GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aspS2 in Pseudomonas simiae WCS417

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 GFF4388 PS417_22465 aspartyl-tRNA synthetase

Query= SwissProt::Q51422
         (591 letters)



>FitnessBrowser__WCS417:GFF4388
          Length = 591

 Score = 1054 bits (2726), Expect = 0.0
 Identities = 521/591 (88%), Positives = 555/591 (93%)

Query: 1   MMRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAK 60
           MMRSHYCGQLNE+L+GQE+TLCGWVHRRRDHGGVIFLD+RDR+GLAQVVFDPDRAE+FA 
Sbjct: 1   MMRSHYCGQLNETLEGQEITLCGWVHRRRDHGGVIFLDIRDRDGLAQVVFDPDRAESFAA 60

Query: 61  ADRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVG 120
           ADRVRSE+VVKITGKVRLRP GA N NMASG IEVLGYELEVLN++ETPPFPL+EYSDVG
Sbjct: 61  ADRVRSEYVVKITGKVRLRPAGAVNKNMASGGIEVLGYELEVLNESETPPFPLNEYSDVG 120

Query: 121 EETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYL 180
           EETRLRYRF+DLRRPEMA KL+LR+R+T+SIRR+LD+NGFLDVETPIL R TPEGARDYL
Sbjct: 121 EETRLRYRFLDLRRPEMAEKLRLRSRMTTSIRRFLDENGFLDVETPILTRATPEGARDYL 180

Query: 181 VPSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240
           VPSRT+ G FFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS
Sbjct: 181 VPSRTHAGSFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETS 240

Query: 241 FLDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300
           FLDE +I+G+TE+M+R LFKEVLD+EF +FPHM FEEAMRRYGSDKPDLR PLELVDVAD
Sbjct: 241 FLDEKEIMGLTEQMIRNLFKEVLDLEFGDFPHMTFEEAMRRYGSDKPDLRNPLELVDVAD 300

Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360
           QLKEV+FKVFSGPANDPK R+AALRVPG ASMPR QIDDYTKFVGIYGAKGLAYIKVNER
Sbjct: 301 QLKEVDFKVFSGPANDPKCRIAALRVPGGASMPRKQIDDYTKFVGIYGAKGLAYIKVNER 360

Query: 361 AKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHDL 420
           A GV+GLQSPIVK IP  NLN ILDRVGAVDGDIVFFGADKAKIV +ALGALRIK+GHDL
Sbjct: 361 ANGVDGLQSPIVKNIPLDNLNAILDRVGAVDGDIVFFGADKAKIVSEALGALRIKLGHDL 420

Query: 421 KLLTREWAPMWVVDFPMFEENDDGSLSALHHPFTSPKCTPAELEANPGAALSRAYDMVLN 480
            LLT EWAPMWVVDFPMFEENDDGS SALHHPFT+PKC+PAELEANP  ALSRAYDMVLN
Sbjct: 421 NLLTCEWAPMWVVDFPMFEENDDGSFSALHHPFTAPKCSPAELEANPAGALSRAYDMVLN 480

Query: 481 GTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLV 540
           GTELGGGSIRIH K MQQAVFR+LGI+EAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLV
Sbjct: 481 GTELGGGSIRIHRKEMQQAVFRLLGINEAEQEEKFGFLLDALKYGAPPHGGLAFGLDRLV 540

Query: 541 MLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591
           MLMTGA SIREVIAFPKTQSA DVMTQAPG VD KALRELHIRLRE PKAE
Sbjct: 541 MLMTGAQSIREVIAFPKTQSAADVMTQAPGVVDAKALRELHIRLRETPKAE 591


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: 1308
Number of extensions: 40
Number of successful extensions: 2
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: 591
Length adjustment: 37
Effective length of query: 554
Effective length of database: 554
Effective search space:   306916
Effective search space used:   306916
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 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