Alignments for a candidate for HSERO_RS05250 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Escherichia coli BW25113

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Keio:16258
          Length = 506

 Score =  439 bits (1128), Expect = e-127
 Identities = 228/504 (45%), Positives = 340/504 (67%), Gaps = 8/504 (1%)

Query: 13  AASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY 72
           + + SS   ++ +  + K FPGV ALDN   ++    +HALMGENGAGKSTL+K L G+Y
Sbjct: 4   STTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIY 63

Query: 73  QRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI 132
           Q+DSG IL  GK ++    ++A   GI ++HQELNL+   S   N+++GR P K  G+F+
Sbjct: 64  QKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GMFV 121

Query: 133 DEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192
           D+D++ R+  AIF  + +D+DP   VG L+V++ QM+EIAKA S++++++IMDEPT++L 
Sbjct: 122 DQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181

Query: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252
             E+  LF IIR L+ +G GIVYISHKM+E+ Q+ D V+V+RDG++IAT P+   +MD I
Sbjct: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKI 241

Query: 253 ISMMVGRALDGEQRIPPDTSR-NDVVLEVRGLN--RGRAIRDVSFTLRKGEILGFAGLMG 309
           I+MMVGR+L+  QR P   ++  +V+LEVR L   R  +IRDVSF L KGEILG AGL+G
Sbjct: 242 IAMMVGRSLN--QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVG 299

Query: 310 AGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQ 369
           A RT++   +FG     AG I +HG +    +  +A+ HG   ++E+R+  G+   +D+ 
Sbjct: 300 AKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIG 359

Query: 370 ANIALSSMGRF-TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428
            N  +S++  +  +VG +D   ++   Q  +  + +KTP    Q   LSGGNQQK++I +
Sbjct: 360 FNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGR 419

Query: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488
           WLL   +IL  DEPTRGIDVGAK EIY+L+  LA++GK I++ISSE+PE+L ++ R+LVM
Sbjct: 420 WLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVM 479

Query: 489 CEGRITGELARADATQEKIMQLAT 512
             G ++G +     TQ +I++LA+
Sbjct: 480 SNGLVSGIVDTKTTTQNEILRLAS 503



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 64/250 (25%), Positives = 120/250 (48%), Gaps = 16/250 (6%)

Query: 272 SRNDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEA 327
           S  + +LE+ G+N+     +A+ +V+  +R   I    G  GAG++ + + +FG    ++
Sbjct: 8   SSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67

Query: 328 GEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG-FM 386
           G I+  G +    S  +A+ +GI  + ++     L +   V  N+ L   GR+   G F+
Sbjct: 68  GTILFQGKEIDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWL---GRYPTKGMFV 121

Query: 387 DQRAIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTR 444
           DQ  +    +    +L I    ++ +AR+  LS    Q I IAK    +  I+  DEPT 
Sbjct: 122 DQDKMYRETKAIFDELDI---DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTS 178

Query: 445 GIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ 504
            +     + ++ ++  L E+G  IV IS ++ E+ ++   V V+ +G+       A  T 
Sbjct: 179 SLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTM 238

Query: 505 EKIMQLATQR 514
           +KI+ +   R
Sbjct: 239 DKIIAMMVGR 248


Lambda     K      H
   0.320    0.135    0.372 

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: 632
Number of extensions: 28
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: 520
Length of database: 506
Length adjustment: 35
Effective length of query: 485
Effective length of database: 471
Effective search space:   228435
Effective search space used:   228435
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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