GapMind for Amino acid biosynthesis

 

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

Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate CA265_RS19975 CA265_RS19975 aspartate--tRNA ligase

Query= uniprot:B8DMM5_DESVM
         (614 letters)



>FitnessBrowser__Pedo557:CA265_RS19975
          Length = 581

 Score =  577 bits (1486), Expect = e-169
 Identities = 289/580 (49%), Positives = 389/580 (67%), Gaps = 6/580 (1%)

Query: 23  VRSHDCATLTAADTGAEVCLMGWVQYRRDHGGLIFVDLRDRQGLTQIVFSPDVNPAAHER 82
           +R+  C  L   + G  V L GWVQ  RD GG+ F+D+RDR G+TQ+VF+ D N    E 
Sbjct: 2   LRTVTCGALNLNNLGESVTLCGWVQKSRDLGGMTFIDIRDRYGITQLVFNMDDNRELCET 61

Query: 83  AHIIRSEYVLAIRGTVRPRPEGMTNPGMKTGEIEVYVSEWKLLNTSKTPAFVIEDRTEAS 142
           A  +  E+V+   GTV  R     NP M TG++E+ +S  ++LN +K P F+I+D T+  
Sbjct: 62  ARTLGREFVIKAIGTVVERSN--KNPKMATGDVEIKISALEILNAAKLPPFMIDDETDGG 119

Query: 143 ENLRLQYRYLDLRRPRMANNFIVRHKAAQATRRYLDELGFLEIETPYLTKSTPEGARDFL 202
           + LR++YRYLDLRR  + NN ++RHK AQ+ RRYLD L F+E+ETP L KSTPEGARDF+
Sbjct: 120 DELRMKYRYLDLRRNPVRNNLVLRHKMAQSVRRYLDALDFIEVETPVLIKSTPEGARDFV 179

Query: 203 VPSRLNQGQFYALPQSPQLFKQLLMMSGMERYYQIVRCFRDEDMRADRQLEFTQIDIEMS 262
           VPSR+N+G+FYALPQSPQ FKQLLM+SG +RY+QIV+CFRDED+RADRQ EFTQID EMS
Sbjct: 180 VPSRMNEGEFYALPQSPQTFKQLLMVSGFDRYFQIVKCFRDEDLRADRQPEFTQIDCEMS 239

Query: 263 FVDEEQVMAMAEGLMARVFRDALDREIATPFPRMSYDDAMARYGVDKPDTRFGLELQDVT 322
           F+++E ++   EGL+  +F++  + ++    PRM Y DAM  YG DKPDTRF ++  ++ 
Sbjct: 240 FIEQEDILNTFEGLIRTLFKEVRNYDL-PEVPRMQYADAMRLYGSDKPDTRFAMQFVELN 298

Query: 323 HIVRGSNFKLFATAELVKAMRVPGGETMTRKEIDEFTEFVK--IYGAQGLAWIKIRPD-E 379
           H+V+G  F +F  AELV  +   G  + TRK++DE T+F+K    GA GL + +   D  
Sbjct: 299 HLVKGKGFPVFDNAELVVGINAKGAASYTRKQLDELTDFIKRPQIGATGLIYARHNEDGT 358

Query: 380 WQSPIAKFLSDEERAGLKDALGLETGDIVFFQAGAPGMVNAALGNLRVRLGEHLGLIDEN 439
            +S + KF ++E+     +A G E GD++   AG+   V   L  LR+ +G  LGL D+N
Sbjct: 359 IKSSVDKFFNEEDLKQWSEAFGTEKGDLLLILAGSTDKVRKQLNELRLEMGSRLGLRDKN 418

Query: 440 AFNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHMDVMVENPAAARARAYDMVLNGYE 499
            F+ LWV DFPL E+DEE +RY A HHPFTSPK   + ++  +P   RA AYDMV+NG E
Sbjct: 419 TFSALWVLDFPLLEWDEETERYHAMHHPFTSPKPEDIALLDTDPKNVRANAYDMVINGTE 478

Query: 500 LGGGSIRNHTAEKQRRMFAALGFSPEEAEAQFGFLTQALEMGAPPHGGIAFGMDRLAMLL 559
           +GGGSIR H    Q  MF  LGFS EEA+ QFGFL  A E GAPPHGGIAFG DRL  + 
Sbjct: 479 VGGGSIRIHDRALQALMFKHLGFSAEEAQKQFGFLMDAFEFGAPPHGGIAFGFDRLTSIF 538

Query: 560 TGSSSIRDVIAFPKTQKATCLLTQAPDSVSARQLRDLGLR 599
            G  SIRDVIAFPK      ++  +P ++  +QL++L ++
Sbjct: 539 AGLDSIRDVIAFPKNNSGRDVMIDSPSTIDEKQLKELKIK 578


Lambda     K      H
   0.321    0.137    0.407 

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: 927
Number of extensions: 24
Number of successful extensions: 4
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: 614
Length of database: 581
Length adjustment: 37
Effective length of query: 577
Effective length of database: 544
Effective search space:   313888
Effective search space used:   313888
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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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:

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