Alignments for a candidate for xylK_Tm in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Cupriavidus basilensis 4G11

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Cup4G11:RR42_RS03360
          Length = 537

 Score =  353 bits (906), Expect = e-102
 Identities = 214/510 (41%), Positives = 308/510 (60%), Gaps = 19/510 (3%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPD-AGEIL 72
           +L  + I K FPGV A+  V+   Y  E+ +L+GENGAGKSTL+KIL+G    D  GE  
Sbjct: 10  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 69

Query: 73  VNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENY 132
           ++G+RV+   P  A   G++VI+QEL+L  N++VAENI+L       Q+R L +R D   
Sbjct: 70  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRAL---QRRGLVARGD--- 123

Query: 133 MYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192
           M       L  +GA FSP A V +L+ AQRQ+VEI +A+  E RI+ MDEPT+ L+  ET
Sbjct: 124 MVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 183

Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252
           +RLF +I  L+  G++++++SHR+ E+  ++DR+ V+RDG  +G L +       ++KMM
Sbjct: 184 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 243

Query: 253 VGREVEFF---PHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTE 309
           VGR++  F    HG +    E+ L VR++    +VK  SF++R GEVLG AGLVGAGRTE
Sbjct: 244 VGRDLSGFYTKTHG-QAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTE 302

Query: 310 TMLLVFGVNQKESGDIYV-----NGRKVEIK--NPEDAIKMGIGLIPEDRKLQGLVLRMT 362
              LVFG + +  G++ +     +G  V +    P  AI  GI  + EDRKLQGL L  +
Sbjct: 303 LARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQS 362

Query: 363 VKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVL 422
           V +NI L    + +     L+       + + +  L I+          LSGGNQQKV+L
Sbjct: 363 VHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVML 422

Query: 423 AKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIV 482
           ++ L     +LI DEPTRG+D+GAK+EI+R+I  LA  G A++MISSELPE++ L DR++
Sbjct: 423 SRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVL 482

Query: 483 VMWEGEITA-VLDNREKRVTQEEIMYYASG 511
           VM EG +   V        TQE I+  A+G
Sbjct: 483 VMREGTLAGEVRPAGSAAETQERIIALATG 512


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: 630
Number of extensions: 35
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 520
Length of database: 537
Length adjustment: 35
Effective length of query: 485
Effective length of database: 502
Effective search space:   243470
Effective search space used:   243470
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