GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Pseudovibrio axinellae Ad2

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_068000812.1 PsAD2_RS00245 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_001623255.1:WP_068000812.1
          Length = 514

 Score =  300 bits (767), Expect = 1e-85
 Identities = 185/505 (36%), Positives = 282/505 (55%), Gaps = 20/505 (3%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           ++L G++K+F  V A     L V  G +  ++GENGAGKST+M +L G Y  D+GT+   
Sbjct: 9   IELIGVNKSFGPVHANKDIDLVVGKGSIHGIIGENGAGKSTLMSILYGFYHADSGTIKID 68

Query: 65  GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124
           GK TT    KS+   GIG++HQ   L+   T+ EN+ LG E     G    K   A A +
Sbjct: 69  GKATTIPDSKSAISQGIGMVHQHFMLVDPFTVLENVVLGAE-----GGALLKDGVANARR 123

Query: 125 LLAKL----NLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180
            L +L    ++    D +VG+L +G QQ VEI K L   + ++I+DEPT  LT +E + L
Sbjct: 124 ELKRLADEYDMTIDPDAVVGELPVGLQQRVEILKALYRGADILILDEPTGVLTPSEADHL 183

Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240
           FR++R L+ QG+ ++ I+H+++EI ++ D V+V R G+ +A R+ A  + + L E+MVGR
Sbjct: 184 FRILRVLRDQGKTVLLITHKLREIMDVTDTVSVMRRGEMVASRKTAQTSMEELAELMVGR 243

Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGPG------VNDVSFTLRKGEILGVSGLMGAGRTEL 294
            +  +    D   G   LKV+ L          V DVSF +R GE+LG++G+ G G++EL
Sbjct: 244 SVLLEVSKPDVEVGKPLLKVEGLNVKDERGVRRVKDVSFEVRAGEVLGIAGVSGNGQSEL 303

Query: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLA---NGIVYISEDRKRDGLVLGMSVKENM 351
           M  L G     SG + L G ++      D       G+ ++ EDR R GLV   S  EN 
Sbjct: 304 MAALAGITRAESGSMELAGQKLDLSEVHDAAQMRDRGMSHVPEDRHRMGLVNKFSEAENS 363

Query: 352 SLTALRYFSRAGGSLKHADE-QQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGL 410
            L   R    + G     D  ++   + I  ++++ P  E      SGGNQQK+ +AR +
Sbjct: 364 ILGYHRESKYSKGMFLDKDAIRKEAKERIEKYDIRPPLTEMTAAKFSGGNQQKIVLAREI 423

Query: 411 MTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHE 470
              P VL++ +PTRGVD+GA + I+  I   +A G +++LVS E+ E+  +SDRIIVM +
Sbjct: 424 ECNPDVLLIGQPTRGVDIGAIEYIHNRIMDMRAQGKAVLLVSVELDEIRSLSDRIIVMFD 483

Query: 471 GHLSGEFTREQATQEV-LMAAAVGK 494
           G++ GE   E   Q++ L+ A V +
Sbjct: 484 GNVVGERGPEATEQDLGLLMAGVNQ 508


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: 594
Number of extensions: 32
Number of successful extensions: 9
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: 514
Length adjustment: 34
Effective length of query: 467
Effective length of database: 480
Effective search space:   224160
Effective search space used:   224160
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