GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaT' in Paucidesulfovibrio gracilis DSM 16080

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_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= TCDB::Q7BSH4
         (512 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  255 bits (652), Expect = 2e-72
 Identities = 157/481 (32%), Positives = 273/481 (56%), Gaps = 17/481 (3%)

Query: 20  ILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEILV 79
           ++ ++G+++ F  V A D++S+ ++PG V AL+GENGAGKSTL+ +L G Y+P+ G I +
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83

Query: 80  DGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTIDWQTMNSRSK 139
           DG+P  F+SA+ AI+AG+  ++Q  +L + +TVAEN+ LG         ++ + M +R +
Sbjct: 84  DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGSF---FLNPKEMRNRVQ 140

Query: 140 ALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRKEIDDLFRI 199
            L      +IDP  R+ DLS+ ++  V I + L  ++R++I DEPTA L+ +E   LF  
Sbjct: 141 ELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEA 200

Query: 200 VRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIVRMMVGRDV 259
           +  + EQGK+I+FISHK +E+  +AD+  +  +         S  T + ++   MVG++V
Sbjct: 201 LWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEV 260

Query: 260 ENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAGRSELSQSLFGI 319
                +  +  G  VL++RN +      DI+F L +GE++ V G+ G G+  L +++ G+
Sbjct: 261 LLEVDREAMPHGDAVLQVRNLT-GIGLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGL 319

Query: 320 TKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQNMTL-PSLARTS 378
            KP    M + G+       + + +  + Y+PE+R      L +   +N+ L  +L  T+
Sbjct: 320 RKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDR------LGLATCRNLNLVDNLLLTT 373

Query: 379 RRGFLRA--ANEFALARKYAE---RLDLRAAALSVPVGTLSGGNQQKVVIGKWLATAPKV 433
           R+GF R    ++   AR   E   + D+R   ++     LSGGN QK V+ + L   P++
Sbjct: 374 RQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRL 433

Query: 434 IILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEGLSAGI 493
           I+ ++PT+G+DI +   V   +   A E   I++V+ +L E + ++DRV V+  G    +
Sbjct: 434 IVAEQPTQGLDIAATEQVWNHLL-AAREMAGILLVTGDLNEALQLADRVAVIYRGRFMDV 492

Query: 494 F 494
           F
Sbjct: 493 F 493



 Score = 48.5 bits (114), Expect = 6e-10
 Identities = 53/245 (21%), Positives = 103/245 (42%), Gaps = 15/245 (6%)

Query: 19  AILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIYRPNEGEIL 78
           A+L++R ++ I      L++++  LH G V A++G  G G+  LV+ + G+ +P    + 
Sbjct: 274 AVLQVRNLTGI-----GLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMF 328

Query: 79  VDGRPTTFASAQAAIDAGVTAIHQETV---LFDELTVAENIFLGHAPRTRFRTIDWQTMN 135
           + G+      A+ +    +  I ++ +       L + +N+ L    R  F    W    
Sbjct: 329 IMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLL--TTRQGFARGPWLDKK 386

Query: 136 SRSKALLTALES-NIDP---TIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSRK 191
             ++     ++  +I P         LS        +AR L    R+++ ++PT  L   
Sbjct: 387 KAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIA 446

Query: 192 EIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEIV 251
             + ++  +   +E    IL ++   +E  ++AD   V  R     V  VS K   + I 
Sbjct: 447 ATEQVWNHLLAAREMA-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIG 505

Query: 252 RMMVG 256
            MM G
Sbjct: 506 LMMAG 510


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: 540
Number of extensions: 31
Number of successful extensions: 7
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: 514
Length adjustment: 35
Effective length of query: 477
Effective length of database: 479
Effective search space:   228483
Effective search space used:   228483
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 Apr 09 2024. 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