GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC' in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_9 Nucleoside ABC transporter, permease protein 2

Query= TCDB::A2RKA5
         (317 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_9 Nucleoside ABC
           transporter, permease protein 2
          Length = 308

 Score =  154 bits (390), Expect = 2e-42
 Identities = 101/304 (33%), Positives = 159/304 (52%), Gaps = 19/304 (6%)

Query: 4   VNTLQIIVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMF 63
           ++ L  I   M+   TPL+  ++G +  E+ G++N+G EG+M  GA    +    T  + 
Sbjct: 3   IDLLSNIFYAMVRCGTPLLLVALGELICEKSGVLNLGQEGMMLFGAVIGFIVAFNTGHL- 61

Query: 64  GSMTPWLSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQG 123
                WL +L   L G L SSL A+  +   A+ + +G  L +    L  F+       G
Sbjct: 62  -----WLGVLLAMLAGMLLSSLFALVALVFNANQVATGLALTIFGVGLSTFV-------G 109

Query: 124 QININEQIGYWN---VPLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRL 180
              + + +  +    +P LS IP+IG++ F Q  L      + A++AW +L K+R GL +
Sbjct: 110 AAWVGKPLAGFEPVAIPYLSEIPLIGRMLFAQDLLVYLSFALFALVAWVIL-KSRVGLII 168

Query: 181 RSVGENPQAADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISL 240
           ++VGENP AA  +G+ V A R   VL  G + G+ GA  + A +  ++ +  AG+G+I+L
Sbjct: 169 QAVGENPDAASAMGLPVLAVRTLAVLFGGAMAGLAGAYLSLAYTPMWAENMSAGRGWIAL 228

Query: 241 AAMIFGKWNPIGAMLSSLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLALFL 300
           A ++F  W     +L + LFGL + L +V  Q  G+  IPSS L M PYV TI VL L  
Sbjct: 229 ALVVFASWRVWRLLLGAYLFGLASILHLV-AQGLGL-AIPSSLLAMLPYVATIGVLVLLS 286

Query: 301 GKAI 304
             A+
Sbjct: 287 RDAV 290


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: 262
Number of extensions: 18
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: 308
Length adjustment: 27
Effective length of query: 290
Effective length of database: 281
Effective search space:    81490
Effective search space used:    81490
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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