GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Paucidesulfovibrio gracilis DSM 16080

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  261 bits (666), Expect = 6e-74
 Identities = 157/485 (32%), Positives = 264/485 (54%), Gaps = 12/485 (2%)

Query: 20  VPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDI 79
           +P+++++ + KRF  V+A D+    +  G V AL+GENGAGKSTLM +L+G YQ D+G I
Sbjct: 22  IPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTI 81

Query: 80  LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNR 139
            LDGKPV  +  R A   GIG+++Q   L+  ++ A+N+ +G+E       F++  E+  
Sbjct: 82  ALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEG----SFFLNPKEMRN 137

Query: 140 QAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAEL 199
           +   +  R  LD+DP+  V +L++  +Q VEI K L  DSRVLI DEPTA L   E   L
Sbjct: 138 RVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHL 197

Query: 200 FRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQE-TSMDTIISMMVG 258
           F  +  +  QG  IV+ISHK++E+  +AD ++++R G+        E TS   +   MVG
Sbjct: 198 FEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVG 257

Query: 259 R--ALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVA 316
           +   L+ ++   P     D VL+VR L  G  + D++F L +GE++   G+ G G+  + 
Sbjct: 258 KEVLLEVDREAMP---HGDAVLQVRNLT-GIGLEDITFDLHQGEVVAVVGVAGNGQKALV 313

Query: 317 RAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376
            AI G        + I G +        +  + + Y+ EDR        +++  N+ L++
Sbjct: 314 EAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTT 373

Query: 377 MGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDI 436
              F R  ++D++         +++  I+   +   A  LSGGN QK V+A+ L R   +
Sbjct: 374 RQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRL 433

Query: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496
           +  ++PT+G+D+ A  +++  L A  E    I++++ +L E L+++ RV V+  GR    
Sbjct: 434 IVAEQPTQGLDIAATEQVWNHLLAAREMA-GILLVTGDLNEALQLADRVAVIYRGRFMDV 492

Query: 497 LARAD 501
            + +D
Sbjct: 493 FSVSD 497



 Score =  105 bits (261), Expect = 5e-27
 Identities = 75/249 (30%), Positives = 128/249 (51%), Gaps = 24/249 (9%)

Query: 270 DTSRNDV------VLEVRGLNR--GRAIR--DVSFTLRKGEILGFAGLMGAGRTEVARAI 319
           D S+ DV      ++ ++GL +  G+ +   D+S  +  G +    G  GAG++ +   +
Sbjct: 11  DRSKRDVPPQGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSML 70

Query: 320 FGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGR 379
            G    +AG I + G      S  DA+  GIG + +   HF L   M V  N+ L   G 
Sbjct: 71  AGRYQPDAGTIALDGKPVRFSSARDAIEAGIGMVYQ---HFMLVESMTVAENVLLGQEGS 127

Query: 380 FTRVGFMDQRAIREAAQMYVRQLAIKTP-SVEQQARL--LSGGNQQKIVIAKWLLRDCDI 436
           F    F++ + +R   Q    +L+++    ++  AR+  LS G +Q++ I K L RD  +
Sbjct: 128 F----FLNPKEMRNRVQ----ELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRV 179

Query: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496
           L FDEPT  +       +++ L  +AEQGK+IV IS +L EVL ++  + ++ +GRI GE
Sbjct: 180 LIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGE 239

Query: 497 LARADATQE 505
            + ++ T +
Sbjct: 240 FSESEVTSK 248



 Score = 52.0 bits (123), Expect = 5e-11
 Identities = 45/228 (19%), Positives = 105/228 (46%), Gaps = 9/228 (3%)

Query: 36  LALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQ 95
           + L++  F+L  GEV A++G  G G+  L++ + G+ +     + + GK       + + 
Sbjct: 284 IGLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSW 343

Query: 96  ALGIGIIHQE---LNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDM 152
              +  I ++   L    +L+   N+ +      A G ++D+ +  R    +  +   D+
Sbjct: 344 KNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKF--DI 401

Query: 153 DPSTPVG---ELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQ 209
            P        +L+    Q   +A+ L    R+++ ++PT  L+ A   +++  +   +  
Sbjct: 402 RPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREM 461

Query: 210 GVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257
             GI+ ++  ++E  Q+ADRV+V+  G+++    + +      I +M+
Sbjct: 462 A-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508


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: 556
Number of extensions: 24
Number of successful extensions: 9
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: 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 Apr 09 2024. 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