GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupC' in Rhodobacter ovatus JA234

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 WP_097031108.1 CRO07_RS12920 ABC transporter permease

Query= TCDB::A2RKA5
         (317 letters)



>NCBI__GCF_900207575.1:WP_097031108.1
          Length = 315

 Score =  172 bits (437), Expect = 7e-48
 Identities = 107/292 (36%), Positives = 151/292 (51%), Gaps = 8/292 (2%)

Query: 18  STPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMFGSMTPWLSILFGAL 77
           ++PLIF ++G +  ER G++N+G+EGIM IGAFS  +     AG+      W  +    L
Sbjct: 21  ASPLIFATMGELICERAGVLNLGIEGIMVIGAFSGWITVWAGAGL------WEGVAVAML 74

Query: 78  IGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQININ-EQIGYWNV 136
            G LF  LHAV  V       V G  + L+A +   F  ++   Q       E    W V
Sbjct: 75  AGMLFGLLHAVLVVPFGLSQHVVGLGVTLLATSTSYFAYRLMLPQVTSPPKIEPFAVWEV 134

Query: 137 PLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGENPQAADTLGIN 196
           P+LS+IP+IG   F QT L  + A  VA L   VL++T  GL +R+ GENP A D  G++
Sbjct: 135 PVLSDIPLIGPALFAQTPLT-YAAFAVAALVALVLWRTPLGLAIRAAGENPSAVDAQGLS 193

Query: 197 VYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIFGKWNPIGAMLS 256
           V   R   V++   L  VGGA    +   +F    + G+G+I +A ++FG W P  A+L 
Sbjct: 194 VTGLRIGAVVVGSGLMAVGGAFLTLSAFSSFFFEMVNGRGWICIALVVFGAWRPGKAVLG 253

Query: 257 SLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLALFLGKAIAPKA 308
           +LLF  F +L V   Q P  + +P     MAPYV +I  L L   +A  P A
Sbjct: 254 ALLFAAFDALQVRLQQTPLGQVVPYQLFLMAPYVLSIAALVLMSRRASVPAA 305


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: 277
Number of extensions: 21
Number of successful extensions: 3
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: 315
Length adjustment: 27
Effective length of query: 290
Effective length of database: 288
Effective search space:    83520
Effective search space used:    83520
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 24 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