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_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  280 bits (715), Expect = 1e-79
 Identities = 175/498 (35%), Positives = 268/498 (53%), Gaps = 30/498 (6%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           IL+  GI KRF  +VA D++  E+   E+++L+GENGAGKSTL+ IL G    DAG + V
Sbjct: 5   ILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEV 64

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
           +G+ +    P  A   GI ++HQ   L DN++V +NI L      G +     R+D +  
Sbjct: 65  DGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIML------GTQPLWQWRLDGHAA 118

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
             +   L +  G    P A V  L+  +RQ VEI KAL +  R++ +DEPT+ LT  E E
Sbjct: 119 RGKVLALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAE 178

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            LF  +  L + G+SV+F+SH+LDEV+R+SDRI V+R GK +      +     + ++MV
Sbjct: 179 TLFSTLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMV 238

Query: 254 GREVEFFPHGIETRPGE-----------IALE---VRNLKWKDKVKNVSFEVRKGEVLGF 299
           GR V   P  +  R  E           +ALE    R    +  ++ VS +VR GE++G 
Sbjct: 239 GRVVA-MPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGI 297

Query: 300 AGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVL 359
           AG+ G G+     L  G+ +   G I + G+ +  K P   I  G+  +PEDR   G+V 
Sbjct: 298 AGVSGNGQAALAELASGMLEASEGRITLAGKPMSAK-PRAWIGAGVARVPEDRHAIGVVG 356

Query: 360 RMTVKDNIVLPSLK--KISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQ 417
            + V +N V   L   + SRWG V+     +  + D V R  ++T  I      +SGGN 
Sbjct: 357 DLAVWENAVSEQLSEPRFSRWG-VIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNM 415

Query: 418 QKVVLAKWLATNAD-----ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELP 472
           QK++L + L+   +     +++  +PT G+D+GA A +   + + A +G AV++IS +L 
Sbjct: 416 QKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLD 475

Query: 473 EILNLSDRIVVMWEGEIT 490
           E+  L+DRI VM  G +T
Sbjct: 476 ELHALADRIAVMHAGHLT 493



 Score = 88.2 bits (217), Expect = 7e-22
 Identities = 61/207 (29%), Positives = 113/207 (54%), Gaps = 7/207 (3%)

Query: 286 NVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGI 345
           ++S E+++GEVL   G  GAG++  + ++FG    ++G + V+G+ +    P  A+  GI
Sbjct: 23  DISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAGI 82

Query: 346 GLIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSI 405
           G++ +   L      ++V DNI+L + + + +W L     + + ++    +R  +     
Sbjct: 83  GMVHQHFTLAD---NLSVLDNIMLGT-QPLWQWRLDGHAARGKVLA--LAERFGLAVRPQ 136

Query: 406 YQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVI 465
            ++ E LS G +Q+V + K L   A +LI DEPT  +       +   + +L A+G +VI
Sbjct: 137 ARVGE-LSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLAQLIAEGLSVI 195

Query: 466 MISSELPEILNLSDRIVVMWEGEITAV 492
            IS +L E+L +SDRI V+  G++ A+
Sbjct: 196 FISHKLDEVLRVSDRIAVLRGGKLVAL 222


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: 644
Number of extensions: 23
Number of successful extensions: 10
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: 530
Length adjustment: 35
Effective length of query: 485
Effective length of database: 495
Effective search space:   240075
Effective search space used:   240075
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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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