GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Pantoea rwandensis LMG 26275

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_084935209.1 HA51_RS14055 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_002095475.1:WP_084935209.1
          Length = 494

 Score =  471 bits (1213), Expect = e-137
 Identities = 242/488 (49%), Positives = 338/488 (69%), Gaps = 2/488 (0%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           L+ +GI K FPGVKAL   +L + PG V AL+GENGAGKST+MK L G+Y  D GT+   
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIK 65

Query: 65  GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124
           G+   F     +  +GI +IHQELNL+P +T+AENI+LGRE + ++G +D   +  +  +
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPYMTVAENIWLGREPM-KYGFVDHGKLNKQTQE 124

Query: 125 LLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVI 184
           LL +LN+R K+D++VG+LSI  QQMVEIAK +S+ S ++IMDEPT ALT+TE   LF +I
Sbjct: 125 LLNRLNIRLKADRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHLFTII 184

Query: 185 RELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLED 244
           R+L+ QG+ I+YISH+M EIF I D++++FRDG ++     +  T  SLI  MVGR+L  
Sbjct: 185 RDLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVGRELTQ 244

Query: 245 QYPHLDKAPGDIRLKVDNL-CGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALP 303
            +P  +   G   L V NL C     D++FT+RKGEILGV+GL+GAGR+E+M+ L+G   
Sbjct: 245 LFPKFNGEIGADVLTVRNLTCKDRFTDINFTVRKGEILGVAGLVGAGRSEVMESLFGMES 304

Query: 304 RTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAG 363
             SG V +DG  V   SP   +  G+ +++EDRK+ GL L +SV ENMS+  +  +    
Sbjct: 305 FDSGEVLIDGVPVKIDSPSTAIEKGMAFLTEDRKKSGLFLVLSVMENMSIVNMPDYVSKA 364

Query: 364 GSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPT 423
           G + H    Q   + IR  N+KTP+M+Q I  LSGGNQQKV IAR L+ +PK+LILDEPT
Sbjct: 365 GFVSHMKMAQDCMEQIRKLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPT 424

Query: 424 RGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQAT 483
           RG+DVGAK EIY+LI++    G++II+VSSE+PE+LGMSDR++VMH G ++G   +E+A 
Sbjct: 425 RGIDVGAKAEIYRLISELANRGVAIIMVSSELPEILGMSDRVMVMHGGRITGILDKEEAN 484

Query: 484 QEVLMAAA 491
           QE +++ A
Sbjct: 485 QETILSLA 492



 Score = 88.2 bits (217), Expect = 6e-22
 Identities = 62/234 (26%), Positives = 113/234 (48%), Gaps = 14/234 (5%)

Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322
           PGV   ++VS  ++ G +  + G  GAG++ LMK L G      G + + G  V  +   
Sbjct: 16  PGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIKGEPVQFQDTM 75

Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSL--TALRYFSRAGGSLKHADEQQAVSDFIR 380
           D L +GI  I ++     LV  M+V EN+ L    ++Y     G + H    +   + + 
Sbjct: 76  DALRSGISMIHQELN---LVPYMTVAENIWLGREPMKY-----GFVDHGKLNKQTQELLN 127

Query: 381 LFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQ 440
             N++  + ++ +G LS   QQ V IA+ +     ++I+DEPT  +       ++ +I  
Sbjct: 128 RLNIRLKA-DRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHLFTIIRD 186

Query: 441 FKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
            +  G +II +S +M E+  ++D I +  +G   G     + T++ L+   VG+
Sbjct: 187 LREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVGR 240


Lambda     K      H
   0.318    0.137    0.380 

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: 685
Number of extensions: 36
Number of successful extensions: 7
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: 501
Length of database: 494
Length adjustment: 34
Effective length of query: 467
Effective length of database: 460
Effective search space:   214820
Effective search space used:   214820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 24 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