Alignments for a candidate for HSERO_RS03640 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Escherichia coli BW25113

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Keio:17809
          Length = 501

 Score =  414 bits (1063), Expect = e-120
 Identities = 219/493 (44%), Positives = 310/493 (62%), Gaps = 6/493 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LLQ++GI K+F    ALS   L + PG + AL+GENGAGKST+MKVL+G++  D G +L 
Sbjct: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            G+      P +S+ AGI +I+QEL + P +++A N+F+G E   R G ID   M +  D
Sbjct: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            +L +L   F +  L G LSI +QQ VEIA+ L   S+++IMDEPT AL++ ETE LF V
Sbjct: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +R L+ +G  I+YISHRM E++ + D VTV RDG F+ E     +  + +++MMVGR L 
Sbjct: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLL 305
           + Y H   AP D       ++V  L G  +   SF +R GE+LG +GL+GAGRTEL ++L
Sbjct: 244 DQYPHLDKAPGDIR-----LKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVL 298

Query: 306 FGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASR 365
           +GA PR+ G + L+G  V    P+  +  GI Y+ EDRK  GL L M+V  N ++     
Sbjct: 299 YGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRY 358

Query: 366 HTRL-GLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424
            +R  G ++           I+  NVK    E  +G LSGGNQQKV +AR L   PKVLI
Sbjct: 359 FSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLI 418

Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484
           LDEPTRGVD+ AK EIYQL+++  + G++++++SSE+PEV+G+ DR++VM EG ++GE  
Sbjct: 419 LDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFT 478

Query: 485 GAAITQENIMRLA 497
               TQE +M  A
Sbjct: 479 REQATQEVLMAAA 491



 Score =  109 bits (272), Expect = 3e-28
 Identities = 70/231 (30%), Positives = 118/231 (51%), Gaps = 14/231 (6%)

Query: 22  LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAA 81
           ++D+  T+R GEI  + G  GAG++ LMKVL G      G + LDG  V  R P    A 
Sbjct: 268 VNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLAN 327

Query: 82  GINLIYQE---------LAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQLG 132
           GI  I ++         ++V  N+S+ A  +         G + HA  +      +R   
Sbjct: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAG----GSLKHADEQQAVSDFIRLFN 383

Query: 133 AGFGASDLA-GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRD 191
               + + A G LS   QQ+V IAR L+ R +++I+DEPT  +     ++++ ++ + + 
Sbjct: 384 VKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKA 443

Query: 192 EGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242
           +GL+II +S  M EV  ++DR+ V+ +G   GE  R++   E ++   VG+
Sbjct: 444 DGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494



 Score =  102 bits (254), Expect = 3e-26
 Identities = 68/247 (27%), Positives = 123/247 (49%), Gaps = 10/247 (4%)

Query: 267 VRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHID 326
           V+AL+G     A+ +V  G V+   G  GAG++ + ++L G   R  G +L  G+     
Sbjct: 17  VKALSG-----AALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFT 71

Query: 327 QPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQ 386
            P+++  AGI  + ++     L  Q+ +A N  +       R G +  +++   A   + 
Sbjct: 72  GPKSSQEAGIGIIHQELN---LIPQLTIAENIFLG-REFVNRFGKIDWKTMYAEADKLLA 127

Query: 387 RLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHR 446
           +LN++    +  VG LS G+QQ V +A+ L    KV+I+DEPT  +       +++++  
Sbjct: 128 KLNLRFKSDKL-VGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRE 186

Query: 447 LASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTA 506
           L SQG  +V IS  + E+  ICD V V R+G    E   A++T+++++ +     +    
Sbjct: 187 LKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLEDQY 246

Query: 507 PASHSSP 513
           P    +P
Sbjct: 247 PHLDKAP 253


Lambda     K      H
   0.320    0.135    0.378 

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: 638
Number of extensions: 23
Number of successful extensions: 7
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: 521
Length of database: 501
Length adjustment: 35
Effective length of query: 486
Effective length of database: 466
Effective search space:   226476
Effective search space used:   226476
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 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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