Alignments for a candidate for aspS2 in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Archaeoglobus veneficus SNP6

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_013682936.1 ARCVE_RS01095 aspartate--tRNA(Asn) ligase

Query= SwissProt::O26328
         (437 letters)



>NCBI__GCF_000194625.1:WP_013682936.1
          Length = 430

 Score =  536 bits (1380), Expect = e-157
 Identities = 256/427 (59%), Positives = 328/427 (76%)

Query: 11  YSKDIEPEMDGDEVTVMGWVHEIRDLGGIIFVLLRDRDGLIQITAPSKKIEKDLFKSIRK 70
           Y+ +I  E  G EVT+ GW+HE+RD GG++FV+LRDR+G IQIT P KK+++++F   +K
Sbjct: 4   YTSEIGEEDVGKEVTLYGWIHEVRDHGGLVFVILRDREGFIQITLPKKKVDREIFNRAKK 63

Query: 71  LKKESVVAFGGTVQESGKAPGGFEIIPSFLKVLNISKQPLPLDPTEKVKAEIDTRLDARF 130
           +++ESVV   G V+   KAPGG+E+IP+   VLN +  PLPLD  EKV AE+DTRLD R+
Sbjct: 64  VRRESVVMVKGIVKAEPKAPGGYEVIPTAFDVLNEADAPLPLDVAEKVPAELDTRLDHRY 123

Query: 131 LDLRKPSVSAIFKIKSRMLHSVRVFLEEQGFLEINTPKLVASATEGGTELFPITYFEREA 190
           LDLRKP + AIF+I+  ML SVR FL E+GF+E+NTPK+V++ATEGGTELFPI+YFE+EA
Sbjct: 124 LDLRKPKIQAIFRIRHCMLQSVRRFLCEEGFIEVNTPKIVSTATEGGTELFPISYFEKEA 183

Query: 191 FLGQSPQLYKQIMMSTGLDRVYEIAPIFRAEEHDTLRHLNEVISIDIEASFVDHEDVMKI 250
           FL QSPQLYKQ++M  GL++V+EI PIFRAEEH+T+RHLNE ISIDIEASF+DHE VM +
Sbjct: 184 FLNQSPQLYKQVLMGAGLEKVFEIGPIFRAEEHNTVRHLNEAISIDIEASFMDHEGVMDV 243

Query: 251 LENLVVRVIEDVNEHCTDALETLGRTLEVPETPFERLEYDEAVEMVNSKGVPMKHGEDLP 310
           LE LV R+ EDV+  C   L  L   L+VPE PFERL+YDEA+E+ +  G  +  GEDL 
Sbjct: 244 LERLVARIYEDVSVECEKFLSWLDIKLDVPEVPFERLKYDEAIEIAHEGGEDIPWGEDLS 303

Query: 311 RAAEKALGEIMDGYYFITSWPTAIKPFYVMPDEDDPERSHAFDLMYRDLEISSGAMRVHQ 370
            AA K + E MD +YFI  WPT  KPFY MP +D PE   +FDLM+  LE++SGA R+H 
Sbjct: 304 TAALKIIAEHMDSHYFIVDWPTESKPFYAMPYDDKPEVCKSFDLMHGWLELASGAQRIHL 363

Query: 371 HDLLVEKIKRQGLNPDSFESYLSAFEYGMPPHAGWGLGAERFNMTLTGLKNIRETVLFPR 430
           +DLLV++I+  G++P+SF  YL AF YGMPPHAGWGLGAER  M++ GLKNIRE ++FPR
Sbjct: 364 YDLLVKRIEECGMSPESFGFYLEAFRYGMPPHAGWGLGAERLLMSMLGLKNIREAIMFPR 423

Query: 431 DRRRLTP 437
           DR RL P
Sbjct: 424 DRHRLVP 430


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: 580
Number of extensions: 28
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: 430
Length adjustment: 32
Effective length of query: 405
Effective length of database: 398
Effective search space:   161190
Effective search space used:   161190
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_013682936.1 ARCVE_RS01095 (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.10383.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-218  711.4   0.0   2.4e-218  711.2   0.0    1.0  1  lcl|NCBI__GCF_000194625.1:WP_013682936.1  ARCVE_RS01095 aspartate--tRNA(As


