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_05270 H281DRAFT_05270 monosaccharide ABC transporter ATP-binding protein, CUT2 family

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



>FitnessBrowser__Burk376:H281DRAFT_05270
          Length = 539

 Score =  483 bits (1242), Expect = e-141
 Identities = 252/491 (51%), Positives = 341/491 (69%), Gaps = 10/491 (2%)

Query: 4   DQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADR 63
           D  + IL T G+SK FPGVKAL  VDF L  GE+  L+G+NGAGKSTLI  LTGV   D 
Sbjct: 30  DPCEPILATTGVSKTFPGVKALQRVDFRLFPGEVHTLMGQNGAGKSTLINVLTGVIAPDT 89

Query: 64  GTIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEME 123
           GTI L G+ ++  +   A+  G+ T+YQEVNL PN+SVA+N+F GR+P+RFG +   +++
Sbjct: 90  GTIRLAGEVVAFASPQEAEAAGVRTLYQEVNLCPNLSVAENIFAGRQPRRFGAIDWPDIK 149

Query: 124 KRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVEL 183
           +RA   +A    SLDV   L+ + +A+QQ+VAI RA+ + A+VLILDEPT+SLD  EV  
Sbjct: 150 RRAQAALARLDISLDVTRSLDAYPIAVQQMVAIARALSVDARVLILDEPTSSLDDSEVAQ 209

Query: 184 LFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
           LF ++R L+  G++++FVTHF++Q Y +SDRITV+RNG   G      L   +LV  M+G
Sbjct: 210 LFKILRHLKQSGIAILFVTHFIEQTYAISDRITVMRNGEREGEYLARNLSADQLVAKMVG 269

Query: 244 RELDTHALQRA-------GRTLLSDKPVAAF---KNYGKKGTIAPFDLEVRPGEIVGLAG 293
            E  +  L+ A       G T   ++  +AF   +  GK+GT+ P DL V  G+I+GLAG
Sbjct: 270 HERMSERLREAAHEASAPGGTERGERAASAFIELRGVGKRGTLQPIDLNVERGQILGLAG 329

Query: 294 LLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAA 353
           LLGSGRTETA ++FG   ADSGT L+ GKP  LRSPH A   GI +C EDRK +GI+A  
Sbjct: 330 LLGSGRTETARLLFGADRADSGTMLVDGKPVRLRSPHDAVRHGIAYCAEDRKKEGIVADL 389

Query: 354 SVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLL 413
           S+RENI+LALQA+RGW R ISR+  +E+A+ +I +LGI+    EQPI  LSGGNQQK LL
Sbjct: 390 SIRENILLALQARRGWWRKISRQRARELADLWIERLGIKASDAEQPIGLLSGGNQQKALL 449

Query: 414 SRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVI 473
           +RWL T P+ LILDEPTRGIDV A  +I+  +  LCA+GL++L ISSE+ E++  + RV 
Sbjct: 450 ARWLATDPKLLILDEPTRGIDVAAKFDIMDRLLALCANGLSILFISSEISEVLRVSHRVA 509

Query: 474 IMRDRKQVAEI 484
           ++RDR+++AE+
Sbjct: 510 VLRDRRKIAEV 520



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 58/220 (26%), Positives = 100/220 (45%), Gaps = 14/220 (6%)

Query: 280 DLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGF 339
           D  + PGE+  L G  G+G++    V+ G+   D+GT  + G+     SP +A   G+  
Sbjct: 55  DFRLFPGEVHTLMGQNGAGKSTLINVLTGVIAPDTGTIRLAGEVVAFASPQEAEAAGVRT 114

Query: 340 CPEDRKTDGIIAAASVRENIILALQAQR----GWLRPISRKEQQEIAERFIRQLGIRTPS 395
             ++     +    SV ENI    Q +R     W  P  ++  Q    R    L +    
Sbjct: 115 LYQEVN---LCPNLSVAENIFAGRQPRRFGAIDW--PDIKRRAQAALARLDISLDVTRSL 169

Query: 396 TEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLAL 455
              PI       QQ V ++R L    + LILDEPT  +D    A++ +++  L   G+A+
Sbjct: 170 DAYPIAV-----QQMVAIARALSVDARVLILDEPTSSLDDSEVAQLFKILRHLKQSGIAI 224

Query: 456 LVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIM 495
           L ++  +E+    +DR+ +MR+ ++  E     LS   ++
Sbjct: 225 LFVTHFIEQTYAISDRITVMRNGEREGEYLARNLSADQLV 264


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: 682
Number of extensions: 26
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: 539
Length adjustment: 35
Effective length of query: 465
Effective length of database: 504
Effective search space:   234360
Effective search space used:   234360
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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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