Alignments for a candidate for aspS2 in Methanobacterium lacus AL-21

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Methanobacterium lacus AL-21

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_013644957.1 METBO_RS06815 aspartate--tRNA(Asn) ligase

Query= SwissProt::O26328
         (437 letters)



>NCBI__GCF_000191585.1:WP_013644957.1
          Length = 439

 Score =  683 bits (1763), Expect = 0.0
 Identities = 330/436 (75%), Positives = 377/436 (86%)

Query: 2   LLGDLRRTHYSKDIEPEMDGDEVTVMGWVHEIRDLGGIIFVLLRDRDGLIQITAPSKKIE 61
           LL D RRTHYSK I+PEM  ++V +MGW+HE+RDLGGIIFVLLRDRDG+ Q+TAPSKKIE
Sbjct: 4   LLEDCRRTHYSKQIKPEMKDEDVVIMGWIHEMRDLGGIIFVLLRDRDGVTQVTAPSKKIE 63

Query: 62  KDLFKSIRKLKKESVVAFGGTVQESGKAPGGFEIIPSFLKVLNISKQPLPLDPTEKVKAE 121
            +LF+ ++KLKKESV+A  G VQES KAPGG EIIP  +K+L+ SK PLPLD TEKV+AE
Sbjct: 64  PELFEELKKLKKESVIAVKGRVQESAKAPGGVEIIPETIKLLSESKLPLPLDTTEKVRAE 123

Query: 122 IDTRLDARFLDLRKPSVSAIFKIKSRMLHSVRVFLEEQGFLEINTPKLVASATEGGTELF 181
           IDTRLD+RF+DLRK SVSAIFK+KSRMLHSVR FLE + + EINTPKLV SATEGGTELF
Sbjct: 124 IDTRLDSRFIDLRKHSVSAIFKVKSRMLHSVRNFLESENYTEINTPKLVGSATEGGTELF 183

Query: 182 PITYFEREAFLGQSPQLYKQIMMSTGLDRVYEIAPIFRAEEHDTLRHLNEVISIDIEASF 241
           PITYFEREAFLGQSPQLYKQ+MM++G D VYEIAPIFRAEEHDTLRHLNEVISID+E +F
Sbjct: 184 PITYFEREAFLGQSPQLYKQMMMASGFDNVYEIAPIFRAEEHDTLRHLNEVISIDVETAF 243

Query: 242 VDHEDVMKILENLVVRVIEDVNEHCTDALETLGRTLEVPETPFERLEYDEAVEMVNSKGV 301
            D  D M ILE +VV+ I DV EHC DAL+TL   L++PETPF R+EYDE VEMVN+KGV
Sbjct: 244 TDQIDAMNILEKMVVKAITDVKEHCKDALDTLEFDLQIPETPFPRIEYDEMVEMVNNKGV 303

Query: 302 PMKHGEDLPRAAEKALGEIMDGYYFITSWPTAIKPFYVMPDEDDPERSHAFDLMYRDLEI 361
            M+HGED+ RAAEK +GE+MDGYYFIT+WPT IKPFYV P  +DP +S AFDLMY+DLEI
Sbjct: 304 KMEHGEDMSRAAEKVMGELMDGYYFITAWPTDIKPFYVQPSAEDPAKSCAFDLMYKDLEI 363

Query: 362 SSGAMRVHQHDLLVEKIKRQGLNPDSFESYLSAFEYGMPPHAGWGLGAERFNMTLTGLKN 421
           SSGAMR+H HDLLVEKIK +GLNPDSF  YL+AFEYGMPPHAGWG+GAERF MT+TG  N
Sbjct: 364 SSGAMRIHNHDLLVEKIKSKGLNPDSFNRYLAAFEYGMPPHAGWGVGAERFTMTMTGQTN 423