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000194625.1:WP_013682936.1  ARCVE_RS01095 aspartate--tRNA(Asn) ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  711.2   0.0  2.4e-218  2.4e-218       2     428 .]       4     430 .]       3     430 .] 1.00

  Alignments for each domain:
  == domain 1  score: 711.2 bits;  conditional E-value: 2.4e-218
                                 TIGR00458   2 ysadikeekdgkevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesvvav 70 
                                               y+ +i ee  gkev+l+gw+he+rd G+l+fv+lrdreg iqi+++kkkv++e+f+ +kk+++esvv+v
  lcl|NCBI__GCF_000194625.1:WP_013682936.1   4 YTSEIGEEDVGKEVTLYGWIHEVRDHGGLVFVILRDREGFIQITLPKKKVDREIFNRAKKVRRESVVMV 72 
                                               7889999999*********************************************************** PP

                                 TIGR00458  71 kGkvkekekapqgleiipeklevlneakeplPldleekveaeldtrldarfldlrrpkvqaifkirsev 139
                                               kG+vk++ kap+g+e+ip+ ++vlnea++plPld++ekv+aeldtrld+r+ldlr+pk+qaif+ir+ +
  lcl|NCBI__GCF_000194625.1:WP_013682936.1  73 KGIVKAEPKAPGGYEVIPTAFDVLNEADAPLPLDVAEKVPAELDTRLDHRYLDLRKPKIQAIFRIRHCM 141
                                               ********************************************************************* PP

                                 TIGR00458 140 lesvreflaeegfievntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyeiaPi 208
                                               l+svr fl eegfievntPk+v++ateGGtelf+i+yfe+eafl+qsPqlykqvl+ agle+v+ei+Pi
  lcl|NCBI__GCF_000194625.1:WP_013682936.1 142 LQSVRRFLCEEGFIEVNTPKIVSTATEGGTELFPISYFEKEAFLNQSPQLYKQVLMGAGLEKVFEIGPI 210
                                               ********************************************************************* PP

                                 TIGR00458 209 fraeehntkrhlnevisidiemafedhkdvldileelvvrvfedvaeklkkelevlevklevpeekler 277
                                               fraeehnt rhlne+isidie++f dh++v+d+le+lv r++edv+ +++k l++l++kl+vpe ++er
  lcl|NCBI__GCF_000194625.1:WP_013682936.1 211 FRAEEHNTVRHLNEAISIDIEASFMDHEGVMDVLERLVARIYEDVSVECEKFLSWLDIKLDVPEVPFER 279
                                               ********************************************************************* PP

                                 TIGR00458 278 ltydeaieilrakGkeikdgedlsteaekllGekmdglyfitdfPteikPfytmPdednPeisksfdll 346
                                               l+ydeaiei++  G++i++gedlst+a k++ e+md++yfi+d+Pte+kPfy+mP++d+Pe++ksfdl+
  lcl|NCBI__GCF_000194625.1:WP_013682936.1 280 LKYDEAIEIAHEGGEDIPWGEDLSTAALKIIAEHMDSHYFIVDWPTESKPFYAMPYDDKPEVCKSFDLM 348
                                               ********************************************************************* PP

                                 TIGR00458 347 yrdleissGaqrihdydllvekikakGlePeslksyleafkyGmPPhaGwGlGaerlvmvlldlknire 415
                                               + +le++sGaqrih+ydllv +i + G++Pes+ +yleaf+yGmPPhaGwGlGaerl m++l+lknire
  lcl|NCBI__GCF_000194625.1:WP_013682936.1 349 HGWLELASGAQRIHLYDLLVKRIEECGMSPESFGFYLEAFRYGMPPHAGWGLGAERLLMSMLGLKNIRE 417
                                               ********************************************************************* PP

                                 TIGR00458 416 avlfPrdrkrltP 428
                                               a++fPrdr+rl+P
  lcl|NCBI__GCF_000194625.1:WP_013682936.1 418 AIMFPRDRHRLVP 430
                                               ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (428 nodes)
Target sequences:                          1  (430 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: 9.43
//
[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