Alignments for a candidate for xylK_Tm in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Escherichia coli BW25113

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Keio:1937256
          Length = 500

 Score =  367 bits (941), Expect = e-106
 Identities = 196/478 (41%), Positives = 301/478 (62%), Gaps = 16/478 (3%)

Query: 13  EILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEIL 72
           EIL+ +G+ K FPGV A+DNVDF +   EI++L+GENGAGKSTLIK LTGV   D G I 
Sbjct: 8   EILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIW 67

Query: 73  VNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENY 132
           + G+ +   +   A + GI  ++QE+NL  NM+VA+N+F+  E  R         +    
Sbjct: 68  LEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR------FGLLRRKE 121

Query: 133 MYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192
           M  R+ EL+   G        +   + A +Q+V IC+A+    +++ +DEPT+SL  +E 
Sbjct: 122 MEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEV 181

Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252
           E LF+++  L+ RG+S++FV+H LD+V ++SDRI V+R+G  +G  +  E     ++KMM
Sbjct: 182 ELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMM 241

Query: 253 VGREVEFFPHGIETRPGEIALE------VRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAG 306
           +GRE++   H ++ R G   L        +N   K  +     EVR GE++G AGL+G+G
Sbjct: 242 LGRELD--THALQ-RAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSG 298

Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDN 366
           RTET  ++FG+   +SG   + G+   +++P  A  +GIG  PEDRK  G++   +V++N
Sbjct: 299 RTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVREN 358

Query: 367 IVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWL 426
           I+L +L+    W   +  ++++EI+E ++++L I+TPS  Q  E LSGGNQQKV+L++WL
Sbjct: 359 IIL-ALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWL 417

Query: 427 ATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVM 484
            T    LI DEPTRGIDVGA AEI R+I  L A G A+++ISSEL E++  +DR+++M
Sbjct: 418 LTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475



 Score = 97.1 bits (240), Expect = 1e-24
 Identities = 60/220 (27%), Positives = 113/220 (51%), Gaps = 8/220 (3%)

Query: 34  DFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGISV 93
           D EV   EIV L G  G+G++   +++ G+   D+G  L+ G+     SP  A   GI  
Sbjct: 280 DLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGF 339

Query: 94  IHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKF-S 149
             ++     +    +V ENI LA +A RG  R +S +  +      ++  +  +G +  S
Sbjct: 340 CPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEI----AERFIRQLGIRTPS 395

Query: 150 PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGISV 209
            +  +  L+   +Q V + + L+  P+ + +DEPT  + V     +  +IE L + G+++
Sbjct: 396 TEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLAL 455

Query: 210 VFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTII 249
           + +S  L+E++  +DR+++MRD K++ E+   E  V  I+
Sbjct: 456 LVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIM 495



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 59/215 (27%), Positives = 108/215 (50%), Gaps = 13/215 (6%)

Query: 286 NVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGI 345
           NV F +R+GE++   G  GAG++  +  + GV   + G I++ G+ +  KN   A ++GI
Sbjct: 27  NVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGI 86

Query: 346 GLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLD---ERKEEEISEDYVKRLSIKT 402
           G + ++     L+  M+V DN+ +    K  R+GL+     E++  E+   Y   L ++ 
Sbjct: 87  GTVYQE---VNLLPNMSVADNLFIGREPK--RFGLLRRKEMEKRATELMASYGFSLDVRE 141

Query: 403 PSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGK 462
           P         S   QQ V + + +  +A +LI DEPT  +D      +  ++R+L  +G 
Sbjct: 142 P-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGV 196

Query: 463 AVIMISSELPEILNLSDRIVVMWEGEITAVLDNRE 497
           ++I ++  L ++  +SDRI V+  G      +  E
Sbjct: 197 SLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCE 231


Lambda     K      H
   0.319    0.138    0.381 

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: 640
Number of extensions: 35
Number of successful extensions: 9
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: 520
Length of database: 500
Length adjustment: 34
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 (21.7 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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