Alignments for a candidate for aspS2 in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Methanococcus maripaludis C5

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_011869534.1 MMARC5_RS09215 aspartate--tRNA(Asn) ligase

Query= SwissProt::O26328
         (437 letters)



>NCBI__GCF_000016125.1:WP_011869534.1
          Length = 438

 Score =  545 bits (1403), Expect = e-159
 Identities = 262/436 (60%), Positives = 333/436 (76%)

Query: 2   LLGDLRRTHYSKDIEPEMDGDEVTVMGWVHEIRDLGGIIFVLLRDRDGLIQITAPSKKIE 61
           L+ D RRTHYS+++ PEMDG EV +MGWVH IR LG + FV+LRDR+G IQ   P +K++
Sbjct: 3   LIADWRRTHYSEEVIPEMDGQEVILMGWVHSIRALGKLAFVILRDREGTIQAVVPKQKVD 62

Query: 62  KDLFKSIRKLKKESVVAFGGTVQESGKAPGGFEIIPSFLKVLNISKQPLPLDPTEKVKAE 121
           ++ F   +KL KE ++A  G V  + KAP GFE+IP  ++VLN +  PLPLDP+EKV AE
Sbjct: 63  EETFAIAKKLGKEDIIAIRGKVVANEKAPKGFEVIPIEIRVLNKADAPLPLDPSEKVAAE 122

Query: 122 IDTRLDARFLDLRKPSVSAIFKIKSRMLHSVRVFLEEQGFLEINTPKLVASATEGGTELF 181
           IDTRLD RFLD+R+P + AIFKI+S ML S+R    + GF+E+NTPKLVASATEGGTELF
Sbjct: 123 IDTRLDKRFLDIRRPKIQAIFKIRSEMLRSIRKTFADGGFVEVNTPKLVASATEGGTELF 182

Query: 182 PITYFEREAFLGQSPQLYKQIMMSTGLDRVYEIAPIFRAEEHDTLRHLNEVISIDIEASF 241
           PI+YFE+EAFLGQSPQLYKQ+MM+ G D+V+EIA IFRAEEH+T RHLNE ISID E SF
Sbjct: 183 PISYFEKEAFLGQSPQLYKQMMMAGGFDKVFEIAQIFRAEEHNTRRHLNEAISIDTEMSF 242

Query: 242 VDHEDVMKILENLVVRVIEDVNEHCTDALETLGRTLEVPETPFERLEYDEAVEMVNSKGV 301
           V+ +D M +LE +V     D+  +    +E L    E+PE  F+++ Y EA+++ N+KGV
Sbjct: 243 VNEKDAMAMLEKVVYNCYADIEYNRPQEIELLELNWEIPEKTFDKITYTEAIDIANAKGV 302

Query: 302 PMKHGEDLPRAAEKALGEIMDGYYFITSWPTAIKPFYVMPDEDDPERSHAFDLMYRDLEI 361
            ++ GEDL RAAE+A+G+ M G YFIT WPT  +PFY +P + D +   AFDLMY++LEI
Sbjct: 303 EIEWGEDLSRAAERAVGDEMGGLYFITEWPTQTRPFYTLPHKHDNKVCKAFDLMYKELEI 362

Query: 362 SSGAMRVHQHDLLVEKIKRQGLNPDSFESYLSAFEYGMPPHAGWGLGAERFNMTLTGLKN 421
           SSGA RVH++DLLVE I   G+NPDSFE+YL AF++GMPPHAGWGLGA+RF M LT   N
Sbjct: 363 SSGAQRVHKYDLLVENISNMGMNPDSFETYLEAFKFGMPPHAGWGLGADRFAMVLTAQDN 422

