Alignments for a candidate for H281DRAFT_01113 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for H281DRAFT_01113 in Burkholderia phytofirmans PsJN

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>FitnessBrowser__BFirm:BPHYT_RS27185
          Length = 516

 Score =  358 bits (919), Expect = e-103
 Identities = 206/501 (41%), Positives = 303/501 (60%), Gaps = 12/501 (2%)

Query: 10  PLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDE 69
           P+S+  L++ GV KRF GV AL G+ L    G+++ + GENG GKSTL+KIISG    DE
Sbjct: 18  PVSREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADE 77

Query: 70  GQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFD 129
           G +   G P    S  +A AAGI  ++Q+L+L+P++SVAEN+ L       E +     D
Sbjct: 78  GVVRYRGAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLA-----REPKRGPFVD 132

Query: 130 RRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTS 189
            R L + A R L+ +GL   +   STL+  L LA +Q+V IA+A++ +A+ +IMDEPT+S
Sbjct: 133 YRTLNSNAQRCLQRIGL---NVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSS 189

Query: 190 LTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKA 249
           LT+ E   L  ++  LRA GV +L++SH+LDE   I   V VLRDG+ +A    A  T  
Sbjct: 190 LTESETVQLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIATSDFASTTVN 249

Query: 250 QISELMTGRHLSNERY--RESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLD 307
           +I   M GR L ++ Y  R+S  +  I+L VR   R G F  +SF+L  GEILG  GL+ 
Sbjct: 250 EIVARMVGRPL-DDAYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMG 308

Query: 308 SGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIR 367
           +GR E ARA+ G     SG + L  + + + +P +A RH I Y+ EDR  +GL L  P+ 
Sbjct: 309 AGRTETARAIFGAERPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVS 368

Query: 368 DNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGR 427
            N+  A + ++  R G +  +   A+AE+ V+EL I TP V +  ++LSGGNQQ+++I +
Sbjct: 369 ANITLANVRAISSR-GFLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISK 427

Query: 428 WLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMM 487
           WL    R+L    PT G+DVG+K  IY +M RL+  G+G++LIS +LPELL   DRI + 
Sbjct: 428 WLYRGSRILFFDEPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVF 487

Query: 488 KKGHVSAEYRADELSEADLYH 508
            +G ++A     + S+ ++ H
Sbjct: 488 HEGRITAVLETRQTSQEEILH 508



 Score = 62.0 bits (149), Expect = 5e-14
 Identities = 59/254 (23%), Positives = 108/254 (42%), Gaps = 12/254 (4%)

Query: 8   SAPLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPP 67
           S P +Q  L V  + +  TGV     +S   ++G+I    G  G G++   + I GA+ P
Sbjct: 269 STPSNQILLRVRDLQR--TGVFG--PLSFELRKGEILGFAGLMGAGRTETARAIFGAERP 324

Query: 68  DEGQLVIEGVPHARLSALEALAAGIETVYQDLS---LLPNMSVAENVALTSELATHEGRL 124
           D G + +   P    S  EA+  GI  + +D     L  +M V+ N+ L +  A      
Sbjct: 325 DSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAISSRGF 384

Query: 125 ARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMD 184
            R  +   +A    R L  +  P   +    +   L    +Q + I++ +   ++ +  D
Sbjct: 385 LRFSEETAIAERYVREL-GIRTPTVKQ----IARNLSGGNQQKIVISKWLYRGSRILFFD 439

Query: 185 EPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIA 244
           EPT  +       +  ++  L A GV V+ +S +L E   +   + V  +G+  A     
Sbjct: 440 EPTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETR 499

Query: 245 EFTKAQISELMTGR 258
           + ++ +I    +GR
Sbjct: 500 QTSQEEILHHASGR 513


Lambda     K      H
   0.319    0.135    0.376 

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: 635
Number of extensions: 24
Number of successful extensions: 7
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: 515
Length of database: 516
Length adjustment: 35
Effective length of query: 480
Effective length of database: 481
Effective search space:   230880
Effective search space used:   230880
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.

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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