GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araVsh in Pseudomonas simiae WCS417

Align ABC transporter related (characterized, see rationale)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= uniprot:A0KWY5
         (499 letters)



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

 Score =  357 bits (915), Expect = e-103
 Identities = 198/501 (39%), Positives = 307/501 (61%), Gaps = 7/501 (1%)

Query: 1   MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60
           MS +L+L+ I K YPGV+AL+ ++L++  GE+HALLGENGAGKSTL+K++ G + +D G 
Sbjct: 1   MSSLLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQ 60

Query: 61  ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYE-PRRLGLIHFKKMYA 119
           IL  G+ Q F T  DA  AGI  V+QE +L+P LT  +N+FLG+E   R GL+  ++M  
Sbjct: 61  ILIDGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVE 120

Query: 120 DARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179
            + A+  +  + ID+   +   S+A QQ + IA+ +A+ A++LVLDEPTA+L   E ++L
Sbjct: 121 ASEALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELL 180

Query: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239
           F I+ +LK +GVA++FI+H L++++Q+ DRI+VLR+G  +G    A+     L+E M+GR
Sbjct: 181 FEIMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGR 240

Query: 240 SLQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSE 299
            L      K  +ER       +LL ++D+ +  +       + KG+ +G AGL+GSGR+E
Sbjct: 241 RLACSFPPKPTRER-----GPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTE 295

Query: 300 VCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL 359
           +   + G     S  + L G+K+ L  P  A++ GI L PE RK +G+I   SIRENI L
Sbjct: 296 LALGMMGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISL 355

Query: 360 -ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIE 418
             L         +   R+    +  + +L I  P ++  +  LSGGNQQKV++ARW+   
Sbjct: 356 NNLPKYQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHH 415

Query: 419 PILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYA 478
             +LV DEPTRGID+GA A+I  L+R+L ++G ++++ SSEL E++   ++V V      
Sbjct: 416 CDVLVFDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAI 475

Query: 479 VRELSGAELTSQHVMQAIAEG 499
           V+ L  + +  Q VM+    G
Sbjct: 476 VKLLEASAVNPQEVMRHATGG 496


Lambda     K      H
   0.319    0.136    0.377 

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: 534
Number of extensions: 24
Number of successful extensions: 8
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: 499
Length of database: 502
Length adjustment: 34
Effective length of query: 465
Effective length of database: 468
Effective search space:   217620
Effective search space used:   217620
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: 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, the preprint on GapMind for carbon sources, 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