GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01113 in Pseudomonas simiae WCS417

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>lcl|FitnessBrowser__WCS417:GFF3463 PS417_17730
           ribonucleotide-diphosphate reductase subunit alpha
          Length = 502

 Score =  321 bits (822), Expect = 4e-92
 Identities = 178/478 (37%), Positives = 284/478 (59%), Gaps = 8/478 (1%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           L++  + KR+ GV AL+ ++L  +RG+I+ LLGENG GKSTL+KI+ G +  DEGQ++I+
Sbjct: 5   LKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILID 64

Query: 76  GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135
           G      +  +A+AAGI  V+Q+ SL+P ++  EN+ L  EL+   G L +    R +  
Sbjct: 65  GQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRK----REMVE 120

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
            +    + +G+  + +     ++ L +A +Q V IA+A+A +A+ +++DEPT +LT  E 
Sbjct: 121 ASEALFKRLGVTIDLQ---CAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEA 177

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
           + L  ++  L+ QGV V+F+SH L+E + +   + VLRDG  +    +A+     + E+M
Sbjct: 178 ELLFEIMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMM 237

Query: 256 TGRHLS-NERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELA 314
            GR L+ +   + +     ++L+V+            F+LH GEILG  GL+ SGR ELA
Sbjct: 238 VGRRLACSFPPKPTRERGPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTELA 297

Query: 315 RALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAM 374
             + G  P+ S DV L G++I L  P+ A  H IG +PE R +EGL  D  IR+N+    
Sbjct: 298 LGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNN 357

Query: 375 ISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPR 434
           +   ++  G ID+ R  A  E  +K+L I  P  +  V +LSGGNQQ+V+I RW+     
Sbjct: 358 LPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCD 417

Query: 435 VLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHV 492
           VL+   PT G+DVG+K  IY +M+ L+++G  II+IS +LPE++  CDR+ +  KG +
Sbjct: 418 VLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAI 475


Lambda     K      H
   0.319    0.135    0.376 

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: 579
Number of extensions: 28
Number of successful extensions: 7
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: 515
Length of database: 502
Length adjustment: 34
Effective length of query: 481
Effective length of database: 468
Effective search space:   225108
Effective search space used:   225108
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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