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 3609577 Dshi_2961 ABC transporter related (RefSeq)

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Dino:3609577
          Length = 511

 Score =  290 bits (742), Expect = 9e-83
 Identities = 181/499 (36%), Positives = 278/499 (55%), Gaps = 21/499 (4%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           T LL++ G+ K++   +A  D+   I  GE+HAL+GENGAGKSTL+K++ G+  PD G +
Sbjct: 2   TALLRVAGLTKAYPGVVANDDVSFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTM 61

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
              G P A  +P A+R+AG+ +++Q  ++   ++VA N+ +G E   ++       + +R
Sbjct: 62  TFGGVPFAPPEPRAARSAGVAMVFQHFSLFEALTVAENIALGMEDPPKM-----RDLAAR 116

Query: 124 TDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLF 183
              V +  G     S L G LS  E+Q+VEI R L+   +++IMDEPT+ L+ +E + LF
Sbjct: 117 ITQVSQAYGLPLDPSRLVGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDILF 176

Query: 184 NVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRS 243
             +R+LRDEG AI+YISH++ E+ AL D  T+LR G  V      E  +  + +MMVG++
Sbjct: 177 ATLRKLRDEGTAILYISHKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVGKT 236

Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALA-------GGKIRPASFDVRAGEVLGFAGLVGA 296
           L      Q+   A  A    V+++R L+       G  +R  S +VRAGEVLG  G+ G 
Sbjct: 237 L------QQTKSAGNAFGAPVLELRGLSQPATTPFGTPLRDISLEVRAGEVLGIGGVAGN 290

Query: 297 GRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAA 356
           G+ EL   + G + R+   I L G P+    P A  + G+   PE+R G      M++  
Sbjct: 291 GQDELLSAISG-ERRAEDAIFLHGTPISKIGPAARRQLGVLSGPEERLGHAAAPDMSLTE 349

Query: 357 NA--TMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLAR 414
           NA  T +V  + TR G +        A   I+  +V+   PE     LSGGN QK ++ R
Sbjct: 350 NALLTGSVREKLTRNGFLDWAKTRAFAERIIETFDVRTPGPEAAARALSGGNLQKFVIGR 409

Query: 415 WLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVM 474
            +   P+VLI+++PT GVD  A + I Q +  LA+ G AVVVIS +L E++ I D    +
Sbjct: 410 EVLQRPEVLIVNQPTWGVDASAAAAIRQALLDLAAGGTAVVVISQDLDELMEISDTFAAL 469

Query: 475 REGMITGELAGAAITQENI 493
             G ++G++  A +T E I
Sbjct: 470 NGGRLSGKVPAAGLTVEQI 488



 Score = 87.8 bits (216), Expect = 9e-22
 Identities = 63/243 (25%), Positives = 108/243 (44%), Gaps = 10/243 (4%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           SF++  GEV    G  GAG++ L ++++G      G +   G P    +PRAA  AG+A 
Sbjct: 24  SFEIAEGEVHALLGENGAGKSTLVKMIYGLVRPDSGTMTFGGVPFAPPEPRAARSAGVAM 83

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETP 398
           V +      LF  + VA N  + +          + R L        Q   + +  P   
Sbjct: 84  VFQHFS---LFEALTVAENIALGMEDPP------KMRDLAARITQVSQAYGLPL-DPSRL 133

Query: 399 VGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVIS 458
           VG LS G +Q+V + R L   PK+LI+DEPT  +       ++  + +L  +G A++ IS
Sbjct: 134 VGTLSAGERQRVEIIRCLLQEPKLLIMDEPTSVLTPQEVDILFATLRKLRDEGTAILYIS 193

Query: 459 SELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSSPTPLAP 518
            +L E+  +CD   ++R G +         +   +  +     + +T  A ++   P+  
Sbjct: 194 HKLEEIRALCDSATILRLGKVVATCDPREKSARELAEMMVGKTLQQTKSAGNAFGAPVLE 253

Query: 519 SHG 521
             G
Sbjct: 254 LRG 256


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: 660
Number of extensions: 39
Number of successful extensions: 8
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: 521
Length of database: 511
Length adjustment: 35
Effective length of query: 486
Effective length of database: 476
Effective search space:   231336
Effective search space used:   231336
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