GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Dino:3608553
          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:

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:

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:

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:

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