Alignments for a candidate for sepS in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for sepS in Methanococcus maripaludis C5

Align O-phosphoserine--tRNA(Cys) ligase; O-phosphoserine--tRNA ligase; Non-canonical O-phosphoseryl-tRNA(Cys) synthetase; O-phosphoseryl-tRNA(Cys) synthetase; SepRS; EC 6.1.1.27 (characterized)
to candidate WP_011868649.1 MMARC5_RS04485 O-phosphoserine--tRNA ligase

Query= SwissProt::Q59054
         (539 letters)



>NCBI__GCF_000016125.1:WP_011868649.1
          Length = 537

 Score =  764 bits (1974), Expect = 0.0
 Identities = 362/537 (67%), Positives = 443/537 (82%), Gaps = 1/537 (0%)

Query: 3   FDIKKVLELAEKDFETAWRETRALIKDKHIDNKYPRLKPVYGKPHPVMETIERLRQAYLR 62
           F  ++++E+A KDFE AW ET+ LIK K ++  YPR+KP +GK HPV +TIE LRQAYLR
Sbjct: 2   FKREEIIEMANKDFEKAWIETKDLIKAKKVNESYPRIKPAFGKTHPVNDTIENLRQAYLR 61

Query: 63  MGFEEMINPVIVDEMEIYKQFGPEAMAVLDRCFYLAGLPRPDVGLGNEKVEIIKNLGIDI 122
           MGFEE INPVIVDE +IYKQFGPEAMAVLDRCFYLAGLPRPDVGL +EK+  I+ LGI +
Sbjct: 62  MGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKLGIKV 121

Query: 123 DEEKKERLREVLHLYKKGAIDGDDLVFEIAKALNVSNEMGLKVLETAFPEFKDLKPESTT 182
            E K E L+++LH YKKG +DGDDLV EI+ AL +S+EMGLK+LE  FPEFKDL   S+ 
Sbjct: 122 SEHK-ESLQKILHGYKKGTLDGDDLVLEISNALEISSEMGLKILEEVFPEFKDLTAVSSK 180

Query: 183 LTLRSHMTSGWFITLSSLIKKRKLPLKLFSIDRCFRREQREDRSHLMSYHSASCVVVGED 242
           LTLRSHMTSGWF+T+S L+ K+ LP KLFSIDRCFRREQ+ED+SHLM+YHSASC + GE 
Sbjct: 181 LTLRSHMTSGWFLTVSDLMNKKPLPFKLFSIDRCFRREQKEDKSHLMTYHSASCAIAGEG 240

Query: 243 VSVDDGKVVAEGLLAQFGFTKFKFKPDEKKSKYYTPETQTEVYAYHPKLGEWIEVATFGV 302
           V ++DGK +AEGLL+QFGFT FKF PDEKKSKYYTPETQTEVYAYHPKL EW+EVATFGV
Sbjct: 241 VDINDGKAIAEGLLSQFGFTNFKFIPDEKKSKYYTPETQTEVYAYHPKLKEWLEVATFGV 300

Query: 303 YSPIALAKYNIDVPVMNLGLGVERLAMIIYGYEDVRAMVYPQFYEYRLSDRDIAGMIRVD 362
           YSP+AL+KY IDVPVMNLGLGVERLAMI   + DVR MVYPQFYE++LSDR +A M+++D
Sbjct: 301 YSPVALSKYGIDVPVMNLGLGVERLAMISGNFADVREMVYPQFYEHKLSDRAVASMVKLD 360

Query: 363 KVPILDEFYNFANELIDICIANKDKESPCSVEVKREFNFNGERRVIKVEIFENEPNKKLL 422
           KVP++DE Y+   ELID C+ NKD +SPC + +++ F+F   ++ +K+ IFE E  K LL
Sbjct: 361 KVPVMDEIYDLTKELIDSCVKNKDLKSPCELTIEKTFSFGKTKKNVKINIFEKEEGKNLL 420

Query: 423 GPSVLNEVYVYDGNIYGIPPTFEGVKEQYIPILKKAKEEGVSTNIRYIDGIIYKLVAKIE 482
           GPS+LNE+YVYDGN+ GIP +F+GVKE++   L+K K EGV T IRYID + +K+ +K+E
Sbjct: 421 GPSILNEIYVYDGNVIGIPESFDGVKEEFKDFLEKGKAEGVPTGIRYIDALCFKITSKLE 480

Query: 483 EALVSNVDEFKFRVPIVRSLSDINLKIDELALKQIMGENKVIDVRGPVFLNAKVEIK 539
           EA VSN  EFK +VPIVRSLSDINLKID++ALKQIM + KVIDVRGPVFLN +V+I+
Sbjct: 481 EAFVSNTTEFKVKVPIVRSLSDINLKIDDIALKQIMSKTKVIDVRGPVFLNVEVKIE 537


Lambda     K      H
   0.320    0.140    0.403 

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: 922
Number of extensions: 33
Number of successful extensions: 2
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: 539
Length of database: 537
Length adjustment: 35
Effective length of query: 504
Effective length of database: 502
Effective search space:   253008
Effective search space used:   253008
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: 52 (24.6 bits)

