Alignments for a candidate for rhaT' in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Rhizobium leguminosarum 3841

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_011651404.1 RL_RS09075 sugar ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>NCBI__GCF_000009265.1:WP_011651404.1
          Length = 492

 Score =  381 bits (978), Expect = e-110
 Identities = 201/490 (41%), Positives = 306/490 (62%), Gaps = 1/490 (0%)

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

Query: 80  DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139
            G+   FA    A+ +G+  I QE      +TVAENI+LG  P TRF  ID++TMN  ++
Sbjct: 64  RGKDVDFAGPADALASGIAIIEQELSPVPHMTVAENIYLGREPSTRFGGIDFRTMNRSAQ 123

Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199
            LL  LE +I  T  + +LS+AQ  LV IA+ALS +A ++ MDEPT+A+  KE   LF  
Sbjct: 124 GLLDDLEFDIRATQYMMNLSVAQMQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQLFAA 183

Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259
           +R LK QG+ I+++SH+  E+++IAD + VF R       G  ++  + +++RM+VGR++
Sbjct: 184 IRRLKGQGRGIVYVSHRLSEIFQIADSYTVF-RDGAYVGSGDLKQISRPDLIRMIVGREL 242

Query: 260 ENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGI 319
              + K +       LE+   S   +  DISF+ RKGEI G+YGL+G+GR+E+   LFG+
Sbjct: 243 AEEYVKTNTPTSETGLEVTALSCPNKIEDISFSARKGEIFGIYGLMGSGRTEIFNCLFGL 302

Query: 320 TKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTLPSLARTSR 379
            K   G++V++G  I++  P DA+ +G+  V E+R   GL L   +  N+ + SL   S 
Sbjct: 303 EKSSDGRIVVDGTRISVSKPADAMASGLALVTEDRKLTGLNLSDSVRANICMASLPEMSP 362

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

Query: 440 TKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAEL 499
           T+G+D+G+K  ++  I + AA G +++M+SSE+ E++GMSDR++VM+ G SAGI+ R E 
Sbjct: 423 TRGVDVGAKREIYRIICDFAAAGGTVVMISSEIDEVLGMSDRIMVMRAGKSAGIYSREET 482

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



 Score = 76.3 bits (186), Expect = 2e-18
 Identities = 65/228 (28%), Positives = 98/228 (42%), Gaps = 13/228 (5%)

Query: 287 RDISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAG 346
           RD  F LR G +  + G  GAG+S   + L GI    +G +   G+++    P DA+ +G
Sbjct: 21  RDGRFELRAGSVHALCGGNGAGKSTFLKILMGIHNRDAGSIRRRGKDVDFAGPADALASG 80

Query: 347 IVYVPEERGRHGLALPMP---IFQNMTLPSLARTSRRGF-LRAANEFALARKYAERLDLR 402
           I  + +E        P+P   + +N+ L     T   G   R  N  A         D+R
Sbjct: 81  IAIIEQELS------PVPHMTVAENIYLGREPSTRFGGIDFRTMNRSAQGLLDDLEFDIR 134

Query: 403 AAALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEG 462
           A    +    LS    Q V I K L+   +VI +DEPT  I       +   I  L  +G
Sbjct: 135 ATQYMM---NLSVAQMQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQLFAAIRRLKGQG 191

Query: 463 LSIIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
             I+ VS  L EI  ++D   V ++G   G  +  ++S   L+R   G
Sbjct: 192 RGIVYVSHRLSEIFQIADSYTVFRDGAYVGSGDLKQISRPDLIRMIVG 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: 591
Number of extensions: 23
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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Protein sequences (fasta format)
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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