL 360

Query: 361 TNTQVDYVINSMKTIINELR 380
           TNTQVDYVINSMKTIINELR
Sbjct: 361 TNTQVDYVINSMKTIINELR 380


Lambda     K      H
   0.318    0.138    0.398 

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: 690
Number of extensions: 16
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: 380
Length of database: 380
Length adjustment: 30
Effective length of query: 350
Effective length of database: 350
Effective search space:   122500
Effective search space used:   122500
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: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011868122.1 MMARC5_RS01795 (O-phospho-L-seryl-tRNA:Cys-tRNA synthase)
to HMM TIGR02539 (pscS: O-phospho-L-seryl-tRNA:Cys-tRNA synthase (EC 2.5.1.73))

# 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/TIGR02539.hmm
# target sequence database:        /tmp/gapView.2674225.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02539  [M=370]
Accession:   TIGR02539
Description: SepCysS: O-phospho-L-seryl-tRNA:Cys-tRNA synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-175  568.2   0.1   4.5e-175  568.0   0.1    1.0  1  NCBI__GCF_000016125.1:WP_011868122.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016125.1:WP_011868122.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  568.0   0.1  4.5e-175  4.5e-175       1     369 [.      12     379 ..      12     380 .] 0.99

  Alignments for each domain:
  == domain 1  score: 568.0 bits;  conditional E-value: 4.5e-175
                             TIGR02539   1 vrkleresinlnplqrGGvlteearkallefgdGysvcdfceGlldevkkppikdfledlaeflgmdvvrvta 73 
                                           +r+lere+inlnp+qrGG+l++e++k ++e++dGysvcd+c+G+ld+++ ppi++fled+++flgmd++r+t+
  NCBI__GCF_000016125.1:WP_011868122.1  12 TRNLEREMINLNPIQRGGILPTESKKIIYEYWDGYSVCDYCSGRLDRIETPPINEFLEDMSKFLGMDITRPTH 84 
                                           6899********************************************************************* PP

                             TIGR02539  74 GareakfavmhalckeGdvvvldglahytsyvaaeraglevkevpetgspeykvkleeykevieevedesgke 146
                                           Gare+k+avm+++ckeGd+vvldg+ahytsyva era+l+ ++    ++p+++v +e+y+e i+ +ed   k+
  NCBI__GCF_000016125.1:WP_011868122.1  85 GARESKYAVMNSICKEGDYVVLDGNAHYTSYVAIERAKLNYEKTDIGEYPTFRVIPESYAEKIDMLEDS-KKN 156
                                           *******************************************************************99.89* PP

                             TIGR02539 147 valallthvdgeyGnladakkvakvcrkkgvplllncaytvGrlpvsakevkadfivgsGhksmaasapvGvl 219
                                           + l+llthvdg+yGn+ad +kv+k+++ kg p+llncay+ Gr+p+++k++++dfi +sGhksmaas+p+G+l
  NCBI__GCF_000016125.1:WP_011868122.1 157 IGLILLTHVDGNYGNVADVEKVGKIAKSKGYPFLLNCAYSAGRMPIDGKKLNVDFIAASGHKSMAASGPCGLL 229
                                           ************************************************************************* PP

                             TIGR02539 220 alkeeyedkvlrksrkfkvkevellGctsrGapivtllasfpevvervkrwdeevkktrylvkeledigvkql 292
                                           +++++yed+vl +s+   vke+++lGctsrG+pi++l+asf +++ervk+wd e++ktr +v+ele +g+kq+
  NCBI__GCF_000016125.1:WP_011868122.1 230 SINKKYEDEVLETSKVNVVKELQMLGCTSRGIPILSLMASFERLIERVKKWDLELEKTRKVVNELEPLGFKQI 302
                                           ************************************************************************* PP

                             TIGR02539 293 GekpkehdlvkfetpvfdeiakkekrrgyflyeelkkrgivGiraGltkeiklsvyGltkeqveyvvdafkei 365
                                           Gekp++hd+++fetp +deia+k+krrg+f+yeelk+rg+ Gir+G+tke+k+svyGlt+ qv+yv++++k i
  NCBI__GCF_000016125.1:WP_011868122.1 303 GEKPRNHDIIRFETPILDEIAEKDKRRGFFFYEELKRRGLGGIRRGVTKEFKMSVYGLTNTQVDYVINSMKTI 375
                                           ************************************************************************* PP

                             TIGR02539 366 veey 369
                                           ++e 
  NCBI__GCF_000016125.1:WP_011868122.1 376 INEL 379
                                           9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (370 nodes)
Target sequences:                          1  (380 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 24.60
//
[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