Alignments for a candidate for aspS2 in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Malonomonas rubra DSM 5091

Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_072904924.1 BUB13_RS01205 aspartate--tRNA ligase

Query= uniprot:SYDND_DESVH
         (610 letters)



>NCBI__GCF_900142125.1:WP_072904924.1
          Length = 595

 Score =  748 bits (1931), Expect = 0.0
 Identities = 355/587 (60%), Positives = 453/587 (77%), Gaps = 4/587 (0%)

Query: 19  LGDWQRTHSCCELTAADVGNDVCIMGWVQYRRDHGGLIFVDLRDRKGLTQVVFSPDFAPE 78
           LG+W+RTH C +LTA ++G DVC+MGWVQ RRDHGGLIF+DLRDR+G+ Q+   PD    
Sbjct: 5   LGNWKRTHRCGDLTAENIGQDVCVMGWVQRRRDHGGLIFIDLRDREGIVQLALDPDRDLA 64

Query: 79  AHKDAHIVRSEYVLAIRGRVRPRPEGMTNPGMKTGEIEVVVSEWKLLNTSKTPPFLIEDR 138
           + + A  VR+E+VLA +G+V PRPEG  NP MKTGE+E+ +SE K+LN S+TPPF++++ 
Sbjct: 65  SLQKAEQVRNEFVLAAKGKVSPRPEGTVNPKMKTGEVEIEISELKILNRSETPPFMLDEF 124

Query: 139 TEASENLRLAWRYLDLRRPRMARNFMLRHRAAQSARRYLDELDFLEIETPYLTKATPEGA 198
           TE +EN+RL +RYLDLRRP +  N +LRH  A++ R YLD   F+E+ETP LTK+TPEGA
Sbjct: 125 TEVAENIRLKYRYLDLRRPALQSNLLLRHLVAKTVRNYLDGQGFIEVETPVLTKSTPEGA 184

Query: 199 RDFLVPSRLNHGMFYALPQSPQIFKQLLMVSGMDRYYQIVRCFRDEDMRADRQLEFTQID 258
           RD+LVPSR+N G FYALPQSPQ+FKQLLMVSG DRY+QIV+CFRDED+RADRQ EFTQID
Sbjct: 185 RDYLVPSRVNTGNFYALPQSPQLFKQLLMVSGFDRYFQIVKCFRDEDLRADRQPEFTQID 244

Query: 259 IEMSFVDEERVMSMAEGLMSRVMKDTLGVDVTVPFPRMTYDQAMGEYGVDKPDTRFDLRL 318
            E+S+V+++ VM + EG+++ + K+ +GVDV +P PR++Y +AM  +GVD PD RF + L
Sbjct: 245 CELSYVNKDDVMGVMEGMIATIFKEAIGVDVQLPMPRLSYAEAMERFGVDNPDMRFGMEL 304

Query: 319 KDVTDAVRGSEFKLF----AKAPLVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLAWIK 374
             +TD V GS+FK+F    A   LVKA+   G  T +RKE+D+ T+FVKIYGA+GLAW+K
Sbjct: 305 ITITDLVAGSDFKVFADVAASGGLVKAVNAKGCATFSRKELDDLTDFVKIYGAKGLAWVK 364

Query: 375 IREGEWQSPIAKFLSEAERAALVAALGLEVGDIVFFQAGEPGMVNAALGNLRVKLGQHLG 434
           + E  WQSPIAKF  E E  AL   LG EVGD++ F A +P + N ALG LR  LGQ LG
Sbjct: 365 VNEDGWQSPIAKFFKEDELKALNEKLGAEVGDLLLFMADKPSIANEALGRLRGHLGQKLG 424

Query: 435 LIPEDTYNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHFDLMTSDPAAARARAYDMV 494
           L  +  Y F W+TDFPLFEYDE+EKR+VA HHPFTSP +    L+ +DP   RA+AYD+V
Sbjct: 425 LADKQNYKFAWITDFPLFEYDEDEKRHVAVHHPFTSPLEEDIPLLDTDPGQVRAQAYDLV 484

Query: 495 LNGYELGGGSIRIHSAEVQRRMFAALGLDPQEAEEKFGFLIQALEHGAPPHGGIAFGMDR 554
           LNG E+GGGSIRIH   VQ RMF  LG+D +E  EKFGFL+ AL  GAPPHGGIAFG+DR
Sbjct: 485 LNGSEVGGGSIRIHDQSVQSRMFELLGIDEEEQREKFGFLLDALSFGAPPHGGIAFGLDR 544

Query: 555 LVMLLTGSPSIRDVIAFPKTQKATCLMTQAPDAVSARQLRDLGIRLR 601
           L+M+LTG+ SIRDVIAFPKTQKATCL+++AP   + +QL++LGIRLR
Sbjct: 545 LMMILTGADSIRDVIAFPKTQKATCLLSEAPSEATEKQLQELGIRLR 591


Lambda     K      H
   0.322    0.138    0.415 

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: 1042
Number of extensions: 33
Number of successful extensions: 2
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: 610
Length of database: 595
Length adjustment: 37
Effective length of query: 573
Effective length of database: 558
Effective search space:   319734
Effective search space used:   319734
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 (21.9 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