Alignments for a candidate for aspS2 in Sulfuricurvum kujiense DSM 16994

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Sulfuricurvum kujiense DSM 16994

Align aspartate-tRNA ligase (EC 6.1.1.12) (characterized)
to candidate WP_013459862.1 SULKU_RS05065 aspartate--tRNA ligase

Query= BRENDA::P56459
         (577 letters)



>NCBI__GCF_000183725.1:WP_013459862.1
          Length = 584

 Score =  773 bits (1995), Expect = 0.0
 Identities = 375/581 (64%), Positives = 465/581 (80%), Gaps = 4/581 (0%)

Query: 1   MRSHFCTEISEKDVGKIVKVAGWCNTYRDHGGVVFIDLRDKSGLVQLVCDPSSKAYEKAL 60
           MRSHFCT++SE +VG  V + GW N+YRDHGG+VFIDLRDKSGL+QLVCDP+  A+   L
Sbjct: 1   MRSHFCTDLSEANVGDNVILCGWANSYRDHGGIVFIDLRDKSGLIQLVCDPADNAHAHKL 60

Query: 61  --EVRSEFVLVAKGKVRLRGAGLENPKLKTGKIEIVLEELIIENKSATPPIEIGNKHVNE 118
             EVR EFVL+A G+VR RG GL NP+LKTG IE+V+EELIIEN+S   P  IG+  V E
Sbjct: 61  ASEVRDEFVLIAHGRVRNRGEGLVNPRLKTGAIEVVVEELIIENRSEPVPFGIGDNSVGE 120

Query: 119 DLRLKYRYLDLRSPNSYEIFKLRSEVALITRNTLAQKGFLEIETPILSKTTPEGARDYLV 178
           ++RLKYRYLDLR+P+ Y  F LRS+ A+  RN L + GFLE+ETPIL+K+TPEGARDYLV
Sbjct: 121 EIRLKYRYLDLRNPSMYNTFMLRSKAAIAARNVLDRLGFLEVETPILTKSTPEGARDYLV 180

Query: 179 PSRVHEGEFFALPQSPQLFKQLLMVGGMDRYFQIARCFRDEDLRADRQPEFTQIDAEMSF 238
           PSRVHEGEF+ALPQSPQLFKQLLMVGG DRYFQIA+CFRDEDLRADRQPEFTQID EMSF
Sbjct: 181 PSRVHEGEFYALPQSPQLFKQLLMVGGFDRYFQIAKCFRDEDLRADRQPEFTQIDVEMSF 240

Query: 239 CDENDVMGVVEDLLQEIFKAVGHTISKPFKRMPYKEAMENYGSDKPDLRFELPLIEVGDC 298
           C++ DV+ V E+L+  +F A GH +  PF R+ Y +AME YGSDKPDLR++L +I+V D 
Sbjct: 241 CNQEDVIRVAEELITGMFAAAGHEVHTPFNRIKYNDAMEWYGSDKPDLRYDLKMIDVIDI 300

Query: 299 FRDSSNAIFSNTAKDPKNKRIKALNVKGADALFSRSVLKELEEFVRQFGAKGLAYLQIKE 358
           F    N IF++ A +PK  RIKAL V GAD +FS+  +K  E++VR+FGAKGL Y Q+KE
Sbjct: 301 FARCDNEIFTSIAANPKMNRIKALRVPGADLVFSKREMKSFEDYVRKFGAKGLGYFQMKE 360

Query: 359 DEIKGPLVKFLSEKGLKNILERTDAQVGDIVFFGAGDKKIVLDYMGRLRLKVA--ETLDL 416
           D +KGPL KF + + L+ ++ERT  +VGD+VFFGAGDKK V DYMGR R+ +A  E ++L
Sbjct: 361 DGLKGPLEKFFAPEDLQLLVERTGMEVGDVVFFGAGDKKTVWDYMGRFRIFIAEHEKMNL 420

Query: 417 IDKDALNFLWVVNFPMFEKTENGYHAAHHPFTMPKNIECEDIEEVEAHAYDVVLNGVELG 476
           ID+D   F+WVV+FPMFE  +    A HHPFTMP+++  E +E++E+ AYD+VLNG ELG
Sbjct: 421 IDQDRFEFVWVVDFPMFEIEDGRVKALHHPFTMPRDLNHEHLEDIESIAYDIVLNGTELG 480

Query: 477 GGSIRIHKEEMQKKVFEKINIHEEEAQKKFGFLLEALKFGAPPHGGFAIGFDRLIMLMTK 536
           GGSIRIHK+ +Q+++F  + I EEEAQ+KFGFLL+ALKFGAPPHGGFAIGFDR +ML++K
Sbjct: 481 GGSIRIHKQALQEQIFTLLGIGEEEAQEKFGFLLDALKFGAPPHGGFAIGFDRFMMLLSK 540

Query: 537 SHSIRDVIAFPKTQKASCLLTNAPSPINEEQLRELHIRLRK 577
             SIRDVIAFPKTQKASC++T APSP+   QLRELHIRLR+
Sbjct: 541 KESIRDVIAFPKTQKASCIMTQAPSPVELTQLRELHIRLRE 581


Lambda     K      H
   0.320    0.139    0.400 

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: 976
Number of extensions: 36
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: 577
Length of database: 584
Length adjustment: 36
Effective length of query: 541
Effective length of database: 548
Effective search space:   296468
Effective search space used:   296468
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: 53 (25.0 bits)

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