GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Echinicola vietnamensis KMM 6221, DSM 17526

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Cola:Echvi_1282
          Length = 502

 Score =  384 bits (985), Expect = e-111
 Identities = 221/508 (43%), Positives = 323/508 (63%), Gaps = 14/508 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L  K I K F GV A+D+V  E+    + +++GENGAGKSTL+KIL+GV     G I  
Sbjct: 1   MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY 60

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
           NG+ V+F +  DA +KGI++IHQELNL   +++ ENIFL  E       T    +D   M
Sbjct: 61  NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREP-----ETPMGLLDVAKM 115

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
           +  + +LL  +     P+  V  L   Q+Q+VEI KAL  E ++I MDEPTS+++ +E E
Sbjct: 116 HKEAAQLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVE 175

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            LF II  L++ G ++ ++SH+LDE+  I+DR VV+RDGK I   +      + +I+ MV
Sbjct: 176 ILFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMV 235

Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWK-----DK--VKNVSFEVRKGEVLGFAGLVGAG 306
           GRE+         +  E  L V++L  K     DK  +++++FE+ KGEVLG  GL+GAG
Sbjct: 236 GREIVIERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAG 295

Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDN 366
           RTE M  +FGV   +  +I + G+  E + P++A+  G+ L+PEDRK  GLVL M +  N
Sbjct: 296 RTELMEALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTN 355

Query: 367 IVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWL 426
             L  +  I   GL LD++KE+ +++ Y+  L IK  S  Q+ E LSGGNQQKVVLAKWL
Sbjct: 356 SSLTVVDSILSGGL-LDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWL 414

Query: 427 ATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWE 486
           AT   +L+ DEPTRGID+ AK EI+++IR+LA +G  +I++SSELPEIL +SDR++VM E
Sbjct: 415 ATRPKVLMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAE 474

Query: 487 GEITAVLDNREKRVTQEEIMYYASGQKK 514
           G +TA +   + + +++EI+  A  +KK
Sbjct: 475 GRLTANIP-IDAQTSEDEILQAAIPKKK 501


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: 686
Number of extensions: 37
Number of successful extensions: 8
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: 502
Length adjustment: 35
Effective length of query: 485
Effective length of database: 467
Effective search space:   226495
Effective search space used:   226495
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.

Links

Downloads

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:

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:

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:

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:

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