Alignments for a candidate for aspS2 in Desulfuromusa kysingii DSM 7343

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Desulfuromusa kysingii DSM 7343

Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_092350869.1 BLU87_RS16475 aspartate--tRNA ligase

Query= uniprot:SYDND_DESVH
         (610 letters)



>NCBI__GCF_900107645.1:WP_092350869.1
          Length = 595

 Score =  736 bits (1900), Expect = 0.0
 Identities = 346/587 (58%), Positives = 452/587 (77%), Gaps = 4/587 (0%)

Query: 19  LGDWQRTHSCCELTAADVGNDVCIMGWVQYRRDHGGLIFVDLRDRKGLTQVVFSPDFAPE 78
           LG W+RTH C +LTA  +G  VC+MGW Q RRDHGGLIF+DLRDR+G+ Q+   PD    
Sbjct: 5   LGSWERTHRCGDLTAEQIGEHVCVMGWAQRRRDHGGLIFIDLRDREGVIQLALDPDRDLA 64

Query: 79  AHKDAHIVRSEYVLAIRGRVRPRPEGMTNPGMKTGEIEVVVSEWKLLNTSKTPPFLIEDR 138
           +H+ A  VRSE+VLA RG+V PRPEG  NP MKTGE+E+ ++E  +LN S+TPPF++++ 
Sbjct: 65  SHQKAEQVRSEFVLAARGKVSPRPEGTVNPKMKTGEVEIEITELLILNRSETPPFMLDEF 124

Query: 139 TEASENLRLAWRYLDLRRPRMARNFMLRHRAAQSARRYLDELDFLEIETPYLTKATPEGA 198
           TE +EN+RL +RYLDLRRP + +N ++RH  A++ R Y D+  F+E+ETP LTK+TPEGA
Sbjct: 125 TEVAENIRLKYRYLDLRRPALQKNMLMRHLVAKTVRNYFDQQGFIEVETPVLTKSTPEGA 184

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

Query: 259 IEMSFVDEERVMSMAEGLMSRVMKDTLGVDVTVPFPRMTYDQAMGEYGVDKPDTRFDLRL 318
            EMSF++  +VM + EG++++V K  LG+D+T+P PR++Y +A+  +GVD PD RF + L
Sbjct: 245 CEMSFINRGQVMDIMEGMVAKVFKAALGIDLTLPMPRLSYAEALDRFGVDNPDLRFGMEL 304

Query: 319 KDVTDAVRGSEFKLF----AKAPLVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLAWIK 374
            D+T+ V GS+FK+F    A+  LVKA+ V  G T +RKE+D+ T+F KIYGA+G+AW+K
Sbjct: 305 IDITEQVAGSQFKVFSSVAAEGGLVKALNVKEGATFSRKELDDLTDFTKIYGAKGMAWVK 364

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

Query: 435 LIPEDTYNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHFDLMTSDPAAARARAYDMV 494
           L  +D + F WVTDFPL E+D+E+ R++A HHPFT+P +    L+ +DP  ARA+AYD+V
Sbjct: 425 LARKDDFQFTWVTDFPLLEWDDEQHRHLAVHHPFTAPLEEDIPLLDTDPTQARAQAYDLV 484

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

Query: 555 LVMLLTGSPSIRDVIAFPKTQKATCLMTQAPDAVSARQLRDLGIRLR 601
           L+M+LTG+ SIRDVIAFPKTQKATCL++ AP+ V  +QL++LGIRLR
Sbjct: 545 LMMILTGADSIRDVIAFPKTQKATCLLSDAPNEVDDKQLQELGIRLR 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: 1021
Number of extensions: 37
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.

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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