Alignments for a candidate for rhaT' in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Dinoroseobacter shibae DFL-12

Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  342 bits (876), Expect = 2e-98
 Identities = 189/487 (38%), Positives = 291/487 (59%), Gaps = 3/487 (0%)

Query: 19  AILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEIL 78
           A +++R I++ + GV ALD+V   + PG    L GENG+GKSTL+KI++G+     G + 
Sbjct: 8   AFIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQ 67

Query: 79  VDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRS 138
           + G+     + + +  AGV  I Q+  LF  L+VAENI       TR R   ++ +   +
Sbjct: 68  IAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIA 127

Query: 139 KALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFR 198
           +A L  +   ID   R++ L +AQ+ LVAI RAL+ +A+++IMDEPT AL+ KE+  L  
Sbjct: 128 RAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQG 187

Query: 199 IVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRD 258
           I+R LKE+G A++F+SHK  E+ E+++  VV  R  ++   G + +     +   M GRD
Sbjct: 188 IIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVL-RNGKKVAEGPASEFDTQSLTYHMTGRD 246

Query: 259 VENVFPKIDVAIGGPVL-EIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLF 317
           V  V P  DVA G   L +++       F DISF LR GE+LG+ GL+G GR+ ++++LF
Sbjct: 247 VPEV-PPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALF 305

Query: 318 GITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLART 377
           G+  P +G ++++G  + +  PQ A  A I YVPE+R   GL L   I +N+ +  L   
Sbjct: 306 GLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAH 365

Query: 378 SRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILD 437
           +  GFL        A  +  RL ++A  +  PV +LSGGNQQ+V + +WL+ AP+V+IL+
Sbjct: 366 TSGGFLDMTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLILN 425

Query: 438 EPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERA 497
            P+ G+D+GSKA +H  I ELA EG+ +I++S +LPE++    RVLVM+EG      E  
Sbjct: 426 GPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALEGT 485

Query: 498 ELSPEAL 504
            L+ + L
Sbjct: 486 ALTEDDL 492



 Score = 87.0 bits (214), Expect = 1e-21
 Identities = 62/236 (26%), Positives = 120/236 (50%), Gaps = 11/236 (4%)

Query: 278 RNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIH 337
           + Y+  T    + FT++ GE + + G  G+G+S L + + G+    +G + + GQE    
Sbjct: 17  KRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQEHVTL 76

Query: 338 SPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSRRGF-LRAANEFALAR--K 394
           +P+ +  AG++ + ++     L   + + +N+   +   T +R F  RA  + A A   +
Sbjct: 77  NPRISAAAGVMVIFQD---FSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARAALDR 133

Query: 395 YAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGF 454
              ++DL A   ++PV       +Q V I + LA+  ++II+DEPT  +       + G 
Sbjct: 134 IGVQIDLDARVETLPVA-----QKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGI 188

Query: 455 ISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
           I  L  EG+++I VS +L E++ +S++V+V++ G        +E   ++L    TG
Sbjct: 189 IRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLTYHMTG 244


Lambda     K      H
   0.320    0.137    0.382 

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: 593
Number of extensions: 26
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: 512
Length of database: 498
Length adjustment: 34
Effective length of query: 478
Effective length of database: 464
Effective search space:   221792
Effective search space used:   221792
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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Steps (tab-delimited)
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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