Alignments for a candidate for aspS2 in Clostridium acetobutylicum ATCC 824

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Clostridium acetobutylicum ATCC 824

Align aspartate-tRNA ligase (EC 6.1.1.12) (characterized)
to candidate NP_350148.2 CA_C3564 aspartyl-tRNA synthetase

Query= BRENDA::Q5SIC2
         (422 letters)



>NCBI__GCF_000008765.1:NP_350148.2
          Length = 425

 Score =  366 bits (940), Expect = e-106
 Identities = 193/427 (45%), Positives = 272/427 (63%), Gaps = 10/427 (2%)

Query: 2   RVLVRDLKAHVGQEVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGGLKLPLPE----S 57
           R LV + +  + + V+L G++H  R LG+I F+LLRDR+G++Q V    K+ + E    S
Sbjct: 3   RCLVNETEKKLEEVVKLQGWVHKLRKLGKIAFVLLRDRTGIIQCVVDAKKIDVKELKLES 62

Query: 58  ALRVRGLVVENAKAPGGLEVQAKEVEVLSPALEPTPVEIPKEEWRANPDTLLEYRYVTLR 117
            + + G+V EN    G  E+Q   ++ LS ALE  P+EI KE+   N DTL+E R +++R
Sbjct: 63  VVEIEGIVKENE---GRFEIQVNSIKTLSKALEKIPIEINKEDMELNIDTLIENRILSMR 119

Query: 118 GEKARAPLKVQAALVRGFRRYLDRQDFTEIFTPKVVRAGAEGGSGLFGVDYFEKRAYLAQ 177
             +  +  K++  +  GF  +L +  FTEI+TPK+V  GAEGG+ LF + YF+K AYLAQ
Sbjct: 120 NSRVNSVFKIETEIAHGFSEFLVKNGFTEIYTPKIVSEGAEGGTELFKLKYFDKEAYLAQ 179

Query: 178 SPQLYKQIMVGV-FERVYEVAPVWRMEEHHTSRHLNEYLSLDVEMGFIADEEDLMRLEEA 236
           SPQ YKQ+MV   +ERV+E+  V+R E H T RHLNEY+S+D+EMGFI DE DL+R E  
Sbjct: 180 SPQFYKQMMVAAGYERVFEIGHVYRAESHDTKRHLNEYISMDLEMGFINDEMDLIRFEIE 239

Query: 237 LLAEMLEEALNTAGDEIRLLGATWPSFPQDIPRLTHAEAKRILKEELGYP-VGQDLSEEA 295
           LL  + +         I LL    P+  Q++P +   EA  IL+E      +  D+  E 
Sbjct: 240 LLKYIFQNVRQKCSKSIELLKVEIPTI-QEVPIMPLNEAITILREVYNKKELTTDIDHEG 298

Query: 296 ERLLGEYAKERWGSDWLFVTRYPRSVRPFYTYPEEDGTTRSFDLLFRGLEITSGGQRIHR 355
           E L+G + KE++ SD++F+T Y +  RP YT P     T SFDL+FRG+EIT+GGQRI+ 
Sbjct: 299 EELIGRFVKEKYNSDFVFLTHYSKDKRPMYTMPCGKNLTHSFDLIFRGMEITTGGQRIND 358

Query: 356 YEELLESLKAKGMDPEAFHGYLEVFKYGMPPHGGFAIGAERLTQKLLGLPNVRYARAFPR 415
           Y+ L +S+  KG+  E+F  YL+VFK+GMPPHGG AIG ER+T KLL L N+R A  F R
Sbjct: 359 YDMLRQSMLDKGLKVESFKSYLDVFKFGMPPHGGLAIGLERITIKLLNLDNIREAAFFVR 418

