Alignments for a candidate for PS417_12065 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_12065 in Dinoroseobacter shibae DFL-12

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= uniprot:A0A1N7TX47
         (495 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  356 bits (914), Expect = e-103
 Identities = 197/489 (40%), Positives = 290/489 (59%), Gaps = 1/489 (0%)

Query: 7   LQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLN 66
           L   H+ K + GV AL D  LSL  G V AL G NGAGKST + IL GI Q D G IL++
Sbjct: 21  LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80

Query: 67  GAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRE 126
           G PV F+ P  A   G+  I QE      ++VAENI+LG  PR A  ++D K      R 
Sbjct: 81  GQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENARA 140

Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186
           LL S+  ++D    +  L +A   LV IA+A S + +V+IMDEPT+A+   E + L++ +
Sbjct: 141 LLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELV 200

Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELTR 246
             L AQG  I+++SH+  E+ +IAD+Y++FRDG  +  G +AD+    LV+ +VG+++++
Sbjct: 201 ESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQ 260

Query: 247 IDHKVGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLT 306
           I  +       +T L V   +   EF DIS  LR+GEILG YGL+G+GRSEF+  ++G+T
Sbjct: 261 IFPQRAPN-VGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGIT 319

Query: 307 VADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRLSSW 366
              +GSV + G    I  P   ++ G+  V EDR   G +L   I  N+ L +  R+S  
Sbjct: 320 RPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRK 379

Query: 367 SLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPT 426
             +   +E  LA +  +RL ++  SL+  V ++SGGNQQKVV+AK L+T P  ++ DEPT
Sbjct: 380 GFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPT 439

Query: 427 RGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDTALS 486
           +G+D G+K  ++  + +    G A I+VSSE PE+L +SDR+ V + GR+V       L 
Sbjct: 440 KGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQ 499

Query: 487 QEALLRLAS 495
            E L+R A+
Sbjct: 500 PETLVRHAA 508



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 67/235 (28%), Positives = 110/235 (46%), Gaps = 9/235 (3%)

Query: 14  KAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFN 73
           + YA      D   +LR G +    G  GAG+S F+  L GIT+  AGS+ + GA  + +
Sbjct: 277 QGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEIS 336

Query: 74  RPSEALAAGIAMITQELEP---IPYMTVAENIWL---GREPRRAGC-IVDNKALNRRTRE 126
            P++A+  GI  + ++      I  + + +N+ L   GR  R+    + +  AL R   E
Sbjct: 337 SPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKGFLRLAEEFALAREYTE 396

Query: 127 LLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAI 186
            LD     +D  + +  LS    Q V IAK  +   +V+I+DEPT  +       +   +
Sbjct: 397 RLDLRAASLD--THVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFM 454

Query: 187 RRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVG 241
             L AQG  ++ VS  + E+  ++D   + R+G  V      D+  + LVR   G
Sbjct: 455 AELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509


Lambda     K      H
   0.319    0.135    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: 582
Number of extensions: 25
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 495
Length of database: 510
Length adjustment: 34
Effective length of query: 461
Effective length of database: 476
Effective search space:   219436
Effective search space used:   219436
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources