GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Burkholderia phytofirmans PsJN

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BPHYT_RS27185 BPHYT_RS27185 D-ribose transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>FitnessBrowser__BFirm:BPHYT_RS27185
          Length = 516

 Score =  401 bits (1030), Expect = e-116
 Identities = 217/494 (43%), Positives = 319/494 (64%), Gaps = 4/494 (0%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L+   + K FPGV ALDG+  D+  G+VH + GENGAGKSTL+KI+ G+Y+ D G V   
Sbjct: 24  LQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGVVRYR 83

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G  V+F+S + + AAGIA+IHQEL  VP L+VAEN+ L + P    +V+ R      +  
Sbjct: 84  GAPVQFSSTSDAQAAGIAIIHQELNLVPHLSVAENIYLAREPKRGPFVDYRTLNSNAQRC 143

Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184
           L+ +G+ + P+  +  LS+AQ+QMVEI KAL  +ARV+ +DEPTSSL+  ET  LF+++R
Sbjct: 144 LQRIGLNVSPSTLVGALSLAQQQMVEIAKALSLDARVLIMDEPTSSLTESETVQLFRIIR 203

Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244
           +LRA   A++YISHR+DE+ E+ D  T+ RDGR IA+       T + IV+ MVGR + D
Sbjct: 204 ELRAGGVAILYISHRLDEMAEIVDRVTVLRDGRHIAT-SDFASTTVNEIVARMVGRPLDD 262

Query: 245 IY-NYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGAD 303
            Y    + P  ++    + ++   +  P SFE+R+GEI+GF GL+GAGR+E    ++GA+
Sbjct: 263 AYPPRQSTPSNQILLRVRDLQRTGVFGPLSFELRKGEILGFAGLMGAGRTETARAIFGAE 322

Query: 304 HKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRV 363
               G + L  +P+ + S  EAIRHGI    EDRK++G+     VS NI ++  R     
Sbjct: 323 RPDSGSITLGDEPVTIGSPREAIRHGIAYLSEDRKKDGLALSMPVSANITLANVRAISSR 382

Query: 364 GMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDE 423
           G FL   +E   A+R+++ L I+TP+ +Q  R LSGGNQQK ++S+WL     +++  DE
Sbjct: 383 G-FLRFSEETAIAERYVRELGIRTPTVKQIARNLSGGNQQKIVISKWLYRGS-RILFFDE 440

Query: 424 PTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKD 483
           PTRGIDVGAK+ IY ++ +LA  G  +V+ISSELPE+LG++DRI V  +GRI+  L  + 
Sbjct: 441 PTRGIDVGAKYAIYGLMDRLAADGVGVVLISSELPELLGMTDRIAVFHEGRITAVLETRQ 500

Query: 484 ATEQSVLSLALPQS 497
            +++ +L  A  +S
Sbjct: 501 TSQEEILHHASGRS 514



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 59/225 (26%), Positives = 108/225 (48%), Gaps = 8/225 (3%)

Query: 250 ARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGE 309
           +R + +++  +K   G         ++  GE+    G  GAG+S LM ++ G      G 
Sbjct: 20  SREILQLKGVSKRFPGVVALDGIDLDLCAGEVHAVCGENGAGKSTLMKIISGQYRADEGV 79

Query: 310 LLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDR 369
           +   G P++  S  +A   GI +     +E  +V   +V+ENI ++      + G F+D 
Sbjct: 80  VRYRGAPVQFSSTSDAQAAGIAII---HQELNLVPHLSVAENIYLA---REPKRGPFVDY 133

Query: 370 KKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGID 429
           +     A R ++ + +   S    +  LS   QQ   +++ L+  D +V+I+DEPT  + 
Sbjct: 134 RTLNSNAQRCLQRIGLNV-SPSTLVGALSLAQQQMVEIAKALS-LDARVLIMDEPTSSLT 191

Query: 430 VGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGR 474
                +++ +I +L   G AI+ IS  L E+  + DR+ V+R GR
Sbjct: 192 ESETVQLFRIIRELRAGGVAILYISHRLDEMAEIVDRVTVLRDGR 236


Lambda     K      H
   0.320    0.136    0.385 

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: 641
Number of extensions: 26
Number of successful extensions: 9
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: 512
Length of database: 516
Length adjustment: 35
Effective length of query: 477
Effective length of database: 481
Effective search space:   229437
Effective search space used:   229437
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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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:

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:

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:

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:

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