GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aspS2 in Lentibacillus jeotgali Grbi

Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate WP_010530794.1 ON01_RS09450 asparagine--tRNA ligase

Query= curated2:A6USZ9
         (438 letters)



>NCBI__GCF_000224785.1:WP_010530794.1
          Length = 430

 Score =  273 bits (698), Expect = 8e-78
 Identities = 158/424 (37%), Positives = 245/424 (57%), Gaps = 11/424 (2%)

Query: 21  DGQEIIIMGWNHSIRKLGKLVFIILRDREGTIQIVAPKQKVSEETFATAKSLGKEDVMAI 80
           + Q++ I  W  + R  GK+ F+ LRD  G IQ V  K  V+EE F  AK++ +E  M I
Sbjct: 12  EDQDVTIGVWLANKRSSGKIAFLQLRDGTGFIQGVVAKNDVTEEVFQLAKNMTQESSMYI 71

Query: 81  KGKVVANEKAPAGFEVIPIEIKILNKADTPLPLDPSEKVSADIDTRLDKRFLDLRRPKIQ 140
            GK+V + ++P G+E+   +IK++ +A    P+ P E  +  +   +D R L LR  +  
Sbjct: 72  SGKIVEDTRSPFGYEMQVKDIKLIQEA-VDYPITPKEHGTEFL---MDHRHLWLRSSRQH 127

Query: 141 SLFKLRSEVLKSIRNTFHDNGFIDVDTPKLVASATEGGTELFPISYFDKEAFLGQSPQLY 200
           ++ K+R+E++++    F+D G++ VD P L  S+ EG TELF   YFD+EA+L QS QLY
Sbjct: 128 AIMKVRNEIIRATYQFFNDQGYVKVDPPILTGSSAEGTTELFHTQYFDEEAYLSQSGQLY 187

Query: 201 KQMMMAAGFDRVFEIGPIFRAEEHNTRRHLNEAISIDCEMSFADEKDAMEILEKVINNAF 260
            +   A    +VF  GP FRAE+  TRRHL E   I+ EM+F D ++++EI E+ ++   
Sbjct: 188 ME-AAAMALGKVFSFGPTFRAEKSKTRRHLIEFWMIEPEMAFVDHEESLEIQEQYVSFVV 246

Query: 261 TDIYNNNQKELQTLGID---LKVQETPFPRIEYTEAVDMVNAKG-VEMEWGEDFSRPAEA 316
             +  N Q EL TLG D   L+  + PFPRI Y  A+ ++  KG  ++EWGEDF  P E 
Sbjct: 247 QSVLENCQLELNTLGRDTSKLEKIKAPFPRISYDGAIKLLKDKGFTDIEWGEDFGAPHET 306

Query: 317 ALGEMMDGFYFITDWPTEIRPFYTLPNEDNPKLCKAFDLMYKD--LEISSGAQRNHKYDL 374
           A+ E  +   FIT++P +I+ FY  P+ +  ++    DL+  +   E+  G+QR   + L
Sbjct: 307 AIAESFEKPVFITNYPADIKSFYMKPDPERSEVVLCADLIAPEGYGEVIGGSQRIDDFKL 366

Query: 375 LVEGIKRMGLNPEGFGTYLEAFKYGMPPHSGWGVGIERLMMIMACQQNIRECVLFPRDRQ 434
           + +  +   L    +  YLE  +YG  PHSG+G+G+ER +  +A   ++RE + FPR   
Sbjct: 367 MEQRYEEHNLTGPAYKWYLELRQYGSVPHSGFGLGLERTVAWIAGVDHVRETIPFPRLLN 426

Query: 435 RLTP 438
           RL P
Sbjct: 427 RLYP 430


Lambda     K      H
   0.320    0.137    0.405 

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: 455
Number of extensions: 27
Number of successful extensions: 6
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: 438
Length of database: 430
Length adjustment: 32
Effective length of query: 406
Effective length of database: 398
Effective search space:   161588
Effective search space used:   161588
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)

This GapMind analysis is from Jul 26 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:

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:

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:

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:

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