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_097028703.1 CRO07_RS00315 ABC transporter permease

Query= TCDB::A2RKA5
         (317 letters)



>NCBI__GCF_900207575.1:WP_097028703.1
          Length = 322

 Score =  207 bits (526), Expect = 4e-58
 Identities = 120/330 (36%), Positives = 190/330 (57%), Gaps = 22/330 (6%)

Query: 1   MNVVNTLQIIVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTA 60
           M++   LQI+  +M+   TPL+   + G+FSER GI ++GLEG M   AF S      T 
Sbjct: 2   MDLPTALQIL-DSMIRLGTPLLLACLAGLFSERAGIFDIGLEGKMLSAAFLSAAVAFVTG 60

Query: 61  GMFGSMTPWLSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFY 120
            +      WL +L G +   + S++H +A++  R + ++SG  +N +A  L V L Q ++
Sbjct: 61  SV------WLGVLAGLVAALMMSAIHGLASITFRGNQLISGVAINFLASGLTVLLGQYWF 114

Query: 121 QQGQININEQIGYWNVPL-------LSNIPVIGKIFFT----QTSLPGFLAIVVAILAWY 169
             G    + +      P+       L  +PV+G I+       T+L  +LA  +  L+W+
Sbjct: 115 ALGGRTPSLEGAARFQPITLPFAQELREVPVLGLIYAELISGHTALV-YLAFALVPLSWW 173

Query: 170 VLFKTRFGLRLRSVGENPQAADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSV 229
           +L++TRFGLRLR+VGENP A DT G++V   R+A V + G+L G+ GA  A  +S  F  
Sbjct: 174 LLYRTRFGLRLRAVGENPAAVDTAGVSVVGIRYAAVAICGLLTGLAGAYLACGLSAGFVK 233

Query: 230 STIAGQGFISLAAMIFGKWNPIGAMLSSLLFGLFTSLA--VVGGQIPGIKEIPSSFLQMA 287
              AG+G+I+LAA+IF KW P  A+ +++LFGL  ++A       + G+  +P  F+Q  
Sbjct: 234 EMTAGRGYIALAALIFAKWRPWQALAATMLFGLLEAVANRYQSLDLWGV-PLPVQFMQAL 292

Query: 288 PYVFTIIVLALFLGKAIAPKADGVNYIKSK 317
           PY+ T+++LA F+GKAI P+A G  Y+K +
Sbjct: 293 PYILTVVILAGFVGKAIPPRAGGQPYVKER 322


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: 246
Number of extensions: 12
Number of successful extensions: 4
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: 322
Length adjustment: 28
Effective length of query: 289
Effective length of database: 294
Effective search space:    84966
Effective search space used:    84966
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