GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Herbaspirillum seropedicae SmR1

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__HerbieS:HSERO_RS05250
          Length = 520

 Score =  440 bits (1132), Expect = e-128
 Identities = 239/498 (47%), Positives = 337/498 (67%), Gaps = 4/498 (0%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           ++ L+ + K FPGV AL      +  G V AL+GENGAGKST+MK+L+G+Y RD+G +L 
Sbjct: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGK-IDWKTMYAEA 122
            GK    T P+ +Q  GIGIIHQELNL+  L+ A+NIF+GRE     G  ID   +  +A
Sbjct: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141

Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182
             + A++ L       VG+L++  QQMVEIAK LSF+S+V+IMDEPT AL + E   LFR
Sbjct: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201

Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKL 242
           +IR+L++QG GIVYISH+M E+ +I D V+V RDG++IA   +   + D++I MMVGR L
Sbjct: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261

Query: 243 E-DQYPHLDKAPGDIRLKVDNLC-GPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYG 300
           + +Q    D +  D+ L+V  L  G  + DVSFTLRKGEILG +GLMGAGRTE+ + ++G
Sbjct: 262 DGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFG 321

Query: 301 ALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360
           A P  +G + + G + V +SP D +A+GI Y+SEDRK  GL +GM V+ N++L+++  F+
Sbjct: 322 ADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFT 381

Query: 361 RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD 420
           R G   + A  ++A   ++R   +KTPS+EQ   LLSGGNQQK+ IA+ L+    +L  D
Sbjct: 382 RVGFMDQRAI-REAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440

Query: 421 EPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTRE 480
           EPTRG+DVGAK EIY+L++     G +I+++SSE+PEVL MS R++VM EG ++GE  R 
Sbjct: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500

Query: 481 QATQEVLMAAAVGKLNRV 498
            ATQE +M  A  + + V
Sbjct: 501 DATQEKIMQLATQRESAV 518


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: 631
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: 501
Length of database: 520
Length adjustment: 34
Effective length of query: 467
Effective length of database: 486
Effective search space:   226962
Effective search space used:   226962
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:

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