Align candidate WP_011868649.1 MMARC5_RS04485 (O-phosphoserine--tRNA ligase)
to HMM TIGR00470 (sepS: O-phosphoserine--tRNA ligase (EC 6.1.1.27))

# 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/TIGR00470.hmm
# target sequence database:        /tmp/gapView.2698659.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00470  [M=533]
Accession:   TIGR00470
Description: sepS: O-phosphoserine--tRNA ligase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-260  851.3   4.3   1.4e-260  851.2   4.3    1.0  1  NCBI__GCF_000016125.1:WP_011868649.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016125.1:WP_011868649.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  851.2   4.3  1.4e-260  1.4e-260       4     533 .]       3     537 .]       1     537 [] 0.97

  Alignments for each domain:
  == domain 1  score: 851.2 bits;  conditional E-value: 1.4e-260
                             TIGR00470   4 ddkkvlelaekdfeaawkeskellkekhidekyprlkfefGkehplfetierlreaylrlGfsevvnplivde 76 
                                           + ++++e+a+kdfe+aw e+k+l+k k+ +e ypr+k+ fGk+hp+ +tie lr+aylr+Gf+e +np+ivde
  NCBI__GCF_000016125.1:WP_011868649.1   3 KREEIIEMANKDFEKAWIETKDLIKAKKVNESYPRIKPAFGKTHPVNDTIENLRQAYLRMGFEEYINPVIVDE 75 
                                           44569******************************************************************** PP

                             TIGR00470  77 veiykqfGpealavldrcfylaglprpdvGlgaekieliedlgidvsdekkerlkevlrrykkGeidGddlvl 149
                                            +iykqfGpea+avldrcfylaglprpdvGl+ eki +ie+lgi+vs++k e+l+++l+ ykkG +dGddlvl
  NCBI__GCF_000016125.1:WP_011868649.1  76 RDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKLGIKVSEHK-ESLQKILHGYKKGTLDGDDLVL 147
                                           ***********************************************999.********************** PP

                             TIGR00470 150 eiaealevedetglkvleevfpefkdlkpvsstltlrshmtsGwfitlssiadklklplklfsidrcfrreqk 222
                                           ei++ale+++e+glk+leevfpefkdl  vss+ltlrshmtsGwf+t+s++++k++lp+klfsidrcfrreqk
  NCBI__GCF_000016125.1:WP_011868649.1 148 EISNALEISSEMGLKILEEVFPEFKDLTAVSSKLTLRSHMTSGWFLTVSDLMNKKPLPFKLFSIDRCFRREQK 220
                                           ************************************************************************* PP

                             TIGR00470 223 edasrlmtyfsascvvvdeevsvddGkavaeglleqlGfekfrfrkdekkskyyipetqtevyayhpklkewi 295
                                           ed+s+lmty+sasc + +e v ++dGka+aegll q+Gf++f+f +dekkskyy+petqtevyayhpklkew+
  NCBI__GCF_000016125.1:WP_011868649.1 221 EDKSHLMTYHSASCAIAGEGVDINDGKAIAEGLLSQFGFTNFKFIPDEKKSKYYTPETQTEVYAYHPKLKEWL 293
                                           ************************************************************************* PP

                             TIGR00470 296 evatfGvyspialakydidvevmnlGlGverlamilygyedvrkmvypqiygeyrlsdrdiaemirvdkvpvt 368
                                           evatfGvysp+al+ky+idv+vmnlGlGverlami  ++ dvr+mvypq+y e++lsdr +a m+++dkvpv+
  NCBI__GCF_000016125.1:WP_011868649.1 294 EVATFGVYSPVALSKYGIDVPVMNLGLGVERLAMISGNFADVREMVYPQFY-EHKLSDRAVASMVKLDKVPVM 365
                                           ***************************************************.********************* PP

                             TIGR00470 369 aeglklaeeivetaeahadkespcsfevf...egellGrrikvevleeeentkllGpavlnevyvydGniyGi 438
                                           +e + l++e+++ + +++d +spc + +    ++  + +++k++++e+ee ++llGp++lne+yvydGn++Gi
  NCBI__GCF_000016125.1:WP_011868649.1 366 DEIYDLTKELIDSCVKNKDLKSPCELTIEktfSFGKTKKNVKINIFEKEEGKNLLGPSILNEIYVYDGNVIGI 438
                                           *************************988631144445567********************************* PP

                             TIGR00470 439 pktkelvkekyi....kakeeGvstgiryidglaykaaakieeavvseaeevkvrarivrslsdinlkieela 507
                                           p+++++vke+++    k k eGv+tgiryid+l +k++ k+eea vs++ e+kv+++ivrslsdinlki++ a
  NCBI__GCF_000016125.1:WP_011868649.1 439 PESFDGVKEEFKdfleKGKAEGVPTGIRYIDALCFKITSKLEEAFVSNTTEFKVKVPIVRSLSDINLKIDDIA 511
                                           **********9977778899***************************************************** PP

                             TIGR00470 508 lryilgknkkidvrGplfvtvkveik 533
                                           l++i+ k k+idvrGp+f++v v+i+
  NCBI__GCF_000016125.1:WP_011868649.1 512 LKQIMSKTKVIDVRGPVFLNVEVKIE 537
                                           **********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (537 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: 25.57
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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