Alignments for a candidate for aspS2 in Methanosarcina barkeri Fusaro

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Methanosarcina barkeri Fusaro

Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate WP_011308097.1 MBAR_RS16835 aspartate--tRNA(Asn) ligase

Query= SwissProt::Q8Q0R2
         (444 letters)



>NCBI__GCF_000195895.1:WP_011308097.1
          Length = 444

 Score =  835 bits (2156), Expect = 0.0
 Identities = 406/444 (91%), Positives = 430/444 (96%)

Query: 1   MSLANLRTHYTADVRPDKVENGQKVTLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKK 60
           MSLA LRTHYTADV+P+KV+NGQK+TLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKK
Sbjct: 1   MSLAKLRTHYTADVKPEKVDNGQKITLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKK 60

Query: 61  IDKDLFDAARRLVRESVISVTGSVKFEEKAPNGYELLPDEINVLNVSGSPLPMDTTGKVE 120
           IDK+LFDAARRLVRESVISVTGSVKFEEKAPNGYELLP+EI VLNV+ SPLPMDTTGKVE
Sbjct: 61  IDKELFDAARRLVRESVISVTGSVKFEEKAPNGYELLPEEITVLNVANSPLPMDTTGKVE 120

Query: 121 AELDTRLDSRFIDLRRAETTAVFKIRHESLRAIREYFVKYNFIETATPKVVATATEGGTA 180
           AELDTRLDSRFIDLRRAETTAVFKIRH++L+A REYFV+  FIETATPKVVATATEGGTA
Sbjct: 121 AELDTRLDSRFIDLRRAETTAVFKIRHQALQATREYFVQNGFIETATPKVVATATEGGTA 180

Query: 181 LFPITYFDREAFLNQSPQLFKQILMSGGFDRVFEIGPIFRAEEHDTRRHLNEATSIDVEV 240
           LFPITYFDREAFLNQSPQLFKQILMSGGFDRVFEIGPIFRAEEHDTRRHLNEATSIDVEV
Sbjct: 181 LFPITYFDREAFLNQSPQLFKQILMSGGFDRVFEIGPIFRAEEHDTRRHLNEATSIDVEV 240

Query: 241 SFADHFDVMELLENLVAYVYTRVIENCKSSLEVLGVDLKVPKTPFLKLTYDEVIEIINSR 300
           SFADHFDVME+LENLVAYVY +VIE CK SLE LG++LKVPKTPFLKLTY+EVIEIIN+R
Sbjct: 241 SFADHFDVMEILENLVAYVYAQVIEKCKPSLETLGIELKVPKTPFLKLTYNEVIEIINAR 300

Query: 301 CEEKMHWGDDLGTLGEHTVGDHVYETTGESHYFIIDWPTEIKPFYAMPYEDRPEFSKSFD 360
            EEKMHWGDDLGT GEH VG++VYETTGESHYFIIDWPTEIKPFYAMPYEDRPE+SKSFD
Sbjct: 301 SEEKMHWGDDLGTFGEHIVGNYVYETTGESHYFIIDWPTEIKPFYAMPYEDRPEYSKSFD 360

Query: 361 MMHRTMELSSGAQRIHIPSLLKNRIESQGLNPDGFEFYLKAFEFGMPPHAGWGMGCERFV 420
           MMHRTMELSSGAQRIHIP LLK+RIESQGLNP+GFEFYLKAFE+GMPPHAGWGMGCERF+
Sbjct: 361 MMHRTMELSSGAQRIHIPDLLKSRIESQGLNPEGFEFYLKAFEYGMPPHAGWGMGCERFI 420

Query: 421 MTMLGTENIRDTVLFPRDRRRLSP 444
           MTMLGTENIRDTVLFPRDRRRLSP
Sbjct: 421 MTMLGTENIRDTVLFPRDRRRLSP 444


Lambda     K      H
   0.321    0.138    0.409 

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: 778
Number of extensions: 15
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 WP_011308097.1 MBAR_RS16835 (aspartate--tRNA(Asn) ligase)
to HMM TIGR00458 (aspS: aspartate--tRNA(Asn) ligase (EC 6.1.1.23))

