Alignments for a candidate for araVsh in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Escherichia coli BW25113

Align ABC transporter related (characterized, see rationale)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__Keio:16258
          Length = 506

 Score =  343 bits (880), Expect = 8e-99
 Identities = 186/474 (39%), Positives = 301/474 (63%), Gaps = 11/474 (2%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +LE+  I+K +PGVKAL++V+L++    +HAL+GENGAGKSTL+K + G   KD G ILF
Sbjct: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G+   F++  +A + GIS V+QE+NLV   +V  N++LG  P +   +   KMY + +A
Sbjct: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132

Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183
           +  +  +DID  A +   S++  Q+I IA+  + +AK++++DEPT+SL  KEV  LF I+
Sbjct: 133 IFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTII 192

Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243
            +LK +G  IV+I+H +++++Q+ D +TVLR+GQ+I     A L   K+I  M+GRSL +
Sbjct: 193 RKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQ 252

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303
           +  DK+ K   V      L SL     + SI+ ++  + KG+ +G+AGL+G+ R+++   
Sbjct: 253 RFPDKENKPGEVILEVRNLTSLR----QPSIRDVSFDLHKGEILGIAGLVGAKRTDIVET 308

Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILA--- 360
           +FG+    +G+I L G+++N     +AI+ G AL  E+R+  GI   L I  N +++   
Sbjct: 309 LFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIR 368

Query: 361 -LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEP 419
             + ++G    L N+R +   Q+ ID +++ TP     I  LSGGNQQKVI+ RWL  +P
Sbjct: 369 NYKNKVG---LLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425

Query: 420 ILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473
            +L+LDEPTRGID+GA  EI +LI  L  +G  +++ SSE+ EL+  +++++V+
Sbjct: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVM 479



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 58/239 (24%), Positives = 112/239 (46%), Gaps = 11/239 (4%)

Query: 3   LILELKQI-SKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDI 61
           +ILE++ + S   P ++   DVS  L  GE+  + G  GA ++ +V+ + G + K  G I
Sbjct: 264 VILEVRNLTSLRQPSIR---DVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTI 320

Query: 62  LFLGEPQHFNTPMDAQKAGISTVYQE---VNLVPNLTVAQNLFLGY---EPRRLGLIHFK 115
              G+  + +   +A   G + V +E     +   L +  N  +        ++GL+   
Sbjct: 321 TLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNS 380

Query: 116 KMYADARAVLTQFKLDIDVS-APLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAK 174
           +M +D + V+   ++        +   S   QQ + I R +    ++L+LDEPT  +D  
Sbjct: 381 RMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVG 440

Query: 175 EVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLI 233
               ++ ++ +L  KG  I+ I+  + ++  I+DRI V+ NG   G   T    Q +++
Sbjct: 441 AKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEIL 499



 Score = 62.4 bits (150), Expect = 4e-14
 Identities = 45/203 (22%), Positives = 96/203 (47%), Gaps = 6/203 (2%)

Query: 273 SIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAIS 332
           ++ ++NL V       L G  G+G+S +   +FG+   DSG+I   G++++     +A+ 
Sbjct: 28  ALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALE 87

Query: 333 AGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATP 392
            GI++  ++  +   +   S+ +N+ L      G   ++   +     +   D+L I   
Sbjct: 88  NGISMVHQELNL---VLQRSVMDNMWLGRYPTKGM--FVDQDKMYRETKAIFDELDIDI- 141

Query: 393 DADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMS 452
           D    +  LS    Q + +A+  +    ++++DEPT  +       +  +IR L + G  
Sbjct: 142 DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCG 201

Query: 453 LLVASSELDELVAFSNKVVVLRD 475
           ++  S +++E+    ++V VLRD
Sbjct: 202 IVYISHKMEEIFQLCDEVTVLRD 224


Lambda     K      H
   0.319    0.136    0.377 

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: 562
Number of extensions: 22
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: 499
Length of database: 506
Length adjustment: 34
Effective length of query: 465
Effective length of database: 472
Effective search space:   219480
Effective search space used:   219480
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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