GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate Pf6N2E2_162 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_162
          Length = 517

 Score =  272 bits (696), Expect = 2e-77
 Identities = 174/481 (36%), Positives = 265/481 (55%), Gaps = 17/481 (3%)

Query: 30  LNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSIADRDAWRE 89
           L D+++ +M GE  AL G NGAGKSTL  I+ GL  P TG+++F G      +   A   
Sbjct: 24  LTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQGQDYRPGSRTQAEEL 83

Query: 90  RVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHWKID-VREDARA 148
            V  V Q   ++  LSVAENLF++  P  GG I  + +R+ A   +    +D +  D   
Sbjct: 84  GVRMVMQELNLLPTLSVAENLFLDNLPNHGGWISRKQLRKAAIEAMAQVGLDAIDPDTLV 143

Query: 149 GDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQREGVTFLFISH 208
           G+L +  +Q+VEIAR L      +ILDEPTA L   E++ LF +I+ LQ  GV+ ++ISH
Sbjct: 144 GELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQARGVSIIYISH 203

Query: 209 HLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADAAARGALPADT 268
            L+E+  + Q + VLRD   +   P++    EQL+  M G   G  +     +   PA  
Sbjct: 204 RLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELGEHIDLGPRQIGAPA-- 261

Query: 269 AVALELKELTGAD-YEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRAAKRGTISVDG 327
              L +K LT +D    VSF V+ GE+ G++G   +GRT +   I G   A  GT+++  
Sbjct: 262 ---LTVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADTADSGTVALGS 318

Query: 328 -----AILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFGIAAPA 382
                +I  P D   ++AHGI  + +DR  EGL+LTQS+A N ++     +   G+    
Sbjct: 319 PAQVVSIRSPAD---AVAHGIALITEDRKGEGLLLTQSIAANIALGNMPEISSAGLVNGD 375

Query: 383 KKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPTAGVDVK 442
            + A  Q+ +DA+ I +  P  +VS LSGGNQQKVV+ R L  +  V++  +PT G+DV 
Sbjct: 376 AELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRGIDVG 435

Query: 443 SKEALLSVVDRVREEGKAVLVVSGELDDLR-TCDRVLVMFRGRVAAEFPA-GWQDHDLIA 500
           +K  + +++  +  +GKA++VVS +L +L   CDR+ V+  GR+   F    W   DL+A
Sbjct: 436 AKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQDDLLA 495

Query: 501 S 501
           +
Sbjct: 496 A 496


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: 596
Number of extensions: 36
Number of successful extensions: 9
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: 517
Length adjustment: 35
Effective length of query: 475
Effective length of database: 482
Effective search space:   228950
Effective search space used:   228950
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