GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaT' in Rhizobium freirei PRF 81

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 WP_004124104.1 RHSP_RS23335 sugar ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>NCBI__GCF_000359745.1:WP_004124104.1
          Length = 492

 Score =  394 bits (1012), Expect = e-114
 Identities = 211/490 (43%), Positives = 310/490 (63%), Gaps = 1/490 (0%)

Query: 20  ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79
           +LE+ G+ + F GV AL +    L PG+V AL G NGAGKST +KIL GI++ + G I  
Sbjct: 4   LLEVEGLKKSFGGVAALRDGCFQLRPGSVHALCGGNGAGKSTFLKILMGIHKRDAGSIRR 63

Query: 80  DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139
            G+   +AS  AA+ AG+  I QE      +TVAENI+LG  P  RF  ID++TMN  ++
Sbjct: 64  RGKDVDYASPAAALAAGIAIIEQELSPIPHMTVAENIYLGREPSARFGGIDFKTMNRNAQ 123

Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199
           ALL  L  NI  T  + +LS+AQ  LV IA+ALS +A ++ MDEPT+A+  KE   LF  
Sbjct: 124 ALLDRLRFNIRATQFMMNLSVAQIQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQLFST 183

Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259
           +  LK +GK ++++SH+  E+++IAD +  F R       G      +  ++RM+VGR++
Sbjct: 184 IERLKAEGKGVVYVSHRLSEIFQIADSYTAF-RDGSYVGSGALADIDRPGLIRMIVGREL 242

Query: 260 ENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGI 319
              + K +V    P LE+   +   +  DISFT  KGEI G+YGL+G+GR+E+   +FG+
Sbjct: 243 GEEYIKTNVPTATPGLEVAGLTAEGKLNDISFTAHKGEIFGIYGLMGSGRTEIFNCIFGL 302

Query: 320 TKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSR 379
               SG++ L GQ IT+  P +A++ GI +V E+R   GL L   +  N+ L SL   S 
Sbjct: 303 DVLNSGQIKLAGQPITVGKPAEAMQHGIAFVTEDRKLTGLNLIDSVRNNICLASLPEMSP 362

Query: 380 RGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEP 439
           R  + +  E + ++   ER  ++AA  S+PV  LSGGNQQKVV+GKW    PKV++LDEP
Sbjct: 363 RFSMDSRAEASASQDMIERFGIKAARDSMPVSGLSGGNQQKVVLGKWFLRKPKVLLLDEP 422

Query: 440 TKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAEL 499
           T+G+D+G+K  ++  I + AAEG ++IM+SSE+ E++GMSDR+LVM++G SAGI +R E 
Sbjct: 423 TRGVDVGAKREIYRIICDFAAEGGTVIMISSEIDEVLGMSDRILVMRQGRSAGILKREEA 482

Query: 500 SPEALVRAAT 509
             ++LV  +T
Sbjct: 483 DAQSLVHLST 492



 Score = 76.3 bits (186), Expect = 2e-18
 Identities = 66/226 (29%), Positives = 99/226 (43%), Gaps = 9/226 (3%)

Query: 287 RDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAG 346
           RD  F LR G +  + G  GAG+S   + L GI K  +G +   G+++   SP  A+ AG
Sbjct: 21  RDGCFQLRPGSVHALCGGNGAGKSTFLKILMGIHKRDAGSIRRRGKDVDYASPAAALAAG 80

Query: 347 IVYVPEERGRHGLALP-MPIFQNMTLPSLARTSRRGF-LRAANEFALARKYAERLDLRAA 404
           I  + +E       +P M + +N+ L         G   +  N  A A     R ++RA 
Sbjct: 81  IAIIEQELS----PIPHMTVAENIYLGREPSARFGGIDFKTMNRNAQALLDRLRFNIRAT 136

Query: 405 ALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLS 464
              +    LS    Q V I K L+   +VI +DEPT  I       +   I  L AEG  
Sbjct: 137 QFMM---NLSVAQIQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQLFSTIERLKAEGKG 193

Query: 465 IIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
           ++ VS  L EI  ++D     ++G   G    A++    L+R   G
Sbjct: 194 VVYVSHRLSEIFQIADSYTAFRDGSYVGSGALADIDRPGLIRMIVG 239


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: 581
Number of extensions: 22
Number of successful extensions: 6
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: 512
Length of database: 492
Length adjustment: 34
Effective length of query: 478
Effective length of database: 458
Effective search space:   218924
Effective search space used:   218924
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 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