Alignments for a candidate for HSERO_RS03640 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 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:D8IZC7
         (521 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  388 bits (996), Expect = e-112
 Identities = 212/492 (43%), Positives = 306/492 (62%), Gaps = 6/492 (1%)

Query: 7   LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLD 66
           L +  I K+F    ALSD+ L++ PG++ AL+GENGAGKST++K+L+G++ PD G IL+D
Sbjct: 21  LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80

Query: 67  GRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDA 126
           G+PV    P A+   G+  I+QE  +   +SVA N+F+G   R   GLID         A
Sbjct: 81  GQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENARA 140

Query: 127 VLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVV 186
           +L  +GA          L IA +  V IARAL   +R+VIMDEPTAALS +E E+L+ +V
Sbjct: 141 LLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELV 200

Query: 187 RRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLSE 246
             L+ +G AI++ISH+  E++ +AD  TV RDG  +G+    ++    +V+MMVGR +S+
Sbjct: 201 ESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQ 260

Query: 247 FYQHQRIAPADAAQLPTVMQVRALAGG-KIRPASFDVRAGEVLGFAGLVGAGRTELARLL 305
            +  +     D     TV+ V+  A   +    SF +R GE+LGF GLVGAGR+E  + L
Sbjct: 261 IFPQRAPNVGD-----TVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSL 315

Query: 306 FGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASR 365
           FG    S G + + G    I  P  A+  GI YVPEDR  QG  L + +  N T+    R
Sbjct: 316 FGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGR 375

Query: 366 HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLIL 425
            +R G +R      +AR   +RL+++ A  +T VG LSGGNQQKV++A+WL   P+V+IL
Sbjct: 376 ISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIIL 435

Query: 426 DEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAG 485
           DEPT+GVDI +K+ ++  +  LA+QG+AV+++SSE+PEV+G+ DRV+VMREG I  ELAG
Sbjct: 436 DEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAG 495

Query: 486 AAITQENIMRLA 497
             +  E ++R A
Sbjct: 496 DDLQPETLVRHA 507



 Score =  105 bits (263), Expect = 3e-27
 Identities = 73/254 (28%), Positives = 127/254 (50%), Gaps = 6/254 (2%)

Query: 255 PADAAQLPTVMQVRALAGGK-IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSG 313
           P   A L      +   G K +   S  +  G+V    G  GAG++ + ++L G     G
Sbjct: 15  PVSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDG 74

Query: 314 GDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVR 373
           G IL++G+PV    P+AA   G+  + ++     LF +++VA N  +  A R    GL+ 
Sbjct: 75  GRILVDGQPVPFSTPQAAADHGVTAIHQETV---LFDELSVAENIFLGHAPRGA-FGLID 130

Query: 374 SRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVD 433
            +     ARA +  +  ++  P+  +  L   N+  V +AR L I  +V+I+DEPT  + 
Sbjct: 131 WKKTTENARALLTSIGAEL-DPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALS 189

Query: 434 IYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENI 493
                E+Y+LV  L +QG A++ IS +  E+  I D   V R+G + G+ A A +T+ ++
Sbjct: 190 HKEIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADL 249

Query: 494 MRLATDTNVPRTAP 507
           +++    +V +  P
Sbjct: 250 VKMMVGRDVSQIFP 263



 Score = 93.2 bits (230), Expect = 2e-23
 Identities = 66/223 (29%), Positives = 108/223 (48%), Gaps = 5/223 (2%)

Query: 24  DMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAAGI 83
           D+  T+R GEI    G  GAG+S  M+ L G+  P  G + + G    +  P  +   GI
Sbjct: 287 DISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHGI 346

Query: 84  NLIYQELA---VAPNISVAANVFMGSELR-TRLGLIDHAAMRSRTDAVLRQLGAGFGASD 139
             + ++        ++ +  NV + S  R +R G +  A   +       +L     + D
Sbjct: 347 VYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKGFLRLAEEFALAREYTERLDLRAASLD 406

Query: 140 L-AGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAIIY 198
              G LS   QQ+V IA+ L  R R++I+DEPT  +       + + +  L  +GLA+I 
Sbjct: 407 THVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIM 466

Query: 199 ISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241
           +S  + EV  ++DRV V+R+G  V EL  D++  E +V+   G
Sbjct: 467 VSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509


Lambda     K      H
   0.320    0.135    0.378 

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: 713
Number of extensions: 41
Number of successful extensions: 6
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: 521
Length of database: 510
Length adjustment: 35
Effective length of query: 486
Effective length of database: 475
Effective search space:   230850
Effective search space used:   230850
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