Query: 416 DRHRLTP 422
           D+ R+ P
Sbjct: 419 DKKRILP 425


Lambda     K      H
   0.320    0.140    0.416 

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: 431
Number of extensions: 22
Number of successful extensions: 4
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: 422
Length of database: 425
Length adjustment: 32
Effective length of query: 390
Effective length of database: 393
Effective search space:   153270
Effective search space used:   153270
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 NP_350148.2 CA_C3564 (aspartyl-tRNA synthetase)
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.8267.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   1.7e-128  415.2   8.4     2e-128  414.9   8.4    1.0  1  lcl|NCBI__GCF_000008765.1:NP_350148.2  CA_C3564 aspartyl-tRNA synthetas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008765.1:NP_350148.2  CA_C3564 aspartyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.9   8.4    2e-128    2e-128      13     428 .]      15     425 .]       5     425 .] 0.95

  Alignments for each domain:
  == domain 1  score: 414.9 bits;  conditional E-value: 2e-128
                              TIGR00458  13 kevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesvvavkGkvkekekapqgl 84 
                                            + v l+gwvh++r+lG+++fvllrdr g+iq +v +kk++      +k+lk+esvv ++G+vke+e   + +
  lcl|NCBI__GCF_000008765.1:NP_350148.2  15 EVVKLQGWVHKLRKLGKIAFVLLRDRTGIIQCVVDAKKID------VKELKLESVVEIEGIVKENE---GRF 77 
                                            44679*********************************96......7899*************987...78* PP

                              TIGR00458  85 eiipeklevlneakeplPldlee.kveaeldtrldarfldlrrpkvqaifkirsevlesvreflaeegfiev 155
                                            ei ++++++l++a e +P+++++  +e ++dt +++r+l +r+ +v+++fki++e+ + + efl ++gf+e+
  lcl|NCBI__GCF_000008765.1:NP_350148.2  78 EIQVNSIKTLSKALEKIPIEINKeDMELNIDTLIENRILSMRNSRVNSVFKIETEIAHGFSEFLVKNGFTEI 149
                                            ********************9754899********************************************* PP

                              TIGR00458 156 ntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyeiaPifraeehntkrhlnevisid 227
                                             tPk+v+  +eGGtelf++ yf++ea+laqsPq+ykq+++aag+erv+ei+ ++rae h+tkrhlne is+d
  lcl|NCBI__GCF_000008765.1:NP_350148.2 150 YTPKIVSEGAEGGTELFKLKYFDKEAYLAQSPQFYKQMMVAAGYERVFEIGHVYRAESHDTKRHLNEYISMD 221
                                            ************************************************************************ PP

                              TIGR00458 228 iemafedh.kdvldileelvvrvfedvaeklkkelevlevklevpeeklerltydeaieilrakGkeikdge 298
                                            +em f ++  d +    el++ +f++v +k++k++e+l+v+++   ++++ +  +eai ilr   ++ +   
  lcl|NCBI__GCF_000008765.1:NP_350148.2 222 LEMGFINDeMDLIRFEIELLKYIFQNVRQKCSKSIELLKVEIPT-IQEVPIMPLNEAITILREVYNKKELTT 292
                                            *****988578999999***********************9998.677889999****************** PP

                              TIGR00458 299 dlsteaekllG....ekmdgly.fitdfPteikPfytmPdednPeisksfdllyrdleissGaqrihdydll 365
                                            d+ +e e l+G    ek+++++ f+t +  + +P+ytmP     + ++sfdl++r++ei++G qri dyd+l
  lcl|NCBI__GCF_000008765.1:NP_350148.2 293 DIDHEGEELIGrfvkEKYNSDFvFLTHYSKDKRPMYTMPC--GKNLTHSFDLIFRGMEITTGGQRINDYDML 362
                                            **************9*****9967888************9..56799************************* PP

                              TIGR00458 366 vekikakGlePeslksyleafkyGmPPhaGwGlGaerlvmvlldlknireavlfPrdrkrltP 428
                                             +++  kGl+ es+ksyl+ fk+GmPPh G  +G+er+++ ll+l+nirea++f rd+kr+ P
  lcl|NCBI__GCF_000008765.1:NP_350148.2 363 RQSMLDKGLKVESFKSYLDVFKFGMPPHGGLAIGLERITIKLLNLDNIREAAFFVRDKKRILP 425
                                            ************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (428 nodes)
Target sequences:                          1  (425 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 7.02
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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