Alignments for a candidate for rbsA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Klebsiella michiganensis M5al

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  472 bits (1214), Expect = e-137
 Identities = 241/488 (49%), Positives = 339/488 (69%), Gaps = 2/488 (0%)

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

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

Query: 125 LLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVI 184
           LL KLN+R  +D+LVG+LSI  QQMVEIAK +S+ + ++IMDEPT ALT++E   LF +I
Sbjct: 125 LLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTII 184

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

Query: 245 QYPHLDKAPGDIRLKVDNLCGPGV-NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALP 303
            +P  + A G+  L V NL   G  +D++F++R+GEILGV+GL+GAGR+E+M+ L+G   
Sbjct: 245 LFPKFNNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEK 304

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

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

Query: 424 RGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQAT 483
           RG+DVGAK EIY LI++    G+++I+VSSE+PE+LGMSDR++VMHEG ++G   +E A 
Sbjct: 425 RGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITGILDKEDAD 484

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



 Score = 92.4 bits (228), Expect = 3e-23
 Identities = 66/234 (28%), Positives = 114/234 (48%), Gaps = 14/234 (5%)

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

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

Query: 381 LFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQ 440
             N++  S ++ +G LS  +QQ V IA+ +     ++I+DEPT  +       ++ +I  
Sbjct: 128 KLNIRL-SADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRD 186

Query: 441 FKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
            +  G +II +S +M E+  ++D I V  +G   G     + T++ L+   VG+
Sbjct: 187 LRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGR 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: 682
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 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