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

GapMind for catabolism of small carbon sources

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

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate H281DRAFT_03380 H281DRAFT_03380 monosaccharide ABC transporter ATP-binding protein, CUT2 family

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__Burk376:H281DRAFT_03380
          Length = 515

 Score =  438 bits (1126), Expect = e-127
 Identities = 232/493 (47%), Positives = 331/493 (67%), Gaps = 4/493 (0%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           +LQLKG+ K FPGV AL G  L++  G V A+ GENGAGKST+MK+++G Y  D G + +
Sbjct: 22  ILQLKGVSKRFPGVVALDGIDLDLRSGEVHAVCGENGAGKSTLMKIISGQYHADDGVICY 81

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
            GK   F     +Q AGI IIHQELNL+P L++AENI+L RE   R   +D++T+ A A 
Sbjct: 82  EGKPVQFASTSDAQAAGIAIIHQELNLVPHLSVAENIYLARE-PKRGPFVDYRTLNANAQ 140

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
           + L ++ L      LVG LSI  QQMVEIAK LS +++V+IMDEPT +LT++ET  LFR+
Sbjct: 141 RCLQRIGLNVSPTTLVGALSIAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRI 200

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243
           IREL++ G  I+YISHR+ E+ EI D VTV RDG+ IA  + AS T + ++  MVGR L+
Sbjct: 201 IRELRADGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTINEIVARMVGRALD 260

Query: 244 DQYPHLDKAPGD-IRLKVDNLCGPGV-NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGA 301
           D YP  +  P + + ++V +L        +SF LRKGEILG +GLMGAGRTE+ + ++GA
Sbjct: 261 DAYPPRESVPTEQVLMRVRDLQRTDTFGPLSFDLRKGEILGFAGLMGAGRTEVARAIFGA 320

Query: 302 LPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSR 361
               SG + L    V  RSP++ + +GI Y+SEDRK+DGL L M V  N++L+ +R  S 
Sbjct: 321 ERLDSGSIQLGDTPVTIRSPREAIRHGIAYLSEDRKKDGLALSMPVAANITLSNVRAIS- 379

Query: 362 AGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDE 421
           + G L+ ++E      ++R   ++TP+++Q    LSGGNQQK+ I++ L    ++L  DE
Sbjct: 380 SRGFLRFSEETAIAERYVRELAIRTPTVKQIARNLSGGNQQKIVISKWLYRGSRILFFDE 439

Query: 422 PTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQ 481
           PTRG+DVGAK  IY+L+++  ADG+ ++L+SSE+PE+LGM+DRI V HEG ++      Q
Sbjct: 440 PTRGIDVGAKYAIYKLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGLITAVLETRQ 499

Query: 482 ATQEVLMAAAVGK 494
            +QE ++  A G+
Sbjct: 500 TSQEEILHYASGR 512


Lambda     K      H
   0.318    0.137    0.380 

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: 637
Number of extensions: 24
Number of successful extensions: 8
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: 501
Length of database: 515
Length adjustment: 34
Effective length of query: 467
Effective length of database: 481
Effective search space:   224627
Effective search space used:   224627
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 (21.7 bits)
S2: 52 (24.6 bits)

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

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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, 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