GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Herbaspirillum seropedicae SmR1

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__HerbieS:HSERO_RS03640
          Length = 502

 Score =  387 bits (993), Expect = e-112
 Identities = 215/502 (42%), Positives = 316/502 (62%), Gaps = 14/502 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L+ +GI K F   +A+ ++   +   EI +L+GENGAGKSTL+K+L+GV  PD GEIL+
Sbjct: 10  LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 69

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
           +G  V    P  +   GI++I+QEL +  N++VA N+F+  E      RT    +D   M
Sbjct: 70  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSEL-----RTRLGLIDHAAM 124

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
            +R+  +L  +GA F    L   L+ A++Q VEI +ALV   RI+ MDEPT++L+  ETE
Sbjct: 125 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 184

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
           +LF ++  L+  G++++++SHR+ EV  ++DR+ V+RDG  +GEL + E D + I++MMV
Sbjct: 185 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 244

Query: 254 GREVEFFPHGIETRPGEIA-----LEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRT 308
           GR +  F       P + A     ++VR L    K++  SF+VR GEVLGFAGLVGAGRT
Sbjct: 245 GRSLSEFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRT 303

Query: 309 ETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIV 368
           E   L+FG + +  GDI + GR V I  P  A++ GI  +PEDRK QGL L+M V  N  
Sbjct: 304 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 363

Query: 369 LPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLAT 428
           +    + +R GLV   R    ++   ++RL++K          LSGGNQQKV+LA+WL  
Sbjct: 364 MNVASRHTRLGLV-RSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEI 422

Query: 429 NADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGE 488
              +LI DEPTRG+D+ AK+EI++++  LA+QG AV++ISSELPE++ + DR++VM EG 
Sbjct: 423 APKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGM 482

Query: 489 ITAVLDNREKRVTQEEIMYYAS 510
           IT  L      +TQE IM  A+
Sbjct: 483 ITGELAG--AAITQENIMRLAT 502


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: 632
Number of extensions: 30
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.

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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:

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