Alignments for a candidate for aspS2 in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Pedobacter sp. GW460-11-11-14-LB5

Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate CA265_RS19975 CA265_RS19975 aspartate--tRNA ligase

Query= BRENDA::Q9KDG1
         (595 letters)



>FitnessBrowser__Pedo557:CA265_RS19975
          Length = 581

 Score =  587 bits (1514), Expect = e-172
 Identities = 300/583 (51%), Positives = 405/583 (69%), Gaps = 11/583 (1%)

Query: 4   RTHHCGQLSEEQVNERVQLKGWVQRRRDLGQVIFVDLRDRSGVVQLVFNSDISQEALETA 63
           RT  CG L+   + E V L GWVQ+ RDLG + F+D+RDR G+ QLVFN D ++E  ETA
Sbjct: 3   RTVTCGALNLNNLGESVTLCGWVQKSRDLGGMTFIDIRDRYGITQLVFNMDDNRELCETA 62

Query: 64  EKVRNEYVLDVEGVVLKRDPSTVNDKIATGTIEVHVERLTILNKAKSLPFQIEANTDASE 123
             +  E+V+   G V++R  S  N K+ATG +E+ +  L ILN AK  PF I+  TD  +
Sbjct: 63  RTLGREFVIKAIGTVVER--SNKNPKMATGDVEIKISALEILNAAKLPPFMIDDETDGGD 120

Query: 124 DIRLKYRYLDLRRPDMQETMKLRHQTTKLIRDFLDGQEFFEIETPMLTKSTPEGARDYLV 183
           ++R+KYRYLDLRR  ++  + LRH+  + +R +LD  +F E+ETP+L KSTPEGARD++V
Sbjct: 121 ELRMKYRYLDLRRNPVRNNLVLRHKMAQSVRRYLDALDFIEVETPVLIKSTPEGARDFVV 180

Query: 184 PSRVHHGEFYALPQSPQIFKQLLMVSGFERYYQIVRCFRDEDLRADRQPEFTQIDIETSF 243
           PSR++ GEFYALPQSPQ FKQLLMVSGF+RY+QIV+CFRDEDLRADRQPEFTQID E SF
Sbjct: 181 PSRMNEGEFYALPQSPQTFKQLLMVSGFDRYFQIVKCFRDEDLRADRQPEFTQIDCEMSF 240

Query: 244 MDKEDLLTMTENMMAKIMKEVKGLDVALPFPRMTYDDAMNRYGSDKPDTRFEMELIELSD 303
           +++ED+L   E ++  + KEV+  D+    PRM Y DAM  YGSDKPDTRF M+ +EL+ 
Sbjct: 241 IEQEDILNTFEGLIRTLFKEVRNYDLP-EVPRMQYADAMRLYGSDKPDTRFAMQFVELNH 299

Query: 304 IVKDSDFKVFSSAIKSGGIVKGLNLKGGAGSLSRKEIDGLAEFVK--PYGAKGLAWLK-V 360
           +VK   F VF +A     +V G+N K GA S +RK++D L +F+K    GA GL + +  
Sbjct: 300 LVKGKGFPVFDNA----ELVVGINAK-GAASYTRKQLDELTDFIKRPQIGATGLIYARHN 354

Query: 361 EEGELKGPIAKFFAGETGAELQQAMGAEDGDLLFFAADKKEVVFDSLGALRLKLGKDFNL 420
           E+G +K  + KFF  E   +  +A G E GDLL   A   + V   L  LRL++G    L
Sbjct: 355 EDGTIKSSVDKFFNEEDLKQWSEAFGTEKGDLLLILAGSTDKVRKQLNELRLEMGSRLGL 414

Query: 421 IDESKFNFLWVVDFPLVEYDEEAKRFVALHHPFTSPKQEDLTKLETDPASVRADAYDLVL 480
            D++ F+ LWV+DFPL+E+DEE +R+ A+HHPFTSPK ED+  L+TDP +VRA+AYD+V+
Sbjct: 415 RDKNTFSALWVLDFPLLEWDEETERYHAMHHPFTSPKPEDIALLDTDPKNVRANAYDMVI 474

Query: 481 NGYELGGGSQRIYQRPVQEKMFAALGFTEEAAQKEFGFLLEAFEYGTPPHGGIALGLDRL 540
           NG E+GGGS RI+ R +Q  MF  LGF+ E AQK+FGFL++AFE+G PPHGGIA G DRL
Sbjct: 475 NGTEVGGGSIRIHDRALQALMFKHLGFSAEEAQKQFGFLMDAFEFGAPPHGGIAFGFDRL 534

Query: 541 VMLLAGRLNLRDTIAFPKTASASCLLTEAPGEVSLEQLLDLNL 583
             + AG  ++RD IAFPK  S   ++ ++P  +  +QL +L +
Sbjct: 535 TSIFAGLDSIRDVIAFPKNNSGRDVMIDSPSTIDEKQLKELKI 577


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: 924
Number of extensions: 33
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: 581
Length adjustment: 37
Effective length of query: 558
Effective length of database: 544
Effective search space:   303552
Effective search space used:   303552
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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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