GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Burkholderia phytofirmans PsJN

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate BPHYT_RS26080 BPHYT_RS26080 ABC transporter ATPase

Query= TCDB::Q8DU37
         (510 letters)



>FitnessBrowser__BFirm:BPHYT_RS26080
          Length = 527

 Score =  361 bits (927), Expect = e-104
 Identities = 204/520 (39%), Positives = 308/520 (59%), Gaps = 29/520 (5%)

Query: 5   VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64
           V+ M  I K+F  F A   ++L+L  GE+H LLGENGAGKSTL N++ G+ +P +G++ +
Sbjct: 10  VLRMDGIVKRFGAFQALTDVSLELFAGEVHCLLGENGAGKSTLCNVMFGVHQPDAGAMWL 69

Query: 65  NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124
           +G+     SP  +   GI MVHQHF LVE  +V +N++LG      G LD K+  Q ++A
Sbjct: 70  DGAPYQPHSPRDALTHGIAMVHQHFSLVEDVSVLDNLLLGQV---RGWLDRKREAQRVRA 126

Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184
           L  + GLA+DP+ ++AD+SVG +QRVEI+K L R   +L+ DEPTAVL P+EI  L+   
Sbjct: 127 LVAELGLALDPDTRVADLSVGEKQRVEIVKCLIREPRLLVLDEPTAVLLPAEIDALLDTC 186

Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMV------ 238
             +V  G +++L+THKL EIR +A R TV++ G+ +            L   M+      
Sbjct: 187 ARVVARGCAVVLVTHKLAEIRRIASRATVLQSGRVVARSSKPSADVDALVRAMIQRPDST 246

Query: 239 --GRSVSFTIEKTP----------TKP-KETILSIKDLVVNENRGIPAIKGLSLEVKAGE 285
             G + +     TP          T+P  +  L I  L V +  G+  ++  +L V  GE
Sbjct: 247 DQGAAANSNASATPRSATRSTSPYTRPLADEALQIDGLTVRDADGVTRLEDCTLVVNRGE 306

Query: 286 IIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRD 345
           I+GIAG++GNGQSEL   + G++K  +G   ++G+D T+ + + +T   VG VPEDRH  
Sbjct: 307 IVGIAGVEGNGQSELGAVLAGMQKASAGRFFVQGKDCTQAAPQTLTRAGVGVVPEDRHAV 366

Query: 346 GLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSG 405
           G + ++++ ENL L        +  G +    +    R LMQ FDVR A+  +  +G SG
Sbjct: 367 GCVPDMSLTENLFLNRL--DDYARGGFMRRRAMRRDARALMQRFDVRAASPDVAFRGLSG 424

Query: 406 GNQQKAIIAREVDRDP-DLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDE 464
           GNQQKA++ARE+  D   +L+ +QPTRGLDVGA+  ++  + A RD G  VLL+S ELDE
Sbjct: 425 GNQQKAVLARELTLDGLAVLVAAQPTRGLDVGAVAAVYDHIRAARDAGVGVLLISSELDE 484

Query: 465 ILNLSDRIAVIHDGQIQGIVTPETT----NKQELGILMAG 500
           ++ ++DR+ V++ G+I G   PE +     ++ +G  MAG
Sbjct: 485 LMAVADRVLVMYRGRIMGTCVPEASQFNLQRERIGAWMAG 524


Lambda     K      H
   0.315    0.135    0.363 

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: 536
Number of extensions: 22
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: 510
Length of database: 527
Length adjustment: 35
Effective length of query: 475
Effective length of database: 492
Effective search space:   233700
Effective search space used:   233700
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: 42 (22.0 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