Alignments for a candidate for rbsA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Escherichia coli BW25113

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Keio:16258
          Length = 506

 Score =  431 bits (1109), Expect = e-125
 Identities = 222/493 (45%), Positives = 325/493 (65%), Gaps = 4/493 (0%)

Query: 2   EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61
           E LL++ GI+K+FPGVKAL    L V P  + AL+GENGAGKST++K L GIY +D+GT+
Sbjct: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70

Query: 62  LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121
           L+ GKE  F   K + E GI ++HQELNL+ Q ++ +N++LGR +  +   +D   MY E
Sbjct: 71  LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGR-YPTKGMFVDQDKMYRE 129

Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181
              +  +L++       VG LS+   QM+EIAK  S+ +K++IMDEPT +LT+ E   LF
Sbjct: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189

Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
            +IR+LK +G GIVYISH+M+EIF++CD+VTV RDGQ+IA   +A LT D +I MMVGR 
Sbjct: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249

Query: 242 LEDQYPHLDKAPGDIRLKVDNLCG---PGVNDVSFTLRKGEILGVSGLMGAGRTELMKVL 298
           L  ++P  +  PG++ L+V NL     P + DVSF L KGEILG++GL+GA RT++++ L
Sbjct: 250 LNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309

Query: 299 YGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRY 358
           +G   +++G +TL G ++   +  + + +G   ++E+R+  G+   + +  N  ++ +R 
Sbjct: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369

Query: 359 FSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLI 418
           +    G L ++  +      I    VKTP     IG LSGGNQQKV I R L+T+P++L+
Sbjct: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429

Query: 419 LDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFT 478
           LDEPTRG+DVGAK EIYQLI +    G  II++SSEMPE+LG++DRI+VM  G +SG   
Sbjct: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489

Query: 479 REQATQEVLMAAA 491
            +  TQ  ++  A
Sbjct: 490 TKTTTQNEILRLA 502



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 61/234 (26%), Positives = 111/234 (47%), Gaps = 14/234 (5%)

Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322
           PGV   ++V+  +R   I  + G  GAG++ L+K L+G   + SG +   G E+   S +
Sbjct: 24  PGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAK 83

Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLF 382
           + L NGI  + ++     LVL  SV +NM L   RY ++        D+ +   +   +F
Sbjct: 84  EALENGISMVHQELN---LVLQRSVMDNMWLG--RYPTKG----MFVDQDKMYRETKAIF 134

Query: 383 NVKTPSMEQA--IGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQ 440
           +     ++    +G LS    Q + IA+      K++I+DEPT  +       ++ +I +
Sbjct: 135 DELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRK 194

Query: 441 FKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
            K  G  I+ +S +M E+  + D + V+ +G           T + ++A  VG+
Sbjct: 195 LKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGR 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: 628
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: 506
Length adjustment: 34
Effective length of query: 467
Effective length of database: 472
Effective search space:   220424
Effective search space used:   220424
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 17 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 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