Alignments for a candidate for aspS2 in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Burkholderia phytofirmans PsJN

Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate BPHYT_RS03200 BPHYT_RS03200 aspartate--tRNA(Asp/Asn) ligase

Query= SwissProt::Q51422
         (591 letters)



>FitnessBrowser__BFirm:BPHYT_RS03200
          Length = 599

 Score =  731 bits (1888), Expect = 0.0
 Identities = 375/597 (62%), Positives = 451/597 (75%), Gaps = 10/597 (1%)

Query: 2   MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61
           MRS YCG + E L GQ V+LCGWV RRRDHGGVIF+D+RDREGL QVV DPDRAE F  A
Sbjct: 3   MRSQYCGLVTEELLGQSVSLCGWVSRRRDHGGVIFIDLRDREGLVQVVCDPDRAEMFKAA 62

Query: 62  DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121
           + VR+EF ++I G VR RPEG  N  + SG IEVL +EL VLN + TPPF LD+  ++ E
Sbjct: 63  EGVRNEFCLQIKGVVRGRPEGTTNAALKSGKIEVLCHELIVLNPSITPPFQLDD-DNLSE 121

Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181
            TRL +R +DLRRP+M   L+LR R+    R+YLD  GF+D+ETP+L + TPEGARDYLV
Sbjct: 122 TTRLTHRVLDLRRPQMQHNLRLRYRVAIEARKYLDSLGFIDIETPMLTKSTPEGARDYLV 181

Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241
           PSRT PG FFALPQSPQLFKQLLMVA FDRYYQI KCFRDEDLRADRQPEFTQID ETSF
Sbjct: 182 PSRTNPGQFFALPQSPQLFKQLLMVANFDRYYQIVKCFRDEDLRADRQPEFTQIDCETSF 241

Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDE-FPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300
           L E +I  + E M+R +FKE + V  DE FP M + EAMRR+GSDKPDLR+ LE  D+ D
Sbjct: 242 LSEQEIRDLFEDMIRHVFKETIGVTLDEKFPVMLYSEAMRRFGSDKPDLRVKLEFTDLTD 301

Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360
            +++V+FKVFS PAN   GRVAA+RVP    + R  ID YT+FV IYGAKGLA+IKVNE 
Sbjct: 302 AVRDVDFKVFSTPANTKDGRVAAIRVPKGGELSRGDIDSYTEFVRIYGAKGLAWIKVNEV 361

Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD- 419
           AKG +GLQSPIVK + +  +  I++R GA DGDI+FF AD+AK+V D+LGALR+K+GH  
Sbjct: 362 AKGRDGLQSPIVKNLHDEAVKAIIERTGAQDGDIIFFAADRAKVVNDSLGALRLKIGHSE 421

Query: 420 ----LKLLTREWAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAE-LEANPGAALSR 473
                 L+   W P+WVVDFPMFE + +D    A HHPFTSPK    E LE +P   L++
Sbjct: 422 FGKANGLVETGWKPLWVVDFPMFEYDEEDNRYVAAHHPFTSPKDEHLEYLETDPARCLAK 481

Query: 474 AYDMVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLA 533
           AYDMVLNG E+GGGS+RIH + +Q  VFR L I+  E + KFGFLLDAL+YGAPPHGG+A
Sbjct: 482 AYDMVLNGWEIGGGSVRIHREEVQSKVFRALKINAEEAQAKFGFLLDALQYGAPPHGGIA 541

Query: 534 FGLDRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLRE-QPK 589
           FGLDR+V +M GA SIR+VIAFPKTQ A  ++TQAP  VD + LRELHIRLR+ +PK
Sbjct: 542 FGLDRIVTMMAGADSIRDVIAFPKTQRAQCLLTQAPSEVDERQLRELHIRLRQPEPK 598


Lambda     K      H
   0.321    0.140    0.411 

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: 1099
Number of extensions: 52
Number of successful extensions: 6
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: 591
Length of database: 599
Length adjustment: 37
Effective length of query: 554
Effective length of database: 562
Effective search space:   311348
Effective search space used:   311348
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 (21.8 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