GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Pseudomonas simiae WCS417

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__WCS417:GFF2673
          Length = 510

 Score =  267 bits (682), Expect = 8e-76
 Identities = 170/483 (35%), Positives = 262/483 (54%), Gaps = 12/483 (2%)

Query: 13  PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG-EV 71
           P++E   ++K F     L  V ++V PGE HAL+G NGAGKSTL+ IL+G  + D G E+
Sbjct: 5   PLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEI 64

Query: 72  RFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDA 131
           R +G   P+     A    +A +YQ  ++  +LSVAEN+++ R+  RG  ID + M    
Sbjct: 65  RIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAGC 124

Query: 132 RALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFR 191
             +L     +     R   LS+  RQLVEIARAL   A+ +++DEPT  L   E  RLF 
Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184

Query: 192 RISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG-ER 250
            I +L+ +G+  ++ISH + E+Y +   V+VLRD  +I      AL  E L++ M G + 
Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGRDL 244

Query: 251 GGLAVADAAARGALPADTAVALELKELT-GADYEGVSFTVKRGEVVGLTGATSSGRTSVA 309
            G    + AA    P +  V + ++++  G      SF +  GEV+G+ G   +GRT +A
Sbjct: 245 SGFYKKEHAAYN--PGN--VVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTELA 300

Query: 310 EAIAGLRAAKRGTISVDGAILPPGDVPA-SLAHGIGCVPKDRHHEGLVLTQSVAENASMT 368
             I        GT+ V G  + P   PA ++  G+  + +DR  +GL L  SVA+N ++ 
Sbjct: 301 RLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINV- 359

Query: 369 IARVLGKFGIAAPAKKNAF--GQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATN 426
            A V          + +A       I +L I     +     LSGGNQQKV++AR L   
Sbjct: 360 CACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVK 419

Query: 427 PNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRV 485
           P+VL+L +PT GVD+ SK  +  +++++ + G  ++V+S EL + + TCDRVL+M  G++
Sbjct: 420 PHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQL 479

Query: 486 AAE 488
            AE
Sbjct: 480 VAE 482


Lambda     K      H
   0.318    0.134    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: 618
Number of extensions: 31
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: 510
Length of database: 510
Length adjustment: 34
Effective length of query: 476
Effective length of database: 476
Effective search space:   226576
Effective search space used:   226576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 (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