GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaT' in Burkholderia phytofirmans PsJN

Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__BFirm:BPHYT_RS27185
          Length = 516

 Score =  408 bits (1049), Expect = e-118
 Identities = 216/506 (42%), Positives = 322/506 (63%), Gaps = 3/506 (0%)

Query: 8   PVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILT 67
           P  + +   +  IL+++G+S+ FPGV ALD + + L  G V A+ GENGAGKSTL+KI++
Sbjct: 11  PAAEPEPPVSREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIIS 70

Query: 68  GIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFR 127
           G YR +EG +   G P  F+S   A  AG+  IHQE  L   L+VAENI+L   P+ R  
Sbjct: 71  GQYRADEGVVRYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPK-RGP 129

Query: 128 TIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAA 187
            +D++T+NS ++  L  +  N+ P+  +  LS+AQ+ +V IA+ALS++AR++IMDEPT++
Sbjct: 130 FVDYRTLNSNAQRCLQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSS 189

Query: 188 LSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQ 247
           L+  E   LFRI+R L+  G AIL+ISH+ DE+ EI D   V  R  R         T  
Sbjct: 190 LTESETVQLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVL-RDGRHIATSDFASTTV 248

Query: 248 DEIVRMMVGRDVENVFPKIDVAIGGPVL-EIRNYSHRTEFRDISFTLRKGEILGVYGLIG 306
           +EIV  MVGR +++ +P         +L  +R+      F  +SF LRKGEILG  GL+G
Sbjct: 249 NEIVARMVGRPLDDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMG 308

Query: 307 AGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIF 366
           AGR+E ++++FG  +P SG + L  + +TI SP++AIR GI Y+ E+R + GLAL MP+ 
Sbjct: 309 AGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVS 368

Query: 367 QNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKW 426
            N+TL ++   S RGFLR + E A+A +Y   L +R   +      LSGGNQQK+VI KW
Sbjct: 369 ANITLANVRAISSRGFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKW 428

Query: 427 LATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMK 486
           L    +++  DEPT+GID+G+K A++G +  LAA+G+ ++++SSELPE++GM+DR+ V  
Sbjct: 429 LYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFH 488

Query: 487 EGLSAGIFERAELSPEALVRAATGNA 512
           EG    + E  + S E ++  A+G +
Sbjct: 489 EGRITAVLETRQTSQEEILHHASGRS 514


Lambda     K      H
   0.320    0.137    0.382 

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: 610
Number of extensions: 31
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: 512
Length of database: 516
Length adjustment: 35
Effective length of query: 477
Effective length of database: 481
Effective search space:   229437
Effective search space used:   229437
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 (21.8 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