GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupC' in Burkholderia phytofirmans PsJN

Align Purine/cytidine ABC transporter permease protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate BPHYT_RS11500 BPHYT_RS11500 ABC transporter permease

Query= TCDB::A2RKA5
         (317 letters)



>FitnessBrowser__BFirm:BPHYT_RS11500
          Length = 309

 Score =  158 bits (400), Expect = 1e-43
 Identities = 91/289 (31%), Positives = 152/289 (52%), Gaps = 12/289 (4%)

Query: 10  IVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMFGSMTPW 69
           + ++ +  + PL+F   G + +E+ G++N+G+EG+M +GA +       T       +PW
Sbjct: 9   LTSSAVTAAIPLMFAGAGELVTEKSGVLNLGVEGMMLMGAVTGYAVTAITG------SPW 62

Query: 70  LSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQININE 129
           L +L     G   S L A  T+ + A+ + +G  L +    L  ++ + +       +  
Sbjct: 63  LGVLAAIGAGLAMSLLFAFLTLTMLANQVATGLSLTIFGIGLSAYVGKPYTSAA---VRA 119

Query: 130 QIGYWNVPLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGENPQA 189
            I  W +P LS IPV+G  FF+ T L     ++ A++ W+ L++TR GL LRSVGE+PQ 
Sbjct: 120 TIDTWTIPGLSKIPVLGPAFFSLTPLDYLAFLMFAVIGWF-LYRTRAGLVLRSVGESPQV 178

Query: 190 ADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIFGKWN 249
           A ++G  V   R+  V   G + G+ G  Y+      +     +G+G+I+LA ++F  W 
Sbjct: 179 AHSVGFPVIGVRYGAVAFGGGMAGLAGGYYSIVNLHLWQEQLTSGRGWIALALVVFATWR 238

Query: 250 PIGAMLSSLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLAL 298
           P   ++ +LLFG  T L     Q  G+  +P+ FL M PYV T++VL L
Sbjct: 239 PGRLLIGALLFGAVTGLQFY-AQAIGV-PVPTQFLAMLPYVATVVVLVL 285


Lambda     K      H
   0.326    0.142    0.419 

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: 271
Number of extensions: 17
Number of successful extensions: 5
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: 317
Length of database: 309
Length adjustment: 27
Effective length of query: 290
Effective length of database: 282
Effective search space:    81780
Effective search space used:    81780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 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