Alignments for a candidate for aspS2 in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Cupriavidus basilensis 4G11

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 RR42_RS02445 RR42_RS02445 aspartyl-tRNA synthetase

Query= SwissProt::Q51422
         (591 letters)



>FitnessBrowser__Cup4G11:RR42_RS02445
          Length = 601

 Score =  757 bits (1954), Expect = 0.0
 Identities = 380/597 (63%), Positives = 459/597 (76%), Gaps = 10/597 (1%)

Query: 2   MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61
           MR+HYCG + E L GQEV L GWV RRRDHGGVIF+D+RDREGL QVV DPDR E F  A
Sbjct: 4   MRTHYCGLVTEQLSGQEVALTGWVQRRRDHGGVIFIDLRDREGLVQVVCDPDRPEMFKAA 63

Query: 62  DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121
           + +R+EF V+ITGKVR RP G  N N+ SG IEVL +EL VLN + TPPF LD+  ++ E
Sbjct: 64  EEIRNEFCVRITGKVRPRPAGTENANLTSGKIEVLCHELTVLNPSVTPPFQLDD-DNLSE 122

Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181
            TRL +R +DLRRP+M   L+LR ++   +R+YLD  GF+D+ETP+LG+ TPEGARDYLV
Sbjct: 123 TTRLTHRVLDLRRPQMQYNLRLRYKVAMEVRKYLDAQGFIDIETPMLGKSTPEGARDYLV 182

Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241
           PSRT PGHFFALPQSPQ+FKQ+LMV+GFDRYYQI KCFRDEDLRADRQPEFTQID ETSF
Sbjct: 183 PSRTNPGHFFALPQSPQIFKQMLMVSGFDRYYQITKCFRDEDLRADRQPEFTQIDCETSF 242

Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFD-EFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300
           L+E +I  + E M+R +FK  +DV+ D  FP M F EAM R+GSDKPDLR+ LE  ++ D
Sbjct: 243 LNEQEIRDLFEDMMRTVFKNAIDVDLDASFPVMEFREAMARFGSDKPDLRVKLEFTELTD 302

Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360
            +K+V+FKVFSGPAN   GRV  L VPG A++ RS+ID YT+FV IYGAKGLA+IKVNE 
Sbjct: 303 AMKDVDFKVFSGPANSENGRVVGLCVPGGAAISRSEIDAYTQFVAIYGAKGLAWIKVNEV 362

Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD- 419
           AKG +GLQSPIVK + +A +  IL R GA DGDI+FFGADKAK+V DA+G LR+K+GH  
Sbjct: 363 AKGRDGLQSPIVKNLHDAAIAEILKRTGAKDGDIIFFGADKAKVVNDAIGGLRLKIGHSE 422

Query: 420 ----LKLLTREWAPMWVVDFPMFE-ENDDGSLSALHHPFTSPKCTPAE-LEANPGAALSR 473
                 L    W P+WV+DFPMFE + +D    A+HHPFTSPK    + LE +PG  +++
Sbjct: 423 FGKTHGLFEDVWKPLWVIDFPMFEYDEEDARWVAMHHPFTSPKDEHLQYLETDPGKCIAK 482

Query: 474 AYDMVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLA 533
           AYDMVLNG E+GGGS+RI  + +Q  VFR L I E E   KFG+LLDAL+YGAPPHGGLA
Sbjct: 483 AYDMVLNGWEMGGGSVRIFREDVQSKVFRALKIGEEEARAKFGYLLDALQYGAPPHGGLA 542

Query: 534 FGLDRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLR-EQPK 589
           FGLDR+V +M GA SIR+VIAFPKTQ A D++TQAP SVD K LRELHIRLR  +PK
Sbjct: 543 FGLDRIVTMMAGADSIRDVIAFPKTQRAQDLLTQAPSSVDEKQLRELHIRLRAAEPK 599


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: 1111
Number of extensions: 56
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: 601
Length adjustment: 37
Effective length of query: 554
Effective length of database: 564
Effective search space:   312456
Effective search space used:   312456
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