Alignments for a candidate for aspS2 in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Echinicola vietnamensis KMM 6221, DSM 17526

Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate Echvi_0841 Echvi_0841 aspartyl-tRNA synthetase, bacterial type

Query= BRENDA::Q9KDG1
         (595 letters)



>FitnessBrowser__Cola:Echvi_0841
          Length = 584

 Score =  587 bits (1514), Expect = e-172
 Identities = 303/586 (51%), Positives = 404/586 (68%), Gaps = 12/586 (2%)

Query: 4   RTHHCGQLSEEQVNERVQLKGWVQRRRDLGQVIFVDLRDRSGVVQLVFNSDISQEAL-ET 62
           RTH CG+L    V E V L GWVQR R+ G +++VDLRDR GV QL+F    S +AL E 
Sbjct: 3   RTHTCGELRIGDVGEEVTLSGWVQRVRNKGGLVWVDLRDRYGVTQLIFEEGSSDQALLEK 62

Query: 63  AEKVRNEYVLDVEGVVLKRDPSTVNDKIATGTIEVHVERLTILNKAKSLPFQIEANTDAS 122
           A  +  E+V+   G V++R  ++ N+KI TG IEV    L +LN AK  PF IE  TD  
Sbjct: 63  AASLGREFVIQAAGEVIER--TSKNNKIPTGDIEVKTTALKVLNAAKVPPFVIEDETDGG 120

Query: 123 EDIRLKYRYLDLRRPDMQETMKLRHQTTKLIRDFLDGQEFFEIETPMLTKSTPEGARDYL 182
           ED+R+KYRYLDLRR  ++E ++LRH+  +  R F+DG +F E+ETP+L KSTPEGARD+L
Sbjct: 121 EDLRMKYRYLDLRRRVVREKLQLRHRMMQETRKFMDGLDFMEVETPVLIKSTPEGARDFL 180

Query: 183 VPSRVHHGEFYALPQSPQIFKQLLMVSGFERYYQIVRCFRDEDLRADRQPEFTQIDIETS 242
           VPSR++ GEFYALPQSPQ FKQLLMVSGF+RY+QIV+CFRDEDLRADRQPEFTQID E S
Sbjct: 181 VPSRINEGEFYALPQSPQTFKQLLMVSGFDRYFQIVKCFRDEDLRADRQPEFTQIDCEMS 240

Query: 243 FMDKEDLLTMTENMMAKIMKEVKGLDVALPFPRMTYDDAMNRYGSDKPDTRFEMELIELS 302
           F+++ED+LT  E ++  +   VK +++     RMT+ DAM  YG+DKPD RF+M+ +EL+
Sbjct: 241 FVEQEDILTTFEGLVRHLFSTVKKVELG-EVERMTFADAMKYYGNDKPDLRFDMKFVELN 299

Query: 303 DIVKDSDFKVFSSAIKSGGIVKGLNLKGGAGSLSRKEIDGLAEFVK--PYGAKGLAWLKV 360
           D+ ++  FK+F  A    GI        GA S +RK++D L E+VK    GAKGL ++K 
Sbjct: 300 DVAQNKGFKIFDEAELVVGIA-----APGAASYTRKQVDALTEWVKRPQIGAKGLVYVKC 354

Query: 361 -EEGELKGPIAKFFAGETGAELQQAMGAEDGDLLFFAADKKEVVFDSLGALRLKLGKDFN 419
            ++G  K  + KF++ E        M A+ GDL+   +  +      L  LRLK+G D  
Sbjct: 355 NDDGTFKSSVDKFYSQEDLKAWADKMNAQPGDLILVLSGDQNATRKQLSELRLKMGSDLG 414

Query: 420 LIDESKFNFLWVVDFPLVEYDEEAKRFVALHHPFTSPKQEDLTKLETDPASVRADAYDLV 479
           L D++ F  LWV+DFPL+E+DE+ KRF A+HHPFTSPKQED+  LE DP +VRA+AYDLV
Sbjct: 415 LRDKNTFKPLWVLDFPLLEWDEDTKRFHAMHHPFTSPKQEDIPLLENDPGAVRANAYDLV 474

Query: 480 LNGYELGGGSQRIYQRPVQEKMFAALGFTEEAAQKEFGFLLEAFEYGTPPHGGIALGLDR 539
           +NG E+GGGS RI+ R  Q+ MF  LGF++E AQ +FGFL+EAFEYG PPHGGIA G DR
Sbjct: 475 INGVEIGGGSIRIHDRDTQKTMFKHLGFSDEEAQAQFGFLMEAFEYGAPPHGGIAFGFDR 534

Query: 540 LVMLLAGRLNLRDTIAFPKTASASCLLTEAPGEVSLEQLLDLNLSI 585
           L  +  G  ++RD IAFPK  S   ++ ++P  ++ EQL +L++ +
Sbjct: 535 LCAIFGGSDSIRDYIAFPKNNSGRDVMIDSPSAIADEQLKELSIQL 580


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: 980
Number of extensions: 38
Number of successful extensions: 5
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: 584
Length adjustment: 37
Effective length of query: 558
Effective length of database: 547
Effective search space:   305226
Effective search space used:   305226
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 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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