Alignments for a candidate for rhaT' in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for rhaT' in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_01057 H281DRAFT_01057 monosaccharide ABC transporter ATP-binding protein, CUT2 family (TC 3.A.1.2.-)

Query= TCDB::Q7BSH4
         (512 letters)



>FitnessBrowser__Burk376:H281DRAFT_01057
          Length = 517

 Score =  388 bits (996), Expect = e-112
 Identities = 215/501 (42%), Positives = 321/501 (64%), Gaps = 6/501 (1%)

Query: 11  DSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKILTGIY 70
           D   GD   +LE+  I++ FPGVK+LD VS+ +  G + AL+GENGAGKSTL KI+ G+Y
Sbjct: 6   DISAGD---LLEVIRITKEFPGVKSLDQVSLGVRAGEIHALVGENGAGKSTLTKIMAGVY 62

Query: 71  RPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTRFRTID 130
            P+ GEI   G+P  + SA  A   G+  IHQE VLF + TVAENIF G  PRTR   +D
Sbjct: 63  APDSGEIRFAGQPLQWKSAADAKRHGIHVIHQELVLFPQSTVAENIFAGAEPRTRIGVLD 122

Query: 131 WQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPTAALSR 190
              MN  ++ALL  L   +D   R+ +LS+A + +V IA+A++ E R++I+DEPTA ++ 
Sbjct: 123 HGRMNRDAQALLGELGVRLDSRERVGNLSVADQQMVEIAKAMAGETRVLILDEPTAVIAG 182

Query: 191 KEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKTPQDEI 250
           KE+  LF  VR L+ +G AI++ISH+ DE++E+ D   V     +   + V+  T +D++
Sbjct: 183 KEVQLLFARVRALRAKGVAIVYISHRLDEIFELCDRVTVMKDGRKVATQSVA-NTTRDQL 241

Query: 251 VRMMVGRDVENVFP-KIDVAIGGP-VLEIRNYSHRTEFRDISFTLRKGEILGVYGLIGAG 308
           VR+MVGR++++++P K  +A G P VLE+          D S T+R GEI+G+ G++G+G
Sbjct: 242 VRLMVGREMKDIYPDKPILAPGVPNVLEVNGLCVGNRVVDASLTVRAGEIVGIAGMVGSG 301

Query: 309 RSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPIFQN 368
           R+EL+  +FG  +   G + + G   T  +P+ AIR G+ +V E+R   GL + + + QN
Sbjct: 302 RTELAAGIFGALRAHRGTVDIGGTRRTRMTPRTAIRLGLGFVTEDRKSQGLLMLLDVAQN 361

Query: 369 MTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGKWLA 428
           +T  +LA+ SR G +R A E A A+       +  A  +  V TLSGGNQQKV+I +W+ 
Sbjct: 362 VTATTLAQVSRFGLMRPALERAAAQAAINEYRIAGAHPAGGVATLSGGNQQKVLISRWVR 421

Query: 429 TAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVMKEG 488
              +V+ILDEPT+G+D+G+KA ++  + EL + GL I+M+SSEL E+IGMSDRVLVM+EG
Sbjct: 422 VCKRVLILDEPTRGVDVGAKAEIYRVMRELTSRGLGILMISSELQEVIGMSDRVLVMREG 481

Query: 489 LSAGIFERAELSPEALVRAAT 509
              G     +++   ++R AT
Sbjct: 482 RINGEVSGEQMTEHDIMRLAT 502



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 72/226 (31%), Positives = 104/226 (46%), Gaps = 13/226 (5%)

Query: 289 ISFTLRKGEILGVYGLIGAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIV 348
           +S  +R GEI  + G  GAG+S L++ + G+  P SG++   GQ +   S  DA R GI 
Sbjct: 31  VSLGVRAGEIHALVGENGAGKSTLTKIMAGVYAPDSGEIRFAGQPLQWKSAADAKRHGIH 90

Query: 349 YVPEERGRHGLALPMPIFQNMTLPSLARTSRRGFLRAA----NEFALARKYAERLDLRAA 404
            + +E     +  P               +R G L       +  AL  +   RLD R  
Sbjct: 91  VIHQEL----VLFPQSTVAENIFAGAEPRTRIGVLDHGRMNRDAQALLGELGVRLDSRER 146

Query: 405 ALSVPVGTLSGGNQQKVVIGKWLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLS 464
                VG LS  +QQ V I K +A   +V+ILDEPT  I       +   +  L A+G++
Sbjct: 147 -----VGNLSVADQQMVEIAKAMAGETRVLILDEPTAVIAGKEVQLLFARVRALRAKGVA 201

Query: 465 IIMVSSELPEIIGMSDRVLVMKEGLSAGIFERAELSPEALVRAATG 510
           I+ +S  L EI  + DRV VMK+G        A  + + LVR   G
Sbjct: 202 IVYISHRLDEIFELCDRVTVMKDGRKVATQSVANTTRDQLVRLMVG 247


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: 619
Number of extensions: 28
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: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
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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Steps (tab-delimited)
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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