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

GapMind for catabolism of small carbon sources

Aligments 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 3608553 Dshi_1947 ABC transporter related (RefSeq)

Query= uniprot:D8J111
         (520 letters)



>lcl|FitnessBrowser__Dino:3608553 Dshi_1947 ABC transporter related
           (RefSeq)
          Length = 514

 Score =  293 bits (750), Expect = 1e-83
 Identities = 181/494 (36%), Positives = 265/494 (53%), Gaps = 11/494 (2%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           PV+ L  + KRF  + A D   F+L AGEV AL+GENGAGK+TLM IL G Y  D G + 
Sbjct: 9   PVLRLDQITKRFGALTANDAISFDLHAGEVVALLGENGAGKTTLMNILFGHYTADEGTVE 68

Query: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140
           + G+ +    PR A A G+G++HQ   L ++LS   N+ +G  P    GL        R+
Sbjct: 69  VFGQTLPPGVPRAALAAGVGMVHQHFTLADNLSVLDNVILGTVPLWRAGL--GSGAARRK 126

Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200
             A+     L +DP   VG L+V  +Q VEI KAL  D+R+LI+DEPTA L   E   LF
Sbjct: 127 LRALAEDFGLQVDPEARVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQEAEALF 186

Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260
             +R   A+G+ +++ISHK+ E+  +A RV V+R G+ +  V   ET    +  MMVG  
Sbjct: 187 ATLRRAVARGMSVIFISHKLHEVMSVAHRVVVLRHGRVVGRVATDETDRHALAEMMVGAE 246

Query: 261 LDGEQRIPPD-----TSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEV 315
           +      P        + + V  + RG   G  +RDVS TLR G+I G AG+ G G+  +
Sbjct: 247 ITAPAPRPATPGAALMTLDRVCTDARGTATG--LRDVSLTLRAGQITGLAGVSGNGQAAL 304

Query: 316 ARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALS 375
           A  I G     AG + +   +    SP  A+A GIG + EDR   G      +  N  L 
Sbjct: 305 ADLIGGLIAPVAGALRLGNAEVADWSPRAALAQGIGRIPEDRHKTGTIADFTLTENAILE 364

Query: 376 S--MGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRD 433
           +    +F+R G+M   A    A+  +    ++ P  E   RLLSGGN QK+++ + L   
Sbjct: 365 AYPKAQFSRSGWMRWGAAESFARDVIASYDVRCPGPETPIRLLSGGNMQKLILGRVLEDG 424

Query: 434 CDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRI 493
             I+  ++P RG+D+GA + + + L A  + G A+++IS +L EVL +S  + VM EGR+
Sbjct: 425 PRIVLANQPVRGLDIGAVTYVQEQLIAARDGGAAVLLISEDLDEVLALSDVIHVMSEGRL 484

Query: 494 TGELARADATQEKI 507
           + E AR   T  ++
Sbjct: 485 SPEFARGSMTPAQL 498



 Score = 93.6 bits (231), Expect = 2e-23
 Identities = 66/229 (28%), Positives = 114/229 (49%), Gaps = 16/229 (6%)

Query: 292 VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIG 351
           +SF L  GE++   G  GAG+T +   +FG    + G + + G       P  A+A G+G
Sbjct: 29  ISFDLHAGEVVALLGENGAGKTTLMNILFGHYTADEGTVEVFGQTLPPGVPRAALAAGVG 88

Query: 352 YLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMD---QRAIREAAQMYVRQLAIKTPS 408
            + +   HF LA  + V  N+ L ++  + R G      +R +R  A+ +  Q       
Sbjct: 89  MVHQ---HFTLADNLSVLDNVILGTVPLW-RAGLGSGAARRKLRALAEDFGLQ------- 137

Query: 409 VEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGK 466
           V+ +AR+  LS G +Q++ I K L RD  IL  DEPT  +       ++  L     +G 
Sbjct: 138 VDPEARVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQEAEALFATLRRAVARGM 197

Query: 467 AIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRE 515
           +++ IS +L EV+ ++HRV+V+  GR+ G +A  +  +  + ++    E
Sbjct: 198 SVIFISHKLHEVMSVAHRVVVLRHGRVVGRVATDETDRHALAEMMVGAE 246


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: 584
Number of extensions: 23
Number of successful extensions: 7
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: 520
Length of database: 514
Length adjustment: 35
Effective length of query: 485
Effective length of database: 479
Effective search space:   232315
Effective search space used:   232315
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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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, or view the source code.

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