Query: 422 IRETVLFPRDRRRLTP 437
           IRE VLFPRDR+RLTP
Sbjct: 423 IRECVLFPRDRQRLTP 438


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: 550
Number of extensions: 20
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: 437
Length of database: 438
Length adjustment: 32
Effective length of query: 405
Effective length of database: 406
Effective search space:   164430
Effective search space used:   164430
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_011869534.1 MMARC5_RS09215 (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.1210049.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.7e-215  699.7   0.5   8.7e-215  699.5   0.5    1.0  1  NCBI__GCF_000016125.1:WP_011869534.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016125.1:WP_011869534.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  699.5   0.5  8.7e-215  8.7e-215       1     428 []      11     438 .]      11     438 .] 1.00

  Alignments for each domain:
  == domain 1  score: 699.5 bits;  conditional E-value: 8.7e-215
                             TIGR00458   1 vysadikeekdgkevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesvvavkGk 73 
                                           +ys ++ +e+dg+ev+l+gwvh+ir+lG+l+fv+lrdreg+iq +v+k+kv++e f  +kkl ke+++a++Gk
  NCBI__GCF_000016125.1:WP_011869534.1  11 HYSEEVIPEMDGQEVILMGWVHSIRALGKLAFVILRDREGTIQAVVPKQKVDEETFAIAKKLGKEDIIAIRGK 83 
                                           79999******************************************************************** PP

                             TIGR00458  74 vkekekapqgleiipeklevlneakeplPldleekveaeldtrldarfldlrrpkvqaifkirsevlesvref 146
                                           v ++ekap+g+e+ip +++vln+a++plPld++ekv ae+dtrld+rfld+rrpk+qaifkirse+l+s+r++
  NCBI__GCF_000016125.1:WP_011869534.1  84 VVANEKAPKGFEVIPIEIRVLNKADAPLPLDPSEKVAAEIDTRLDKRFLDIRRPKIQAIFKIRSEMLRSIRKT 156
                                           ************************************************************************* PP

                             TIGR00458 147 laeegfievntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyeiaPifraeehntkrh 219
                                           +a+ gf+evntPklvasateGGtelf+i+yfe+eafl+qsPqlykq+++a g+++v+eia ifraeehnt+rh
  NCBI__GCF_000016125.1:WP_011869534.1 157 FADGGFVEVNTPKLVASATEGGTELFPISYFEKEAFLGQSPQLYKQMMMAGGFDKVFEIAQIFRAEEHNTRRH 229
                                           ************************************************************************* PP

                             TIGR00458 220 lnevisidiemafedhkdvldileelvvrvfedvaeklkkelevlevklevpeeklerltydeaieilrakGk 292
                                           lne+isid em+f+++kd++ +le++v++ + d++ ++ +e+e+le++ e+pe+ ++++ty eai+i++akG+
  NCBI__GCF_000016125.1:WP_011869534.1 230 LNEAISIDTEMSFVNEKDAMAMLEKVVYNCYADIEYNRPQEIELLELNWEIPEKTFDKITYTEAIDIANAKGV 302
                                           ************************************************************************* PP

                             TIGR00458 293 eikdgedlsteaekllGekmdglyfitdfPteikPfytmPdednPeisksfdllyrdleissGaqrihdydll 365
                                           ei++gedls++ae+++G++m+glyfit++Pt+ +Pfyt+P++++ +++k+fdl+y++leissGaqr+h+ydll
  NCBI__GCF_000016125.1:WP_011869534.1 303 EIEWGEDLSRAAERAVGDEMGGLYFITEWPTQTRPFYTLPHKHDNKVCKAFDLMYKELEISSGAQRVHKYDLL 375
                                           ************************************************************************* PP

                             TIGR00458 366 vekikakGlePeslksyleafkyGmPPhaGwGlGaerlvmvlldlknireavlfPrdrkrltP 428
                                           ve+i + G++P+s+++yleafk+GmPPhaGwGlGa+r+ mvl+ ++nire+vlfPrdr+rltP
  NCBI__GCF_000016125.1:WP_011869534.1 376 VENISNMGMNPDSFETYLEAFKFGMPPHAGWGLGADRFAMVLTAQDNIRECVLFPRDRQRLTP 438
                                           **************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (428 nodes)
Target sequences:                          1  (438 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: 14.50
//
[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