Alignments for a candidate for ytfR in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Paraburkholderia bryophila 376MFSha3.1

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate H281DRAFT_02712 H281DRAFT_02712 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__Burk376:H281DRAFT_02712
          Length = 505

 Score =  381 bits (979), Expect = e-110
 Identities = 198/492 (40%), Positives = 319/492 (64%), Gaps = 7/492 (1%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRG-TIWL 68
           L    +S+ FPGVKALD V+  +R GE++AL GENGAGKSTL+K LTG+Y  D G TI +
Sbjct: 10  LEMRNISRTFPGVKALDRVNLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILV 69

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPK-RFGLLRRKEMEKRAT 127
           EGQ ++  ++ HA+ LG+  +YQE+ ++ N++V +N+F+ REP+ R GL+ R  M + A 
Sbjct: 70  EGQEVALADSHHARTLGVNIIYQELAVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAR 129

Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187
           E++A+    +D    ++  SV  QQ++ I +A+   +K +I+DEPTASL   E  +L  +
Sbjct: 130 EVLATIDMDIDPATRVSELSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGI 189

Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247
           +++LR+R +++++++H L+++++++DR+TVLR+G  VG     ++ +  LV++M+ REL 
Sbjct: 190 VKRLRERNIAVVYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVARELS 249

Query: 248 T---HALQRAGRTLLSDKPVAAFKNYGK-KGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303
                    A R  + +    + K   K +  I      +  GE++G+AGL+GSGRTE  
Sbjct: 250 ELYGEPQSHASRDPVLEVRALSLKPVRKAEPRIRDISFTLHRGEVLGIAGLVGSGRTEIM 309

Query: 304 EVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILAL 363
           E+IFG++ A +G+  I+GKP ++R+PH A   GIGF  EDRK  G+I   +VREN  L  
Sbjct: 310 EMIFGMR-ACTGSVKIEGKPVSIRNPHDAIRSGIGFVTEDRKAQGLILGMTVRENFSLTH 368

Query: 364 QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423
             +    + +    ++E   RF+R LGI+TP  EQ +  LSGGNQQK+++++W+   P+ 
Sbjct: 369 LERYSPFQFVQHARERESCRRFVRMLGIKTPGVEQKVVNLSGGNQQKIVIAKWVARSPKV 428

Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAE 483
           LI+DEPTRGIDVGA AE+  LI  L A+G+ ++VISS+L E++  +DR++ +R+ +   E
Sbjct: 429 LIVDEPTRGIDVGAKAEVHALIARLAAEGIGVIVISSDLLEVLAVSDRILTVREGRISGE 488

Query: 484 IPLAELSVPAIM 495
           +  A+ S   +M
Sbjct: 489 LSRAQASQEKVM 500



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 64/225 (28%), Positives = 119/225 (52%), Gaps = 12/225 (5%)

Query: 280 DLEVRPGEIVGLAGLLGSGRTETAEVIFGI-KPADSGTALIKGKPQNLRSPHQASVLGIG 338
           +LE+R GE++ LAG  G+G++   +++ GI  P   GT L++G+   L   H A  LG+ 
Sbjct: 29  NLEIRAGEVLALAGENGAGKSTLMKILTGIYAPDPGGTILVEGQEVALADSHHARTLGVN 88

Query: 339 FCPEDRKTDGIIAAASVRENIILALQAQR--GWL-RPISRKEQQEIAERFIRQLGIRTPS 395
              ++     ++   +V ENI LA + +   G + RP   +E +E+       +   T  
Sbjct: 89  IIYQEL---AVVGNLTVGENIFLAREPRTRLGLIDRPRMYREAREVLATIDMDIDPATRV 145

Query: 396 TEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLAL 455
           +E     LS G QQ + +++ L  R + +I+DEPT  +     + ++ +++ L    +A+
Sbjct: 146 SE-----LSVGQQQMIEIAKALCARSKAIIMDEPTASLSHHETSVLLGIVKRLRERNIAV 200

Query: 456 LVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIMNAIAA 500
           + IS  LEE+   ADRV ++RD + V   P+A+++   ++  + A
Sbjct: 201 VYISHRLEEIFELADRVTVLRDGRTVGTAPIADMTRETLVRLMVA 245


Lambda     K      H
   0.321    0.138    0.391 

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: 598
Number of extensions: 34
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 500
Length of database: 505
Length adjustment: 34
Effective length of query: 466
Effective length of database: 471
Effective search space:   219486
Effective search space used:   219486
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.

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
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