GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS26080 BPHYT_RS26080 ABC
           transporter ATPase
          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 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