GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_11890 in Pseudomonas simiae WCS417

Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= reanno::pseudo3_N2E3:AO353_21385
         (521 letters)



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

 Score =  403 bits (1035), Expect = e-117
 Identities = 214/494 (43%), Positives = 313/494 (63%), Gaps = 2/494 (0%)

Query: 27  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 86
           LL++ N+ K +PGV AL  + L+V  G + AL+GENGAGKSTLMKI+ G+   D G++ +
Sbjct: 4   LLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILI 63

Query: 87  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRCTA 146
            G+   F T   A+ AGI ++ QE +L+P+++  ENI++G E  N F ++  REM   + 
Sbjct: 64  DGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVEASE 123

Query: 147 QLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 206
            L +RL + +D +  V +LS+AE+Q VEIAKA++ D+ +L++DEPT+ +T  E   LF I
Sbjct: 124 ALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFEI 183

Query: 207 IADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 266
           + +LK QG  +I+I+H + E+F + D ++V RDG  +G+      D D L+ MMVGR L+
Sbjct: 184 MRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGRRLA 243

Query: 267 QLFPVR-EKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGI 325
             FP +  +  G LL+ V+D++L        F LH GEILG AGL+GSGRT +A  + G 
Sbjct: 244 CSFPPKPTRERGPLLLEVKDIQLVRNGPHNRFQLHKGEILGFAGLVGSGRTELALGMMGA 303

Query: 326 TPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYA- 384
            PS   ++ L G+ + + DP  A+  G  LL E RK  GL    S+ EN+ +  LP Y  
Sbjct: 304 LPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPKYQN 363

Query: 385 GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDE 444
            +G I +    A  E + K+L +K PS E  +  LSGGNQQK ++ARW+  +  +L+ DE
Sbjct: 364 ASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLVFDE 423

Query: 445 PTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSE 504
           PTRGIDVGAKA+IY L+  L  +G A+IMISSELPE++GM DRV V H+G ++  L+ S 
Sbjct: 424 PTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLEASA 483

Query: 505 ATQERVMQLASGMS 518
              + VM+ A+G S
Sbjct: 484 VNPQEVMRHATGGS 497


Lambda     K      H
   0.321    0.137    0.391 

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: 596
Number of extensions: 27
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: 521
Length of database: 502
Length adjustment: 35
Effective length of query: 486
Effective length of database: 467
Effective search space:   226962
Effective search space used:   226962
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