Alignments for a candidate for aspS2 in Ferroglobus placidus DSM 10642

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Ferroglobus placidus DSM 10642

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_012966017.1 FERP_RS07595 aspartate--tRNA(Asn) ligase

Query= SwissProt::Q8Q0R2
         (444 letters)



>NCBI__GCF_000025505.1:WP_012966017.1
          Length = 429

 Score =  536 bits (1380), Expect = e-157
 Identities = 258/423 (60%), Positives = 329/423 (77%), Gaps = 7/423 (1%)

Query: 22  GQKVTLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKKIDKDLFDAARRLVRESVISVT 81
           G+KVTL GW+HEVRDLGG+ FVVLRDREG AQ+TL KKK+ +++F+ A+ + RESV+ V 
Sbjct: 14  GKKVTLYGWIHEVRDLGGLVFVVLRDREGFAQITLPKKKVKQEVFERAKNVRRESVVKVV 73

Query: 82  GSVKFEEKAPNGYELLPDEINVLNVSGSPLPMDTTGKVEAELDTRLDSRFIDLRRAETTA 141
           G VK EE+APNG+E++P+E  VLN + +PLP+D T KV AELDTRLD RF+DLR+    A
Sbjct: 74  GEVKKEERAPNGFEIIPEEFEVLNEADAPLPLDVTEKVPAELDTRLDHRFLDLRKHRVFA 133

Query: 142 VFKIRHESLRAIREYFVKYNFIETATPKVVATATEGGTALFPITYFDREAFLNQSPQLFK 201
           +F++R E L A RE+F +  FIE  TPK+V+TATEGGT LFPITYF+REAFLNQSPQL+K
Sbjct: 134 IFRVRSEVLNATREFFHERGFIEVNTPKIVSTATEGGTELFPITYFEREAFLNQSPQLYK 193

Query: 202 QILMSGGFDRVFEIGPIFRAEEHDTRRHLNEATSIDVEVSFADHFDVMELLENLVAYVYT 261
           Q LM+ GFDRVFEIGPIFRAEEH+T RHLNEATSID+EVSF DH  VM+ LE L+ Y++ 
Sbjct: 194 QTLMAAGFDRVFEIGPIFRAEEHNTVRHLNEATSIDIEVSFTDHNGVMKYLEELIVYIHE 253

Query: 262 RVIENCKSSLEVLGVDLKVPKTPFLKLTYDEVIEIINSRCEEKMHWGDDLGTLGEHTVGD 321
           RV+ENC+  L  L V L+VP+ PF ++TYDE +EI++ +  E++ WG+D  T     + +
Sbjct: 254 RVVENCEKYLNWLNVKLEVPEKPFERITYDEALEIVSRK--EEIPWGEDFSTPALKVLAE 311

Query: 322 HVYETTGESHYFIIDWPTEIKPFYAMPYEDRPEFSKSFDMMHRTMELSSGAQRIHIPSLL 381
           H+     + +YFI DWPTE KPFYAMPYE+R E  KSFD+M   +EL+SGAQRIH   LL
Sbjct: 312 HM-----QGYYFITDWPTESKPFYAMPYENRKEICKSFDLMKGWLELASGAQRIHKYDLL 366

Query: 382 KNRIESQGLNPDGFEFYLKAFEFGMPPHAGWGMGCERFVMTMLGTENIRDTVLFPRDRRR 441
             RI++QGL+P+ F FYL+AF +GMPPHAGWG+G ER +M ML  +NIR+ VLFPRDR+R
Sbjct: 367 VERIKAQGLDPESFGFYLEAFRYGMPPHAGWGLGVERLLMAMLDLKNIREAVLFPRDRQR 426

Query: 442 LSP 444
           L P
Sbjct: 427 LVP 429


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: 566
Number of extensions: 21
Number of successful extensions: 3
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: 429
Length adjustment: 32
Effective length of query: 412
Effective length of database: 397
Effective search space:   163564
Effective search space used:   163564
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_012966017.1 FERP_RS07595 (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.24653.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-216  704.2   1.1   3.6e-216  704.1   1.1    1.0  1  lcl|NCBI__GCF_000025505.1:WP_012966017.1  FERP_RS07595 aspartate--tRNA(Asn


