Alignments for a candidate for aspS2 in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for aspS2 in Acidovorax sp. GW101-3H11

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 Ac3H11_4801 Aspartyl-tRNA synthetase (EC 6.1.1.12) @ Aspartyl-tRNA(Asn) synthetase (EC 6.1.1.23)

Query= SwissProt::Q51422
         (591 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4801
          Length = 600

 Score =  725 bits (1871), Expect = 0.0
 Identities = 363/591 (61%), Positives = 453/591 (76%), Gaps = 8/591 (1%)

Query: 2   MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61
           MRSHYCG + E+L GQ VTL GWV+RRRDHGGVIF+D+RDREG  QVV DPDRAE F  A
Sbjct: 3   MRSHYCGLVTEALMGQTVTLSGWVNRRRDHGGVIFIDLRDREGYVQVVCDPDRAEMFKTA 62

Query: 62  DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121
           + VR+EF V++ G VR RP+G  N  + SG IEVL +EL+VLN + TPPF +D+  ++ E
Sbjct: 63  EDVRNEFCVQVVGLVRPRPDGTTNDKLKSGQIEVLCHELKVLNPSVTPPFQMDD-ENLSE 121

Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181
            TRL +R +DLRRP M   + LR +    +R +LD  GF+D+ETP+LG+ TPEGARDYLV
Sbjct: 122 TTRLTHRVMDLRRPHMQRNMMLRYKTAIQVRNFLDKEGFIDIETPMLGKSTPEGARDYLV 181

Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241
           PSR + G FFALPQSPQL+KQ+LMVAG+DRYYQI KCFRDEDLRADRQPEFTQID ETSF
Sbjct: 182 PSRVHDGQFFALPQSPQLYKQMLMVAGYDRYYQITKCFRDEDLRADRQPEFTQIDCETSF 241

Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301
           L+E +I  I ++M+ ++F++ L V+  EFP M ++EA  R+GSDKPDLR+ LE  ++ + 
Sbjct: 242 LNEEEIRAIFQRMITEVFQQQLGVDLGEFPIMTYQEAAFRFGSDKPDLRVKLEFTELTEV 301

Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361
           +K+V+FKVFS PA    GRV ALRVPG + + R +ID YT+FV IYGAKGLA+IKVNE A
Sbjct: 302 MKDVDFKVFSAPATTKGGRVVALRVPGGSQISRGEIDAYTEFVKIYGAKGLAWIKVNEVA 361

Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD-- 419
           +G EGLQSPIVK + +A +  IL R GA DGD++FFGADK KIV D++GALR+KVGH   
Sbjct: 362 QGREGLQSPIVKNLHDAAIAEILKRTGAQDGDLLFFGADKEKIVNDSIGALRLKVGHSEF 421

Query: 420 ---LKLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTPAEL-EANPGAALSRA 474
                L   +WAP+WVVDFPMFE +++    +A+HHPFTSPK    +L + +PG  +++A
Sbjct: 422 GKKNGLFEAKWAPLWVVDFPMFEHDEENDRWAAVHHPFTSPKDGHEDLMDTDPGKCIAKA 481

Query: 475 YDMVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAF 534
           YDMVLNG ELGGGS+RIH   +Q+ VF  L I   + + KFG+LLDAL+YGAPPHGGLAF
Sbjct: 482 YDMVLNGWELGGGSVRIHRADVQKKVFDALKITPEDAQAKFGYLLDALQYGAPPHGGLAF 541

Query: 535 GLDRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLR 585
           GLDRL+ LMTGA SIR+VIAFPKTQ A D++TQAP  VD K LRELHIRLR
Sbjct: 542 GLDRLITLMTGAESIRDVIAFPKTQRAQDLLTQAPSPVDEKQLRELHIRLR 592


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: 1117
Number of extensions: 55
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: 591
Length of database: 600
Length adjustment: 37
Effective length of query: 554
Effective length of database: 563
Effective search space:   311902
Effective search space used:   311902
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