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

GapMind for catabolism of small carbon sources

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

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__Dino:3609044
          Length = 510

 Score =  437 bits (1123), Expect = e-127
 Identities = 223/500 (44%), Positives = 335/500 (67%), Gaps = 10/500 (2%)

Query: 10  EVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQI 69
           +  L   +ITKTFPGV A+++V+L +Y G+V AL+GENGAGKST++KIL G+Y    G+I
Sbjct: 18  QAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRI 77

Query: 70  FLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQ 129
            ++G+ V F  P+ A ++G+  I QE  L   LS AENIFL   P   FG+I+++K  E 
Sbjct: 78  LVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTEN 137

Query: 130 ASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLF 189
           A  L + +G  +DP  K++DL  + + +VAIA+ALS++A+++IMDEPT+A+  +E E+L+
Sbjct: 138 ARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELY 197

Query: 190 NIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRS 249
            ++ SLK +GK++++ISH+ +EIF IAD   V RDG+ +G+G I +     LV++MVGR 
Sbjct: 198 ELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRD 257

Query: 250 IDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTEL 309
           + Q F +    + D +  V+G             DD+SF +R+GE+LG YGLVGAGR+E 
Sbjct: 258 VSQIFPQRAPNVGDTVLTVQGY------AHPTEFDDISFTLREGEILGFYGLVGAGRSEF 311

Query: 310 LEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNITL 369
           ++++FG     + G V IGG   +I SP DAV +GI  VPEDR   G IL + +  N+TL
Sbjct: 312 MQSLFGI-TRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTL 370

Query: 370 PSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWLA 429
           PS  +  I RK G +    E  + R + E+L+++  S    V NLSGGNQQKVV+AKWLA
Sbjct: 371 PS--LGRISRK-GFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLA 427

Query: 430 IKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSEG 489
            +P+V++LDEPT+G+D+ +K+ ++  ++E+A  G+ V+MVSSE+PE+L MSDR++VM EG
Sbjct: 428 TRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREG 487

Query: 490 RKTAEFLREEVTEEDLLKAA 509
           R  AE   +++  E L++ A
Sbjct: 488 RIVAELAGDDLQPETLVRHA 507



 Score = 94.0 bits (232), Expect = 1e-23
 Identities = 62/224 (27%), Positives = 113/224 (50%), Gaps = 5/224 (2%)

Query: 29  NNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYPDYEGQIFLEGKEVRFRNPREAQENG 88
           ++++  + +GE+    G  GAG+S  M+ L G+     G + + G      +P +A ++G
Sbjct: 286 DDISFTLREGEILGFYGLVGAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHG 345

Query: 89  IALIPQELD---LVPNLSSAENIFL-SREPVNEFGVIEYQKMFEQASKLFSKLGVNIDP- 143
           I  +P++      + +L   +N+ L S   ++  G +   + F  A +   +L +     
Sbjct: 346 IVYVPEDRGKQGAILDLPIFQNVTLPSLGRISRKGFLRLAEEFALAREYTERLDLRAASL 405

Query: 144 KTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLFNIIRSLKNEGKSVI 203
            T V +LS   QQ V IAK L+   ++II+DEPT  +       + + +  L  +G +VI
Sbjct: 406 DTHVGNLSGGNQQKVVIAKWLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVI 465

Query: 204 YISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVG 247
            +S  + E+  ++DRV+VMR+GR V E   ++   + LVR   G
Sbjct: 466 MVSSEIPEVLGMSDRVIVMREGRIVAELAGDDLQPETLVRHAAG 509



 Score = 90.9 bits (224), Expect = 1e-22
 Identities = 59/239 (24%), Positives = 120/239 (50%), Gaps = 9/239 (3%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342
           + DVS  +  G+V  + G  GAG++ +++ + G +     G++ + G+ +   +P+ A  
Sbjct: 36  LSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQP-DGGRILVDGQPVPFSTPQAAAD 94

Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNI 402
           +G+  + ++     L  ++SV  NI L           FGLID +   E  R+ +  +  
Sbjct: 95  HGVTAIHQETV---LFDELSVAENIFLGHAPRGA----FGLIDWKKTTENARALLTSIGA 147

Query: 403 KTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVS 462
           +    +++ ++L   N+  V +A+ L+I+ +V+++DEPT  +      E+Y+L+  +   
Sbjct: 148 ELDPDHKL-KDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESLKAQ 206

Query: 463 GMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVETTQR 521
           G  ++ +S +  EI  ++D   V  +G+   +    +VTE DL+K  + R V     QR
Sbjct: 207 GKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQIFPQR 265


Lambda     K      H
   0.317    0.137    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: 596
Number of extensions: 28
Number of successful extensions: 8
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: 523
Length of database: 510
Length adjustment: 35
Effective length of query: 488
Effective length of database: 475
Effective search space:   231800
Effective search space used:   231800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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