Query: 422 IRETVLFPRDRRRLTP 437
           IRETVLFPRDRRRLTP
Sbjct: 424 IRETVLFPRDRRRLTP 439


Lambda     K      H
   0.320    0.139    0.402 

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: 620
Number of extensions: 19
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: 437
Length of database: 439
Length adjustment: 32
Effective length of query: 405
Effective length of database: 407
Effective search space:   164835
Effective search space used:   164835
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_013644957.1 METBO_RS06815 (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.4038588.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-217  708.7   1.4   1.6e-217  708.5   1.4    1.0  1  NCBI__GCF_000191585.1:WP_013644957.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000191585.1:WP_013644957.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  708.5   1.4  1.6e-217  1.6e-217       1     428 []      12     439 .]      12     439 .] 1.00

  Alignments for each domain:
  == domain 1  score: 708.5 bits;  conditional E-value: 1.6e-217
                             TIGR00458   1 vysadikeekdgkevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesvvavkGk 73 
                                           +ys+ ik+e++ ++v+++gw+he+rdlG++ifvllrdr+g+ q+++++kk++ elf+  kklkkesv+avkG+
  NCBI__GCF_000191585.1:WP_013644957.1  12 HYSKQIKPEMKDEDVVIMGWIHEMRDLGGIIFVLLRDRDGVTQVTAPSKKIEPELFEELKKLKKESVIAVKGR 84 
                                           799********************************************************************** PP

                             TIGR00458  74 vkekekapqgleiipeklevlneakeplPldleekveaeldtrldarfldlrrpkvqaifkirsevlesvref 146
                                           v+e+ kap+g+eiipe+++ l+e+k plPld +ekv+ae+dtrld rf+dlr+ +v+aifk++s++l+svr+f
  NCBI__GCF_000191585.1:WP_013644957.1  85 VQESAKAPGGVEIIPETIKLLSESKLPLPLDTTEKVRAEIDTRLDSRFIDLRKHSVSAIFKVKSRMLHSVRNF 157
                                           ************************************************************************* PP

                             TIGR00458 147 laeegfievntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyeiaPifraeehntkrh 219
                                           l+ e+++e+ntPklv+sateGGtelf+ityfereafl+qsPqlykq+++a+g++ vyeiaPifraeeh+t rh
  NCBI__GCF_000191585.1:WP_013644957.1 158 LESENYTEINTPKLVGSATEGGTELFPITYFEREAFLGQSPQLYKQMMMASGFDNVYEIAPIFRAEEHDTLRH 230
                                           ************************************************************************* PP

                             TIGR00458 220 lnevisidiemafedhkdvldileelvvrvfedvaeklkkelevlevklevpeeklerltydeaieilrakGk 292
                                           lnevisid+e af+d+ d+++ile++vv++++dv+e++k++l++le++l++pe++++r++yde +e++++kG+
  NCBI__GCF_000191585.1:WP_013644957.1 231 LNEVISIDVETAFTDQIDAMNILEKMVVKAITDVKEHCKDALDTLEFDLQIPETPFPRIEYDEMVEMVNNKGV 303
                                           ************************************************************************* PP

                             TIGR00458 293 eikdgedlsteaekllGekmdglyfitdfPteikPfytmPdednPeisksfdllyrdleissGaqrihdydll 365
                                           ++++ged+s++aek++Ge mdg+yfit +Pt+ikPfy+ P+ ++P  s +fdl+y+dleissGa+rih++dll
  NCBI__GCF_000191585.1:WP_013644957.1 304 KMEHGEDMSRAAEKVMGELMDGYYFITAWPTDIKPFYVQPSAEDPAKSCAFDLMYKDLEISSGAMRIHNHDLL 376
                                           ************************************************************************* PP

                             TIGR00458 366 vekikakGlePeslksyleafkyGmPPhaGwGlGaerlvmvlldlknireavlfPrdrkrltP 428
                                           vekik kGl+P+s++ yl af+yGmPPhaGwG+Gaer++m+++++ nire+vlfPrdr+rltP
  NCBI__GCF_000191585.1:WP_013644957.1 377 VEKIKSKGLNPDSFNRYLAAFEYGMPPHAGWGVGAERFTMTMTGQTNIRETVLFPRDRRRLTP 439
                                           **************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (428 nodes)
Target sequences:                          1  (439 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: 16.09
//
[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