Alignments for a candidate for ytfR in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Burkholderia phytofirmans PsJN

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate BPHYT_RS23875 BPHYT_RS23875 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__BFirm:BPHYT_RS23875
          Length = 549

 Score =  483 bits (1244), Expect = e-141
 Identities = 249/496 (50%), Positives = 345/496 (69%), Gaps = 13/496 (2%)

Query: 2   TTDQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHA 61
           TT+  + IL T G+SK FPGVKAL  VDF L  GEI  L+G+NGAGKSTLI  LTGV   
Sbjct: 35  TTNALEPILATAGVSKTFPGVKALQRVDFRLFPGEIHTLMGQNGAGKSTLINVLTGVLAP 94

Query: 62  DRGTIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKE 121
           D GTI L G+ ++  +   A+  G+ T+YQEVNL PN+SVA+N+F GR+P+RFG +   +
Sbjct: 95  DEGTIRLGGELVAFASPQEAEGAGVRTLYQEVNLCPNLSVAENIFAGRQPRRFGAIDWPD 154

Query: 122 MEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEV 181
           +++RA   +A    +LDV   L+ + +A+QQ+VAI RA+ + A+VLILDEPT+SLD  EV
Sbjct: 155 IKRRAQAALARLDVTLDVTRSLDAYPIAVQQMVAIARALSVDARVLILDEPTSSLDDGEV 214

Query: 182 ELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMM 241
             LF ++R L+  G++++FVTHF++Q Y +SDRITV+RNG   G     +LP  +LV  M
Sbjct: 215 SQLFKILRHLKQSGIAILFVTHFIEQTYAISDRITVMRNGEREGEYLARDLPADQLVSKM 274

Query: 242 LGRELDTHALQRAG-------------RTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEI 288
           +G E  +  L+ A              +   + +P    +  G++GT+ P DL+V+PG+I
Sbjct: 275 VGHERMSARLREAAHEGHQGHEAHAGPQAAQAVQPFVELRGVGRRGTMQPIDLDVQPGQI 334

Query: 289 VGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDG 348
           +GLAGLLGSGRTETA ++FG   ADSGT L++G+P  LRSP  A   GIG+C EDRK +G
Sbjct: 335 LGLAGLLGSGRTETARLLFGADRADSGTILVEGRPVRLRSPRDAVRHGIGYCAEDRKKEG 394

Query: 349 IIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQ 408
           I+A  S+R+NI+LALQA+RGW R ISR+  +E+A+ +I +LGI+    EQPI  LSGGNQ
Sbjct: 395 IVAELSIRDNILLALQARRGWWRKISRQRARELADLWIERLGIKAADAEQPIGLLSGGNQ 454

Query: 409 QKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGY 468
           QK LL+RWL T P+ LILDEPTRGIDV A  +I+  +  LCA GL++L ISSE+ E++  
Sbjct: 455 QKALLARWLATDPKLLILDEPTRGIDVAAKFDIMDRLLALCASGLSILFISSEISEVLRV 514

Query: 469 ADRVIIMRDRKQVAEI 484
           + RV ++RDR+++AE+
Sbjct: 515 SHRVAVLRDRRKIAEV 530



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 65/255 (25%), Positives = 113/255 (44%), Gaps = 18/255 (7%)

Query: 250 ALQRAGRTLLSDKPVAAFKNYGKK----GTIAPFDLEVRPGEIVGLAGLLGSGRTETAEV 305
           A  +AG T  + +P+ A     K       +   D  + PGEI  L G  G+G++    V
Sbjct: 28  AATQAGGTTNALEPILATAGVSKTFPGVKALQRVDFRLFPGEIHTLMGQNGAGKSTLINV 87

Query: 306 IFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQA 365
           + G+   D GT  + G+     SP +A   G+    ++     +    SV ENI    Q 
Sbjct: 88  LTGVLAPDEGTIRLGGELVAFASPQEAEGAGVRTLYQEVN---LCPNLSVAENIFAGRQP 144

Query: 366 QR----GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRP 421
           +R     W  P  ++  Q    R    L +       PI       QQ V ++R L    
Sbjct: 145 RRFGAIDW--PDIKRRAQAALARLDVTLDVTRSLDAYPIAV-----QQMVAIARALSVDA 197

Query: 422 QFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQV 481
           + LILDEPT  +D G  +++ +++  L   G+A+L ++  +E+    +DR+ +MR+ ++ 
Sbjct: 198 RVLILDEPTSSLDDGEVSQLFKILRHLKQSGIAILFVTHFIEQTYAISDRITVMRNGERE 257

Query: 482 AEIPLAELSVPAIMN 496
            E    +L    +++
Sbjct: 258 GEYLARDLPADQLVS 272


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: 697
Number of extensions: 32
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: 500
Length of database: 549
Length adjustment: 35
Effective length of query: 465
Effective length of database: 514
Effective search space:   239010
Effective search space used:   239010
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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