Alignments for a candidate for fruK in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Burkholderia phytofirmans PsJN

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__BFirm:BPHYT_RS20740
          Length = 503

 Score =  347 bits (890), Expect = e-100
 Identities = 185/476 (38%), Positives = 301/476 (63%), Gaps = 10/476 (2%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P++ +K ++  FPGV+AL  V   L  GEVHALMGENGAGKST++K L GVY  + G I+
Sbjct: 3   PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEIL 62

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGI--DWKKTHEA 123
            +G+P  F    +AQ  G+  ++QE+ L  +L++ +N+ +G E RG  G+  D  K +  
Sbjct: 63  YEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNAQ 122

Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183
           A   LA+M + ++DP   +SS+++A QQ+V IA+A+  +++VLI+DEPTS+L+  E+ +L
Sbjct: 123 AHDILARMHV-TLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAEL 181

Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGK 243
           F I+R ++  GV I+++SH +D++ +I DR+T+LR+G+++  V  KDT    +IGMM+G+
Sbjct: 182 FRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMMVGR 241

Query: 244 SAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303
           +  +     A  ++     GE  + +V  L     +  V   + KGE++GFAGL+G+GRT
Sbjct: 242 TLTD-----AAPSQHIANQGEVAL-EVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRT 295

Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363
           E+ R ++GAD  +SG   + G K  I +P  A+   I Y +E+R+  G+   ++V  NI+
Sbjct: 296 EVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIV 355

Query: 364 IA-LQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422
           ++ L+    +   + + +       ++  L +R     + V+ LSGGNQQK++I +WL  
Sbjct: 356 MSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWLER 415

Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
             ++L  DEPTRGID+GAK+EI +++  LA QG  +V ISSEL E++R+SD I V+
Sbjct: 416 DCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVM 471



 Score = 95.1 bits (235), Expect = 5e-24
 Identities = 63/244 (25%), Positives = 123/244 (50%), Gaps = 8/244 (3%)

Query: 266 PIVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321
           P++ VK L K+      ++ V  ++  GEV    G  G+G++ L ++L G    D+G   
Sbjct: 3   PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEIL 62

Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEA 381
             G+ V+   P  A    +    +  +   ++  LT+ QN+ I  +    +   + + + 
Sbjct: 63  YEGQPVDFQSPREAQAVGVGIIHQELQ---LMNHLTIAQNMFIGREPRGRLGLFLDEDKL 119

Query: 382 DAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAK 441
           +A     +  ++V   DP   V +L+   QQ V I + L+    +LI+DEPT  ++    
Sbjct: 120 NAQAHDILARMHVT-LDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEI 178

Query: 442 AEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVET 501
           AE+ +++ DL  +G+G+++IS +++E+ +++D + VL+D   +A +   DT  QA I   
Sbjct: 179 AELFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIGMM 238

Query: 502 IANT 505
           +  T
Sbjct: 239 VGRT 242



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 50/218 (22%), Positives = 103/218 (47%), Gaps = 6/218 (2%)

Query: 26  VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85
           V   L  GE+    G  GAG++ + +A+ G   I +G I+V G         DA   GI 
Sbjct: 274 VSFALRKGEILGFAGLMGAGRTEVARAVFGADPIESGEIVVKGVKATIRNPSDAVARGIG 333

Query: 86  TVYQE---VNLCTNLSVGENVMLGHEKRG---PFGIDWKKTHEAAKKYLAQMGLESIDPH 139
            + ++     L T +SV  N+++ + ++     F +   +  + A  ++  + + +    
Sbjct: 334 YLSEDRKRFGLATGMSVESNIVMSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSAT 393

Query: 140 TPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILF 199
             +  +S   QQ + IA+ +  +  VL  DEPT  +D     +++ ++R + D G AI+ 
Sbjct: 394 QEVRLLSGGNQQKIVIAKWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVM 453

Query: 200 VSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237
           +S  L +I  ++DR+ ++  G+   E+      ++ ++
Sbjct: 454 ISSELPEILRMSDRIVVMCEGRITGELAAAGATQERIM 491


Lambda     K      H
   0.316    0.135    0.376 

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: 577
Number of extensions: 26
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 513
Length of database: 503
Length adjustment: 34
Effective length of query: 479
Effective length of database: 469
Effective search space:   224651
Effective search space used:   224651
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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, or view the source code.

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