GapMind for catabolism of small carbon sources

 

Aligments 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 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= uniprot:Q9WXX0
         (520 letters)



>lcl|FitnessBrowser__Dino:3609044 Dshi_2433 ABC transporter related
           (RefSeq)
          Length = 510

 Score =  405 bits (1041), Expect = e-117
 Identities = 216/493 (43%), Positives = 322/493 (65%), Gaps = 10/493 (2%)

Query: 20  IVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVE 79
           I K FPGV A+ +V   +Y  ++ +LIGENGAGKST++KILTG+ +PD G ILV+G+ V 
Sbjct: 26  ITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVP 85

Query: 80  FHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKE 139
           F +P  A   G++ IHQE  L D ++VAENIFL + A RG        +D       ++ 
Sbjct: 86  FSTPQAAADHGVTAIHQETVLFDELSVAENIFLGH-APRGA----FGLIDWKKTTENARA 140

Query: 140 LLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEII 199
           LL  IGA+  PD  +++L  A + +V I +AL  E R++ MDEPT++L+ +E E L+E++
Sbjct: 141 LLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELV 200

Query: 200 EMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREV-E 258
           E LK++G +++F+SH+ DE+ RI+D   V RDG+ IG+    +     ++KMMVGR+V +
Sbjct: 201 ESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQ 260

Query: 259 FFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVN 318
            FP       G+  L V+      +  ++SF +R+GE+LGF GLVGAGR+E M  +FG+ 
Sbjct: 261 IFPQRAPN-VGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGIT 319

Query: 319 QKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRW 378
           +  +G + + G + EI +P DA+  GI  +PEDR  QG +L + +  N+ LPSL +ISR 
Sbjct: 320 RPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRK 379

Query: 379 GLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDEP 438
           G  L   +E  ++ +Y +RL ++  S+     NLSGGNQQKVV+AKWLAT   ++I DEP
Sbjct: 380 GF-LRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEP 438

Query: 439 TRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLDNREK 498
           T+G+D+G+KA +H  + ELAAQG AVIM+SSE+PE+L +SDR++VM EG I A L   + 
Sbjct: 439 TKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDD- 497

Query: 499 RVTQEEIMYYASG 511
            +  E ++ +A+G
Sbjct: 498 -LQPETLVRHAAG 509


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: 634
Number of extensions: 30
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 520
Length of database: 510
Length adjustment: 35
Effective length of query: 485
Effective length of database: 475
Effective search space:   230375
Effective search space used:   230375
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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