Alignments for a candidate for rbsA in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Rhodobacter johrii JA192

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_069330948.1 C8J29_RS15005 autoinducer 2 ABC transporter ATP-binding protein LsrA

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_003046325.1:WP_069330948.1
          Length = 491

 Score =  311 bits (796), Expect = 4e-89
 Identities = 181/487 (37%), Positives = 275/487 (56%), Gaps = 17/487 (3%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           L +L+ + K++  V+ L G   +V  G + AL+G NGAGKST+MK+L G+     G +  
Sbjct: 5   LAELRSVSKSYAAVRVLKGVHFSVRAGEIHALLGGNGAGKSTLMKILAGLVAPSGGEVRL 64

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
            G+      P  +Q  G+ ++ QE ++ P  T+ +NI +G        +       A   
Sbjct: 65  GGEPLVPATPAQAQAMGLYLVPQEAHIFPNQTVLQNIAVGMPKPAGAYR-------ARVQ 117

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
            L+A+L +    D     L I D+Q+VEI + L  E+KV+I+DEPT ALT  E  +LF  
Sbjct: 118 ALIAQLGVSLSPDAKAATLEIADRQIVEILRGLLREAKVLILDEPTSALTPHEVRTLFGH 177

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFI-AEREVASLTEDSLIEMMVGRKL 242
           +R L++QG G+V+ISH++ E+  + D +TV RDG  + AE    S   + L  M  G   
Sbjct: 178 MRALRAQGHGLVFISHKLHELRAVADRITVLRDGHVVFAEAMETSPDAEILAAMSPGVTA 237

Query: 243 EDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302
            D    + +  G   L ++ L G G  ++S +LR GEILG++G++GAGRTEL + L G  
Sbjct: 238 LDARERMREIEGAPVLALERLSGEGFVEISLSLRPGEILGLTGVVGAGRTELAETLVGLR 297

Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTA---LRYF 359
             + G VTL G +   R P D +  G+V++SEDR++ GL L   +  N+S      L +F
Sbjct: 298 TPSGGRVTLGGRDFRARGPADAMRAGLVHLSEDRQQYGLFLEAPLYWNVSALVHGTLPFF 357

Query: 360 SRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419
            R G   +  ++ +A         ++    +Q +G LSGGNQQKV +A+ L   PKVLIL
Sbjct: 358 LRPGRERRRFEQYRAQ------LGIRCEEADQPVGRLSGGNQQKVLLAKCLAAAPKVLIL 411

Query: 420 DEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTR 479
           DEPTRGVDVGA+ +IY+++      G +++L+SS+  EV  ++DRI VM  GHL+GE   
Sbjct: 412 DEPTRGVDVGARNDIYRIVEDLAEQGTAVLLISSDFDEVRRLADRIAVMAGGHLAGELPA 471

Query: 480 EQATQEV 486
             +T E+
Sbjct: 472 GASTDEI 478



 Score = 82.0 bits (201), Expect = 4e-20
 Identities = 62/221 (28%), Positives = 107/221 (48%), Gaps = 15/221 (6%)

Query: 271 VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIV 330
           V F++R GEI  + G  GAG++ LMK+L G +  + G V L G  +V  +P    A G+ 
Sbjct: 24  VHFSVRAGEIHALLGGNGAGKSTLMKILAGLVAPSGGEVRLGGEPLVPATPAQAQAMGLY 83

Query: 331 YISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQA-VSDFIRLFNVKTPSM 389
            + ++     +    +V +N+++          G  K A   +A V   I    V   S 
Sbjct: 84  LVPQEAH---IFPNQTVLQNIAV----------GMPKPAGAYRARVQALIAQLGVSL-SP 129

Query: 390 EQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSII 449
           +     L   ++Q V I RGL+   KVLILDEPT  +     + ++  +   +A G  ++
Sbjct: 130 DAKAATLEIADRQIVEILRGLLREAKVLILDEPTSALTPHEVRTLFGHMRALRAQGHGLV 189

Query: 450 LVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAA 490
            +S ++ E+  ++DRI V+ +GH+      E +    ++AA
Sbjct: 190 FISHKLHELRAVADRITVLRDGHVVFAEAMETSPDAEILAA 230


Lambda     K      H
   0.318    0.137    0.380 

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: 602
Number of extensions: 36
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: 501
Length of database: 491
Length adjustment: 34
Effective length of query: 467
Effective length of database: 457
Effective search space:   213419
Effective search space used:   213419
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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:

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 2024 update 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