GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Rhodobacter johrii JA192

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  392 bits (1007), Expect = e-113
 Identities = 221/492 (44%), Positives = 311/492 (63%), Gaps = 7/492 (1%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           PV+A+R V + F  V  L +  F+L  GEVHAL+GENGAGKST MKIL+G     +G++L
Sbjct: 4   PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVL 63

Query: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140
           LDG+PV     R+A+A G+ +IHQE NL   L+  +NIF+GRE ++  G F+D   +  +
Sbjct: 64  LDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKR--GPFLDHRAMQAE 121

Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200
           +  +  R+   +DP   V  L+V  +QMVEIAKAL   +RVLIMDEPTA L + E   L 
Sbjct: 122 SRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLL 181

Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260
             +  L+A G  I+Y SHK+DE+ +IADRV+V+RDG+ + T P +  S D +   MVGR 
Sbjct: 182 EQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRE 241

Query: 261 LDGEQRIPPDTS-RNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAI 319
           L G    PP +S   + VLEV GL     +RD SFTLR+GE+LGFAGL+G+GRTE+   I
Sbjct: 242 LSG--LFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGI 299

Query: 320 FGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGR 379
            G  P   GE+ + G      S + A A G+ YL+EDRK  GL +G  +  N+ L ++ R
Sbjct: 300 VGLRP-ATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDR 358

Query: 380 FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFF 439
           F RV  +D+ A   A    +    I+       A  LSGGNQQK+++AK +L +  ++  
Sbjct: 359 FGRV-LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVII 417

Query: 440 DEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELAR 499
           DEPTRGIDVG K +IY  +  LA +G++++++SSELPEV+ +++RV+VM  GRI GE+  
Sbjct: 418 DEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEG 477

Query: 500 ADATQEKIMQLA 511
              T+E I++LA
Sbjct: 478 EAITEENIVRLA 489



 Score = 85.9 bits (211), Expect = 3e-21
 Identities = 72/246 (29%), Positives = 123/246 (50%), Gaps = 16/246 (6%)

Query: 277 VLEVRGLNR----GRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           VL +R ++R     + + DV F LR GE+    G  GAG++   + + G     AGE+++
Sbjct: 5   VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG-FMDQRAI 391
            G      S  +A A G+  + ++   F LA  + V+ NI L   GR  + G F+D RA+
Sbjct: 65  DGRPVHFPSSREAEAAGVVMIHQE---FNLATPLTVEENIFL---GRELKRGPFLDHRAM 118

Query: 392 REAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVG 449
           +  ++  + +L     +V+ +AR+  LS  N+Q + IAK L     +L  DEPT  +   
Sbjct: 119 QAESRRLLERLHC---AVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHR 175

Query: 450 AKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQ 509
               + + +D L   G AI+  S +L EV R++ RV V+ +GR          +++++ +
Sbjct: 176 ETDTLLEQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAE 235

Query: 510 LATQRE 515
               RE
Sbjct: 236 TMVGRE 241



 Score = 72.0 bits (175), Expect = 5e-17
 Identities = 65/270 (24%), Positives = 123/270 (45%), Gaps = 18/270 (6%)

Query: 1   MQEDKETST------TGVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALM 54
           + ED+   T      +G+    SS  P   L       PG +   +  F L  GEV    
Sbjct: 228 LSEDRMAETMVGRELSGLFPPKSSPAPEPVLEVAGLTVPGFVR--DASFTLRRGEVLGFA 285

Query: 55  GENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII---HQELNLMNH 111
           G  G+G++ LM+ + G+ +  +G++ ++G P+       A+A G+  +    +E  L+  
Sbjct: 286 GLVGSGRTELMEGIVGL-RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLG 344

Query: 112 LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDM---DPSTPVGELTVARQQM 168
               +N+ +    R    L    D+   + A   A    D+   D     G L+   QQ 
Sbjct: 345 KPLGENLTLLALDRFGRVLI---DKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQK 401

Query: 169 VEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIAD 228
           + +AK +  + RV+I+DEPT  ++     +++  I  L A+G  ++ +S ++ E+  +A+
Sbjct: 402 LLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLAN 461

Query: 229 RVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           RV VM  G+    V  +  + + I+ + +G
Sbjct: 462 RVVVMSAGRIAGEVEGEAITEENIVRLAMG 491


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: 652
Number of extensions: 33
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: 499
Length adjustment: 34
Effective length of query: 486
Effective length of database: 465
Effective search space:   225990
Effective search space used:   225990
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 24 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