GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Dinoroseobacter shibae DFL-12

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  340 bits (871), Expect = 9e-98
 Identities = 189/477 (39%), Positives = 289/477 (60%), Gaps = 6/477 (1%)

Query: 18  KGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGER 77
           + I KR+ GV A+D+VDF V   E V L GENG+GKSTLIKI++GV    AG + + G+ 
Sbjct: 13  RAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQE 72

Query: 78  VEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRS 137
               +P  +   G+ VI Q+ +L  N++VAENI    + +  ++R    R   +     +
Sbjct: 73  HVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQ-LSTRQRLFKFRAVRDI----A 127

Query: 138 KELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFE 197
           +  LD IG +   DA V  L  AQ+Q+V IC+AL  + ++I MDEPT++LT +E  RL  
Sbjct: 128 RAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQG 187

Query: 198 IIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREV 257
           II MLK  G++V+FVSH+L EV+ +S+++VV+R+GK++ E    EFD  ++   M GR+V
Sbjct: 188 IIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTGRDV 247

Query: 258 EFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGV 317
              P        +  ++V+ L       ++SF++R GEVLG  GL+G GRT     +FG+
Sbjct: 248 PEVPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGL 307

Query: 318 NQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISR 377
              ++G I V+G  V + +P+ A    IG +PEDR  +GL L  ++  N+ +  L   + 
Sbjct: 308 VTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAHTS 367

Query: 378 WGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDE 437
            G  LD     + + D+++RL +K P +    ++LSGGNQQ+V LA+WL+    +LI + 
Sbjct: 368 GGF-LDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILNG 426

Query: 438 PTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLD 494
           P+ G+DVG+KA+IH +IRELA +G  VI+IS +LPE+L    R++VM EG I   L+
Sbjct: 427 PSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALE 483


Lambda     K      H
   0.319    0.138    0.381 

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: 565
Number of extensions: 25
Number of successful extensions: 6
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: 520
Length of database: 498
Length adjustment: 34
Effective length of query: 486
Effective length of database: 464
Effective search space:   225504
Effective search space used:   225504
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 (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