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

GapMind for catabolism of small carbon sources

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

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Burk376:H281DRAFT_03380
          Length = 515

 Score =  435 bits (1119), Expect = e-126
 Identities = 240/501 (47%), Positives = 334/501 (66%), Gaps = 10/501 (1%)

Query: 13  EILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEIL 72
           EIL+ KG+ KRFPGVVA+D +D ++   E+ ++ GENGAGKSTL+KI++G    D G I 
Sbjct: 21  EILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVIC 80

Query: 73  VNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENY 132
             G+ V+F S  DA   GI++IHQELNL  +++VAENI+LA E  RG        VD   
Sbjct: 81  YEGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPF------VDYRT 134

Query: 133 MYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192
           +   ++  L  IG   SP  LV  L+ AQ+QMVEI KAL  + R++ MDEPTSSLT  ET
Sbjct: 135 LNANAQRCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESET 194

Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252
            +LF II  L++ G++++++SHRLDE+  I DR+ V+RDG+ I         ++ I+  M
Sbjct: 195 VQLFRIIRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARM 254

Query: 253 VGREVEFFPHGIETRPGE-IALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETM 311
           VGR ++      E+ P E + + VR+L+  D    +SF++RKGE+LGFAGL+GAGRTE  
Sbjct: 255 VGRALDDAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVA 314

Query: 312 LLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371
             +FG  + +SG I +    V I++P +AI+ GI  + EDRK  GL L M V  NI L +
Sbjct: 315 RAIFGAERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSN 374

Query: 372 LKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNAD 431
           ++ IS  G  L   +E  I+E YV+ L+I+TP++ QI  NLSGGNQQK+V++KWL   + 
Sbjct: 375 VRAISSRGF-LRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSR 433

Query: 432 ILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITA 491
           IL FDEPTRGIDVGAK  I++++  LAA G  V++ISSELPE+L ++DRI V  EG ITA
Sbjct: 434 ILFFDEPTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITA 493

Query: 492 VLDNREKRVTQEEIMYYASGQ 512
           VL+ R+   +QEEI++YASG+
Sbjct: 494 VLETRQ--TSQEEILHYASGR 512


Lambda     K      H
   0.319    0.138    0.381 

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: 645
Number of extensions: 29
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 520
Length of database: 515
Length adjustment: 35
Effective length of query: 485
Effective length of database: 480
Effective search space:   232800
Effective search space used:   232800
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 (21.7 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