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025505.1:WP_012966017.1  FERP_RS07595 aspartate--tRNA(Asn) ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  704.1   1.1  3.6e-216  3.6e-216       3     428 .]       5     429 .]       3     429 .] 0.99

  Alignments for each domain:
  == domain 1  score: 704.1 bits;  conditional E-value: 3.6e-216
                                 TIGR00458   3 sadikeekdgkevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesvvavk 71 
                                               + +i ee  gk+v+l+gw+he+rdlG+l+fv+lrdreg  qi+++kkkv++e+f+ +k++++esvv v 
  lcl|NCBI__GCF_000025505.1:WP_012966017.1   5 TSEISEEDFGKKVTLYGWIHEVRDLGGLVFVVLRDREGFAQITLPKKKVKQEVFERAKNVRRESVVKVV 73 
                                               568999999************************************************************ PP

                                 TIGR00458  72 GkvkekekapqgleiipeklevlneakeplPldleekveaeldtrldarfldlrrpkvqaifkirsevl 140
                                               G+vk++e+ap+g+eiipe++evlnea++plPld++ekv+aeldtrld+rfldlr+ +v aif++rsevl
  lcl|NCBI__GCF_000025505.1:WP_012966017.1  74 GEVKKEERAPNGFEIIPEEFEVLNEADAPLPLDVTEKVPAELDTRLDHRFLDLRKHRVFAIFRVRSEVL 142
                                               ********************************************************************* PP

                                 TIGR00458 141 esvreflaeegfievntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyeiaPif 209
                                               ++ ref++e+gfievntPk+v++ateGGtelf+ityfereafl+qsPqlykq l+aag++rv+ei+Pif
  lcl|NCBI__GCF_000025505.1:WP_012966017.1 143 NATREFFHERGFIEVNTPKIVSTATEGGTELFPITYFEREAFLNQSPQLYKQTLMAAGFDRVFEIGPIF 211
                                               ********************************************************************* PP

                                 TIGR00458 210 raeehntkrhlnevisidiemafedhkdvldileelvvrvfedvaeklkkelevlevklevpeeklerl 278
                                               raeehnt rhlne++sidie++f+dh++v++ leel+v + e v e+++k+l++l+vklevpe+++er+
  lcl|NCBI__GCF_000025505.1:WP_012966017.1 212 RAEEHNTVRHLNEATSIDIEVSFTDHNGVMKYLEELIVYIHERVVENCEKYLNWLNVKLEVPEKPFERI 280
                                               ********************************************************************* PP

                                 TIGR00458 279 tydeaieilrakGkeikdgedlsteaekllGekmdglyfitdfPteikPfytmPdednPeisksfdlly 347
                                               tydea+ei+++k +ei++ged+st a k+l e+m+g+yfitd+Pte+kPfy+mP+e++ ei+ksfdl+ 
  lcl|NCBI__GCF_000025505.1:WP_012966017.1 281 TYDEALEIVSRK-EEIPWGEDFSTPALKVLAEHMQGYYFITDWPTESKPFYAMPYENRKEICKSFDLMK 348
                                               *********987.89****************************************************** PP

                                 TIGR00458 348 rdleissGaqrihdydllvekikakGlePeslksyleafkyGmPPhaGwGlGaerlvmvlldlknirea 416
                                                +le++sGaqrih+ydllve+ika+Gl+Pes+ +yleaf+yGmPPhaGwGlG+erl m++ldlknirea
  lcl|NCBI__GCF_000025505.1:WP_012966017.1 349 GWLELASGAQRIHKYDLLVERIKAQGLDPESFGFYLEAFRYGMPPHAGWGLGVERLLMAMLDLKNIREA 417
                                               ********************************************************************* PP

                                 TIGR00458 417 vlfPrdrkrltP 428
                                               vlfPrdr+rl+P
  lcl|NCBI__GCF_000025505.1:WP_012966017.1 418 VLFPRDRQRLVP 429
                                               **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (428 nodes)
Target sequences:                          1  (429 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: 9.39
//
[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