Alignments for a candidate for rbsA in Bradyrhizobium sp. BTAi1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Bradyrhizobium sp. BTAi1

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_012044568.1 BBTA_RS21220 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_000015165.1:WP_012044568.1
          Length = 501

 Score =  350 bits (898), Expect = e-101
 Identities = 197/497 (39%), Positives = 303/497 (60%), Gaps = 12/497 (2%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           LL+L+ I K+F GV AL G    + PG +  LVGENGAGKST+MK++ G++T  +G  L 
Sbjct: 8   LLELQDITKSFGGVTALRGVDFTLRPGEIHGLVGENGAGKSTLMKIIAGVHTGFSGRFLL 67

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
            G+E  F   + ++ AGI ++HQEL++ P LT+AEN+FLG +  N  G + W+ M  EA 
Sbjct: 68  DGREVHFNSARDARAAGIAMVHQELSVAPDLTVAENVFLGNQPTNALGIVQWRRMAREAA 127

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
           + L KL +       +GDL IG QQ++EIA+VL   +++II+DEPT AL+  E E LF  
Sbjct: 128 EQLKKLGIDADPMSRLGDLPIGVQQLIEIARVLFSGARIIILDEPTSALSPPEVERLFAA 187

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR--- 240
           +R+L+ QG GI++ISH +++I  I D+VTVFR+G+ I E   A  ++ +LIE M+G+   
Sbjct: 188 LRKLREQGTGIIFISHFIEDILLISDEVTVFRNGRKIMETRAADTSKAALIEAMIGKGRD 247

Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGPGVN------DVSFTLRKGEILGVSGLMGAGRTEL 294
            LE  Y H    P     K   L   G++       VSF+++ GE+LG+ G MG G+ EL
Sbjct: 248 ALEGSYTHDITLPAPPAGKPVVLEAAGLSLARSLKRVSFSVQAGEVLGIYGFMGCGQLEL 307

Query: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLT 354
            ++L+G L   +G + L G     +S  D    GI ++ E R RD L L   V +N+S++
Sbjct: 308 ARILFGKLAPDAGELRLAGERNRFKSTADARRAGIAFVPESR-RDMLFLQEPVYKNVSIS 366

Query: 355 ALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP 414
            L   +     LK + E+      +    ++   +E  +GLLSGGNQQKVA+A+ L   P
Sbjct: 367 ILDRINAV--LLKPSRERALAKRQVEQLQIRPADVEIDLGLLSGGNQQKVALAKWLSHPP 424

Query: 415 KVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLS 474
           ++L+L EPTRG+DVGAK ++  ++ Q +  G++++++S+E   VL ++DR+IV+  G + 
Sbjct: 425 RLLVLCEPTRGMDVGAKSDVIGIVRQLRDQGIAVVVLSTEPETVLSLADRVIVLKRGQVV 484

Query: 475 GEFTREQATQEVLMAAA 491
            EF  E  +++ L+ AA
Sbjct: 485 REFAGETISKDRLLEAA 501



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 65/224 (29%), Positives = 111/224 (49%), Gaps = 6/224 (2%)

Query: 271 VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIV 330
           V FTLR GEI G+ G  GAG++ LMK++ G     SG   LDG EV   S +D  A GI 
Sbjct: 27  VDFTLRPGEIHGLVGENGAGKSTLMKIIAGVHTGFSGRFLLDGREVHFNSARDARAAGIA 86

Query: 331 YISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSME 390
            + ++     +   ++V EN+ L      + A G ++     +  ++ ++   +    M 
Sbjct: 87  MVHQELS---VAPDLTVAENVFLG--NQPTNALGIVQWRRMAREAAEQLKKLGIDADPMS 141

Query: 391 QAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIIL 450
           + +G L  G QQ + IAR L +  +++ILDEPT  +     + ++  + + +  G  II 
Sbjct: 142 R-LGDLPIGVQQLIEIARVLFSGARIIILDEPTSALSPPEVERLFAALRKLREQGTGIIF 200

Query: 451 VSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           +S  + ++L +SD + V   G    E      ++  L+ A +GK
Sbjct: 201 ISHFIEDILLISDEVTVFRNGRKIMETRAADTSKAALIEAMIGK 244


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: 558
Number of extensions: 25
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: 501
Length of database: 501
Length adjustment: 34
Effective length of query: 467
Effective length of database: 467
Effective search space:   218089
Effective search space used:   218089
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 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:

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