Alignments for a candidate for aspS2 in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Bacteroides thetaiotaomicron VPI-5482

Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate 350400 BT0872 aspartyl-tRNA synthetase (NCBI ptt file)

Query= BRENDA::Q9KDG1
         (595 letters)



>FitnessBrowser__Btheta:350400
          Length = 587

 Score =  589 bits (1519), Expect = e-173
 Identities = 300/586 (51%), Positives = 403/586 (68%), Gaps = 11/586 (1%)

Query: 4   RTHHCGQLSEEQVNERVQLKGWVQRRRDLGQVIFVDLRDRSGVVQLVFNSDISQEALETA 63
           RTH CG+L    VN+++ L GWVQR R +G + F+DLRDR G+ QLVFN +I+ E  + A
Sbjct: 3   RTHTCGELRISDVNKQITLSGWVQRSRKMGGMTFIDLRDRYGITQLVFNEEINAELCDRA 62

Query: 64  EKVRNEYVLDVEGVVLKRDPSTVNDKIATGTIEVHVERLTILNKAKSLPFQIEANTDASE 123
            K+  E+V+ + G V +R     N  I TG IE+ V  L +LN A + PF IE NTD  +
Sbjct: 63  NKLGREFVIQITGTVNERFSKNAN--IPTGDIEIIVSELNVLNTAMTPPFTIEDNTDGGD 120

Query: 124 DIRLKYRYLDLRRPDMQETMKLRHQTTKLIRDFLDGQEFFEIETPMLTKSTPEGARDYLV 183
           DIR+KYRYLDLRR  ++  ++LRH+ T  +R +LD   F E+ETP+L  STPEGARD++V
Sbjct: 121 DIRMKYRYLDLRRNAVRSNLELRHKMTIEVRKYLDSLGFIEVETPVLIGSTPEGARDFVV 180

Query: 184 PSRVHHGEFYALPQSPQIFKQLLMVSGFERYYQIVRCFRDEDLRADRQPEFTQIDIETSF 243
           PSR++ G+FYALPQSPQ  KQLLMVSGF+RY+QI +CFRDEDLRADRQPEFTQID E SF
Sbjct: 181 PSRMNPGQFYALPQSPQTLKQLLMVSGFDRYFQIAKCFRDEDLRADRQPEFTQIDCEMSF 240

Query: 244 MDKEDLLTMTENMMAKIMKEVKGLDVALPFPRMTYDDAMNRYGSDKPDTRFEMELIELSD 303
           +++ED+++  E M   + K ++G+++  PF RM + DAM  YGSDKPD RF M+ +EL D
Sbjct: 241 VEQEDIISTFEGMAKHLFKTLRGVELTEPFQRMPWADAMKYYGSDKPDLRFGMKFVELMD 300

Query: 304 IVKDSDFKVFSSAIKSGGIVKGLNLKGGAGSLSRKEIDGLAEFVK--PYGAKGLAWLKVE 361
           I+K   F VF +A   GGI        GA + +RK++D L EFVK    GAKG+ + +VE
Sbjct: 301 IMKGHGFSVFDNAAYVGGI-----CAEGAATYTRKQLDALTEFVKKPQIGAKGMVYARVE 355

Query: 362 -EGELKGPIAKFFAGETGAELQQAMGAEDGDL-LFFAADKKEVVFDSLGALRLKLGKDFN 419
            +G +K  + KF+  E   ++++A GA+ GDL L  + D        L  LRL++G    
Sbjct: 356 ADGTVKSSVDKFYTQEVLQQMKEAFGAKPGDLILILSGDDVMKTRKQLCELRLEMGSQLG 415

Query: 420 LIDESKFNFLWVVDFPLVEYDEEAKRFVALHHPFTSPKQEDLTKLETDPASVRADAYDLV 479
           L D++KF  LWV+DFP+ E+ EE  R +A+HHPFT PK+ED+  L+TDPA+VRADAYD+V
Sbjct: 416 LRDKNKFVCLWVIDFPMFEWSEEEGRLMAMHHPFTHPKEEDIPLLDTDPAAVRADAYDMV 475

Query: 480 LNGYELGGGSQRIYQRPVQEKMFAALGFTEEAAQKEFGFLLEAFEYGTPPHGGIALGLDR 539
           +NG E+GGGS RI+   +Q +MF  LGFT E AQ +FGFL+ AF+YG PPHGG+A GLDR
Sbjct: 476 VNGVEVGGGSIRIHDAQLQARMFEILGFTPEKAQAQFGFLMNAFKYGAPPHGGLAYGLDR 535

Query: 540 LVMLLAGRLNLRDTIAFPKTASASCLLTEAPGEVSLEQLLDLNLSI 585
            V L AG  ++RD IAFPK  S   ++ +AP E+   QL +LNL +
Sbjct: 536 WVSLFAGLDSIRDCIAFPKNNSGRDVMLDAPSEIDQTQLDELNLIV 581


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: 913
Number of extensions: 40
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: 587
Length adjustment: 37
Effective length of query: 558
Effective length of database: 550
Effective search space:   306900
Effective search space used:   306900
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.

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