# 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/TIGR00458.hmm
# target sequence database:        /tmp/gapView.1152.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00458  [M=428]
Accession:   TIGR00458
Description: aspS_nondisc: aspartate--tRNA(Asn) 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.9e-198  643.3   0.1   1.1e-197  643.1   0.1    1.0  1  lcl|NCBI__GCF_000195895.1:WP_011308097.1  MBAR_RS16835 aspartate--tRNA(Asn


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195895.1:WP_011308097.1  MBAR_RS16835 aspartate--tRNA(Asn) ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  643.1   0.1  1.1e-197  1.1e-197       1     428 []       9     444 .]       9     444 .] 0.98

  Alignments for each domain:
  == domain 1  score: 643.1 bits;  conditional E-value: 1.1e-197
                                 TIGR00458   1 vysadikeek..dgkevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesv 67 
                                               +y+ad+k+ek  +g++++l gwvhe+rdlG++ fv+lrdreg  q+++ kkk++kelf  +++l +esv
  lcl|NCBI__GCF_000195895.1:WP_011308097.1   9 HYTADVKPEKvdNGQKITLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKKIDKELFDAARRLVRESV 77 
                                               79******975456******************************************************* PP

                                 TIGR00458  68 vavkGkvkekekapqgleiipeklevlneakeplPldleekveaeldtrldarfldlrrpkvqaifkir 136
                                               + v+G vk +ekap+g+e++pe++ vln a++plP+d + kveaeldtrld rf+dlrr+++ a+fkir
  lcl|NCBI__GCF_000195895.1:WP_011308097.1  78 ISVTGSVKFEEKAPNGYELLPEEITVLNVANSPLPMDTTGKVEAELDTRLDSRFIDLRRAETTAVFKIR 146
                                               ********************************************************************* PP

                                 TIGR00458 137 sevlesvreflaeegfievntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyei 205
                                               ++ l++ re++ ++gfie  tPk+va+ateGGt lf+ityf+reafl+qsPql+kq+l++ g++rv+ei
  lcl|NCBI__GCF_000195895.1:WP_011308097.1 147 HQALQATREYFVQNGFIETATPKVVATATEGGTALFPITYFDREAFLNQSPQLFKQILMSGGFDRVFEI 215
                                               ********************************************************************* PP

                                 TIGR00458 206 aPifraeehntkrhlnevisidiemafedhkdvldileelvvrvfedvaeklkkelevlevklevpeek 274
                                               +Pifraeeh+t+rhlne++sid+e++f+dh dv++ile+lv  v+ +v ek+k +le+l+++l+vp+++
  lcl|NCBI__GCF_000195895.1:WP_011308097.1 216 GPIFRAEEHDTRRHLNEATSIDVEVSFADHFDVMEILENLVAYVYAQVIEKCKPSLETLGIELKVPKTP 284
                                               ********************************************************************* PP

                                 TIGR00458 275 lerltydeaieilrakGke.ikdgedlsteaekllG.....ekmdglyfitdfPteikPfytmPdednP 337
                                               + +lty+e iei++a+ +e +++g+dl t  e ++G      + +++yfi+d+PteikPfy+mP+ed+P
  lcl|NCBI__GCF_000195895.1:WP_011308097.1 285 FLKLTYNEVIEIINARSEEkMHWGDDLGTFGEHIVGnyvyeTTGESHYFIIDWPTEIKPFYAMPYEDRP 353
                                               **************9986549***************77764455789********************** PP

                                 TIGR00458 338 eisksfdllyrdleissGaqrihdydllvekikakGlePeslksyleafkyGmPPhaGwGlGaerlvmv 406
                                               e+sksfd+++r++e+ssGaqrih  dll+ +i  +Gl+Pe++++yl+af+yGmPPhaGwG+G er++m+
  lcl|NCBI__GCF_000195895.1:WP_011308097.1 354 EYSKSFDMMHRTMELSSGAQRIHIPDLLKSRIESQGLNPEGFEFYLKAFEYGMPPHAGWGMGCERFIMT 422
                                               ********************************************************************* PP

                                 TIGR00458 407 lldlknireavlfPrdrkrltP 428
                                               +l+ +nir++vlfPrdr+rl P
  lcl|NCBI__GCF_000195895.1:WP_011308097.1 423 MLGTENIRDTVLFPRDRRRLSP 444
                                               ********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (428 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: 11.83
//
[ok]

This GapMind analysis is from Apr 10 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