Alignments for a candidate for H281DRAFT_01113 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Dinoroseobacter shibae DFL-12

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  339 bits (870), Expect = 1e-97
 Identities = 190/498 (38%), Positives = 294/498 (59%), Gaps = 10/498 (2%)

Query: 10  PLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDE 69
           P+SQ  L +  + K F GV AL  VSLS   G++  L+GENG GKST++KI++G   PD 
Sbjct: 15  PVSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDG 74

Query: 70  GQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLA-RTF 128
           G+++++G P    +   A   G+  ++Q+  L   +SVAEN+ L      H  R A    
Sbjct: 75  GRILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLG-----HAPRGAFGLI 129

Query: 129 DRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTT 188
           D +     A   L ++G   + + +   ++ L +A + LVAIARA++ EA+ VIMDEPT 
Sbjct: 130 DWKKTTENARALLTSIGAELDPDHK---LKDLGIANKHLVAIARALSIEARVVIMDEPTA 186

Query: 189 SLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTK 248
           +L+ KE++ L  ++ +L+AQG  +LF+SHK DE + I     V RDGQ +  G IA+ T+
Sbjct: 187 ALSHKEIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTE 246

Query: 249 AQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDS 308
           A + ++M GR +S    + + +  D VL V+G+    +F D+SF L  GEILG  GL+ +
Sbjct: 247 ADLVKMMVGRDVSQIFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGA 306

Query: 309 GRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRD 368
           GR+E  ++L G+    +G V + G +  + +P+DA  H I YVPEDR  +G  LD PI  
Sbjct: 307 GRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQ 366

Query: 369 NVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRW 428
           NV    +  +  R G +      ALA +  + L +    +D  V +LSGGNQQ+V+I +W
Sbjct: 367 NVTLPSLGRI-SRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKW 425

Query: 429 LAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMK 488
           LA  PRV+IL  PT GVD+GSK  ++  M  L+ +G+ +I++S ++PE+L   DR+++M+
Sbjct: 426 LATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMR 485

Query: 489 KGHVSAEYRADELSEADL 506
           +G + AE   D+L    L
Sbjct: 486 EGRIVAELAGDDLQPETL 503



 Score = 83.6 bits (205), Expect = 2e-20
 Identities = 62/251 (24%), Positives = 115/251 (45%), Gaps = 6/251 (2%)

Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELAR 315
           T R L +E    S  A  +    + F      SDVS  L+ G++  + G   +G++ + +
Sbjct: 5   TQRPLPSEDPPVSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVK 64

Query: 316 ALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 375
            L G+     G +L+DGQ +   TP  A  H +  + ++ +   LF +  + +N+     
Sbjct: 65  ILTGIYQPDGGRILVDGQPVPFSTPQAAADHGVTAIHQETV---LFDELSVAENIFLG-- 119

Query: 376 SSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV 435
            + R  FG ID  +    A   +  +  A    D  ++ L   N+  V I R L+I+ RV
Sbjct: 120 HAPRGAFGLIDWKKTTENARALLTSIG-AELDPDHKLKDLGIANKHLVAIARALSIEARV 178

Query: 436 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAE 495
           +I+  PT  +     + +Y +++ L  +G  I+ IS    E+ +  D   + + G +  +
Sbjct: 179 VIMDEPTAALSHKEIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGD 238

Query: 496 YRADELSEADL 506
               +++EADL
Sbjct: 239 GAIADVTEADL 249


Lambda     K      H
   0.319    0.135    0.376 

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: 648
Number of extensions: 26
Number of successful extensions: 7
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: 515
Length of database: 510
Length adjustment: 35
Effective length of query: 480
Effective length of database: 475
Effective search space:   228000
Effective search space used:   228000
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:

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