Alignments for a candidate for rbsA in Stutzerimonas stutzeri A1501

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Stutzerimonas stutzeri A1501

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_011914604.1 PST_RS17845 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_000013785.1:WP_011914604.1
          Length = 525

 Score =  242 bits (618), Expect = 2e-68
 Identities = 162/501 (32%), Positives = 255/501 (50%), Gaps = 24/501 (4%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           +QL G+ K+F G  ALS A      G V AL+GENGAGKS++M +  G+Y  ++G+LL  
Sbjct: 7   IQLSGVSKSFDGFMALSQADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPESGSLLIN 66

Query: 65  GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFL------GREFVNRFGKIDWKTM 118
                 +GP+ +    IG++HQ   L+   T+AENI L      G    +   +     +
Sbjct: 67  DNAVRLSGPRDASRYHIGMVHQHFKLVKPFTVAENIQLALPEGPGNHAFSGSHRQRLAAL 126

Query: 119 YAEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETE 178
                   A+L       K+   LS+ +QQ VEI KVL   ++++I+DEPT  LTD E E
Sbjct: 127 EQRISDKAAELGFSIDPRKITESLSVAEQQRVEILKVLLAGARILILDEPTAVLTDGEAE 186

Query: 179 SLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMV 238
            L   +R    QG  ++ ++H+M ++    D VTV R G+ I   +  +++   L+ + V
Sbjct: 187 RLLETVRAFARQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTVSVPELVRLTV 246

Query: 239 GRKLEDQYPHLDKAPGDIRLKVDNLCGPG------VNDVSFTLRKGEILGVSGLMGAGRT 292
           G        +    PG++RL+V +L   G      +N V+ +LR GEI G++G+ G G++
Sbjct: 247 GESAPAS-EYQPAIPGEVRLQVRDLRSTGAGGQGVLNGVNLSLRAGEIYGIAGVGGNGQS 305

Query: 293 ELMKVLYGALPRTSGYVTLDGHEVVTR-SPQDGLANGIVYISEDRKRDGLVLGMSVKENM 351
           EL  VL G      G + L G   + R S +      I  I  DR    L   +SV EN 
Sbjct: 306 ELANVLMGLPEPCDGTLELTGFGDLRRASAEQRRELRIAAIPADRYGAALAGELSVAENF 365

Query: 352 SLTAL---RY--FSRAGGSLKHADEQQAVSDFIRLFNVK-TPSMEQAIGLLSGGNQQKVA 405
            +  +   RY  F R       A+  +AV+     F+V+   S++Q   LLSGGN QK+ 
Sbjct: 366 GVGQVHSGRYGSFFRLRRKRLEAEAAEAVAG----FDVQGVRSLKQKAALLSGGNAQKLV 421

Query: 406 IARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRI 465
           IAR     P ++++  P+RG+DV A   ++  +   +  G +++++S ++ EVL ++DRI
Sbjct: 422 IAREFSRDPLLVLVHSPSRGLDVRATAAVHARLRAAREAGAAVLVISEDLDEVLALADRI 481

Query: 466 IVMHEGHLSGEFTREQATQEV 486
            VM  G +  EF R    Q +
Sbjct: 482 GVMSGGRIVAEFDRPADRQAI 502



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 61/233 (26%), Positives = 105/233 (45%), Gaps = 12/233 (5%)

Query: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLAN 327
           ++   FT R GE+  + G  GAG++ LM +  G     SG + ++ + V    P+D    
Sbjct: 22  LSQADFTARWGEVHALLGENGAGKSSLMNIAAGLYAPESGSLLINDNAVRLSGPRDASRY 81

Query: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADE----QQAVSDFIRL-- 381
            I  + +  K   LV   +V EN+ L           S  H       +Q +SD      
Sbjct: 82  HIGMVHQHFK---LVKPFTVAENIQLALPEGPGNHAFSGSHRQRLAALEQRISDKAAELG 138

Query: 382 FNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQF 441
           F++    + ++   LS   QQ+V I + L+   ++LILDEPT  +  G  + + + +  F
Sbjct: 139 FSIDPRKITES---LSVAEQQRVEILKVLLAGARILILDEPTAVLTDGEAERLLETVRAF 195

Query: 442 KADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
              G ++ILV+ +M +V   +DR+ VM  G        +  +   L+   VG+
Sbjct: 196 ARQGAAVILVTHKMSDVKRFADRVTVMRGGRTIQTLDPQTVSVPELVRLTVGE 248


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: 608
Number of extensions: 35
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: 525
Length adjustment: 35
Effective length of query: 466
Effective length of database: 490
Effective search space:   228340
Effective search space used:   228340
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