GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aspS2 in Lentibacillus jeotgali Grbi

Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_010531090.1 ON01_RS10970 aspartate--tRNA ligase

Query= BRENDA::Q9KDG1
         (595 letters)



>NCBI__GCF_000224785.1:WP_010531090.1
          Length = 588

 Score =  780 bits (2015), Expect = 0.0
 Identities = 386/581 (66%), Positives = 467/581 (80%)

Query: 9   GQLSEEQVNERVQLKGWVQRRRDLGQVIFVDLRDRSGVVQLVFNSDISQEALETAEKVRN 68
           G LSE  V++ V LKGWVQ RRDLG +IF+DLRDRSG+VQ+VFN D S+ ALE AE VR 
Sbjct: 8   GTLSENDVDQSVLLKGWVQTRRDLGGLIFIDLRDRSGLVQVVFNPDHSKAALEAAEAVRT 67

Query: 69  EYVLDVEGVVLKRDPSTVNDKIATGTIEVHVERLTILNKAKSLPFQIEANTDASEDIRLK 128
           EYVL++ G V+KRD  TVN  + TG IEV  + LTILNKAK+ PF I+  TD +ED+RLK
Sbjct: 68  EYVLEITGSVVKRDEGTVNPAMGTGRIEVIAKDLTILNKAKTPPFLIQEETDVAEDLRLK 127

Query: 129 YRYLDLRRPDMQETMKLRHQTTKLIRDFLDGQEFFEIETPMLTKSTPEGARDYLVPSRVH 188
           YRY+DLRR  +QET K+RH+TT+ IR+FL+   F E+ETP+LTKSTPEGARDYLVPSRVH
Sbjct: 128 YRYIDLRRNKLQETFKMRHRTTQAIRNFLNDDGFLEMETPILTKSTPEGARDYLVPSRVH 187

Query: 189 HGEFYALPQSPQIFKQLLMVSGFERYYQIVRCFRDEDLRADRQPEFTQIDIETSFMDKED 248
           HG+FYALPQSPQ+FKQL+M+ GFE+YYQI RCFRDEDLRADRQPEFTQ+DIETSF+  ++
Sbjct: 188 HGQFYALPQSPQLFKQLIMMGGFEKYYQIARCFRDEDLRADRQPEFTQVDIETSFLTSDE 247

Query: 249 LLTMTENMMAKIMKEVKGLDVALPFPRMTYDDAMNRYGSDKPDTRFEMELIELSDIVKDS 308
           ++ MTE MM  ++KEVK +D++LP PRM YD+AM+R+GSDKPDTRF MELI +SDIVKDS
Sbjct: 248 IMDMTEQMMRHVLKEVKNVDISLPLPRMPYDEAMSRFGSDKPDTRFGMELIHVSDIVKDS 307

Query: 309 DFKVFSSAIKSGGIVKGLNLKGGAGSLSRKEIDGLAEFVKPYGAKGLAWLKVEEGELKGP 368
            FKVF  A++SGG V  LN KG A + SRK+ID L +FVK Y AKG+AWLKV+ G+L GP
Sbjct: 308 SFKVFKGAVESGGKVCLLNAKGQAANYSRKDIDQLTDFVKIYDAKGMAWLKVDGGQLTGP 367

Query: 369 IAKFFAGETGAELQQAMGAEDGDLLFFAADKKEVVFDSLGALRLKLGKDFNLIDESKFNF 428
           IAKF + +    L +   AEDGDLL F +DK  VV+DSLGALRLKLG++ NLIDE+KFNF
Sbjct: 368 IAKFLSDDETNGLIERSAAEDGDLLLFGSDKSSVVYDSLGALRLKLGRELNLIDETKFNF 427

Query: 429 LWVVDFPLVEYDEEAKRFVALHHPFTSPKQEDLTKLETDPASVRADAYDLVLNGYELGGG 488
           LWV D+PL+EYDE+ +R+ A HHPFT P +EDL KL+ DP+ VRA+AYDLVLNGYELGGG
Sbjct: 428 LWVTDWPLLEYDEDLERYFAAHHPFTMPVEEDLDKLDMDPSDVRANAYDLVLNGYELGGG 487

Query: 489 SQRIYQRPVQEKMFAALGFTEEAAQKEFGFLLEAFEYGTPPHGGIALGLDRLVMLLAGRL 548
           S RI+++  Q KM   LGFT+E A ++FGFLLEA EYG PPHGGIALGLDR+VMLLAG  
Sbjct: 488 SLRIHKKDQQMKMLDVLGFTQEEADEQFGFLLEALEYGAPPHGGIALGLDRIVMLLAGSS 547

Query: 549 NLRDTIAFPKTASASCLLTEAPGEVSLEQLLDLNLSIIGHK 589
           NLRDTI FPKTASAS LLT+AP +VS  QL +L + I   K
Sbjct: 548 NLRDTILFPKTASASDLLTDAPNDVSKGQLDELAIQINDEK 588


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: 1025
Number of extensions: 35
Number of successful extensions: 1
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: 588
Length adjustment: 37
Effective length of query: 558
Effective length of database: 551
Effective search space:   307458
Effective search space used:   307458
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 Jul 26 2024. The underlying query database was built on Jul 25 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:

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