Alignments for a candidate for HSERO_RS05250 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Dinoroseobacter shibae DFL-12

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  408 bits (1048), Expect = e-118
 Identities = 223/495 (45%), Positives = 318/495 (64%), Gaps = 6/495 (1%)

Query: 19  SVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGD 78
           S   +AL ++ K FPGV AL +    L  G+V AL+GENGAGKST++KIL+G+YQ D G 
Sbjct: 17  SQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGR 76

Query: 79  ILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELN 138
           IL+DG+PV  + P+ A   G+  IHQE  L + LS A+NIF+G  PR A GL ID  +  
Sbjct: 77  ILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGL-IDWKKTT 135

Query: 139 RQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198
             A A+   +  ++DP   + +L +A + +V IA+ALS ++RV+IMDEPTAAL++ EI E
Sbjct: 136 ENARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEE 195

Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           L+ ++  L+AQG  I++ISHK DE+ +IAD  +V RDG+ I    + + +   ++ MMVG
Sbjct: 196 LYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVG 255

Query: 259 RALDGEQRIPPDTSRN--DVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVA 316
           R +    +I P  + N  D VL V+G        D+SFTLR+GEILGF GL+GAGR+E  
Sbjct: 256 RDVS---QIFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFM 312

Query: 317 RAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376
           +++FG     AG + I G +A I SPADAV HGI Y+ EDR   G  + + +  N+ L S
Sbjct: 313 QSLFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPS 372

Query: 377 MGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDI 436
           +GR +R GF+        A+ Y  +L ++  S++     LSGGNQQK+VIAKWL     +
Sbjct: 373 LGRISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRV 432

Query: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496
           +  DEPT+G+D+G+K+ ++  +  LA QG A++M+SSE+PEVL MS RV+VM EGRI  E
Sbjct: 433 IILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAE 492

Query: 497 LARADATQEKIMQLA 511
           LA  D   E +++ A
Sbjct: 493 LAGDDLQPETLVRHA 507



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 67/226 (29%), Positives = 111/226 (49%), Gaps = 8/226 (3%)

Query: 39  DNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALG 98
           D+  F L  GE+    G  GAG+S  M+ L G+ +  +G + + G   EI+ P  A   G
Sbjct: 286 DDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHG 345

Query: 99  IGIIHQELNLMN---HLSAAQNIFI---GREPRKAMGLFIDEDELNRQAAAIFARMRLDM 152
           I  + ++         L   QN+ +   GR  RK      +E  L R+           +
Sbjct: 346 IVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKGFLRLAEEFALAREYTERLDLRAASL 405

Query: 153 DPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVG 212
           D  T VG L+   QQ V IAK L+   RV+I+DEPT  ++    A +   + +L AQG+ 
Sbjct: 406 D--THVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLA 463

Query: 213 IVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           ++ +S ++ E+  ++DRV VMR+G+ +A +   +   +T++    G
Sbjct: 464 VIMVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509



 Score = 91.3 bits (225), Expect = 8e-23
 Identities = 59/229 (25%), Positives = 113/229 (49%), Gaps = 5/229 (2%)

Query: 287 RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAV 346
           +A+ DVS +L  G++    G  GAG++ V + + G    + G I++ G      +P  A 
Sbjct: 34  KALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVPFSTPQAAA 93

Query: 347 AHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKT 406
            HG+  + ++   F     + V  NI L    R    G +D +   E A+  +  +  + 
Sbjct: 94  DHGVTAIHQETVLFD---ELSVAENIFLGHAPRGA-FGLIDWKKTTENARALLTSIGAEL 149

Query: 407 PSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGK 466
              + + + L   N+  + IA+ L  +  ++  DEPT  +      E+Y+L+++L  QGK
Sbjct: 150 DP-DHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESLKAQGK 208

Query: 467 AIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515
           AI+ IS +  E+ R++    V  +G++ G+ A AD T+  ++++   R+
Sbjct: 209 AILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRD 257


Lambda     K      H
   0.320    0.135    0.372 

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: 647
Number of extensions: 27
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
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 (21.8 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