Alignments for a candidate for aspS2 in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Desulfitobacterium hafniense DCB-2

Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_015944679.1 DHAF_RS17885 aspartate--tRNA ligase

Query= BRENDA::Q9KDG1
         (595 letters)



>NCBI__GCF_000021925.1:WP_015944679.1
          Length = 592

 Score =  694 bits (1791), Expect = 0.0
 Identities = 353/575 (61%), Positives = 431/575 (74%), Gaps = 3/575 (0%)

Query: 9   GQLSEEQVNERVQLKGWVQRRRDLGQVIFVDLRDRSGVVQLVFNSDISQEALETAEKVRN 68
           G L        + L GWVQRRRD G VIFVDLRDRSG VQ+VFN D+   A   AE++R+
Sbjct: 11  GSLRLSHAGAVIHLLGWVQRRRDHGGVIFVDLRDRSGFVQVVFNPDMPDFA--AAERLRS 68

Query: 69  EYVLDVEGVVLKRDPSTVNDKIATGTIEVHVERLTILNKAKSLPFQIEANTDASEDIRLK 128
           EYV+ ++G V  R     N  + TG IEV  E LTILN AK+ PF I+ + D  E +RLK
Sbjct: 69  EYVVAIKGKVRPRPEGATNPNLETGEIEVVAESLTILNGAKTPPFYIQDDVDVDEMVRLK 128

Query: 129 YRYLDLRRPDMQETMKLRHQTTKLIRDFLDGQEFFEIETPMLTKSTPEGARDYLVPSRVH 188
           YRYLDLRRP+MQ+  K+RHQ T+++R+F D Q F+EIETPML KS+PEGARDYLVPSRVH
Sbjct: 129 YRYLDLRRPEMQQVFKIRHQVTQVMRNFFDSQGFYEIETPMLIKSSPEGARDYLVPSRVH 188

Query: 189 HGEFYALPQSPQIFKQLLMVSGFERYYQIVRCFRDEDLRADRQPEFTQIDIETSFMDKED 248
            GEFYALPQSPQIFKQLLMVSG E+Y+QIVRCFRDEDLRADRQPEFTQ+D+E SF + ED
Sbjct: 189 PGEFYALPQSPQIFKQLLMVSGMEKYFQIVRCFRDEDLRADRQPEFTQLDVEMSFAEVED 248

Query: 249 LLTMTENMMAKIMKEVKGLDVALPFPRMTYDDAMNRYGSDKPDTRFEMELIELSDIVKDS 308
           +L M E +MA+I KE  G D+  PFPRMTY +AM  YGSDKPD RF ME++++++ VKDS
Sbjct: 249 ILPMMEELMARIFKETIGRDIPRPFPRMTYQEAMELYGSDKPDIRFGMEMVDVAECVKDS 308

Query: 309 DFKVFSSAIKSGGIVKGLNLKGGAGSLSRKEIDGLAEFVKPYGAKGLAWLKVEEGELKGP 368
           +FKVF+  +  GG VK L  KG AG + R+E+DGL +FV  YGAKGLA++ + E  +K P
Sbjct: 309 NFKVFTDTLAKGGRVKALCAKGCAG-MPRRELDGLIQFVSIYGAKGLAYIVLAEEGIKSP 367

Query: 369 IAKFFAGETGAELQQAMGAEDGDLLFFAADKKEVVFDSLGALRLKLGKDFNLIDESKFNF 428
           IAKFF+ E    L   +  E GD+LFF ADK+ VV D+LG LRL+LGK   LI E   NF
Sbjct: 368 IAKFFSEEQLNGLIAKLKGETGDILFFVADKEAVVADALGHLRLELGKRLGLIPEDALNF 427

Query: 429 LWVVDFPLVEYDEEAKRFVALHHPFTSPKQEDLTKLETDPASVRADAYDLVLNGYELGGG 488
           LWV +FPL+++DEE KRFVA+HHPFTSP  EDL  L T+P  VRA AYD+VLNG ELGGG
Sbjct: 428 LWVTEFPLLQWDEEDKRFVAIHHPFTSPMTEDLPLLPTEPGKVRAKAYDMVLNGTELGGG 487

Query: 489 SQRIYQRPVQEKMFAALGFTEEAAQKEFGFLLEAFEYGTPPHGGIALGLDRLVMLLAGRL 548
           S RI+QR VQE+MF  LG T E A+ +FG+LL+AFEYGTPPHGGIA GLDRL+MLL G+ 
Sbjct: 488 SIRIHQREVQEQMFDLLGLTPEEAKAKFGYLLDAFEYGTPPHGGIAFGLDRLIMLLTGKD 547

Query: 549 NLRDTIAFPKTASASCLLTEAPGEVSLEQLLDLNL 583
           N+RD IAFPKT SAS L+ +AP  V  +QL +L++
Sbjct: 548 NIRDVIAFPKTQSASDLMIQAPSSVDEKQLKELHI 582


Lambda     K      H
   0.319    0.138    0.393 

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: 1054
Number of extensions: 46
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: 595
Length of database: 592
Length adjustment: 37
Effective length of query: 558
Effective length of database: 555
Effective search space:   309690
Effective search space used:   309690
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 (21.7 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