GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC' in Dinoroseobacter shibae DFL-12

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 3609462 Dshi_2846 inner-membrane translocator (RefSeq)

Query= TCDB::A2RKA5
         (317 letters)



>lcl|FitnessBrowser__Dino:3609462 Dshi_2846 inner-membrane
           translocator (RefSeq)
          Length = 321

 Score =  219 bits (557), Expect = 9e-62
 Identities = 126/329 (38%), Positives = 191/329 (58%), Gaps = 20/329 (6%)

Query: 1   MNVVNTLQIIVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTA 60
           M+    LQ++ + + + +TPL+   + G+FSER GI ++GLEG M + AF S       A
Sbjct: 1   MDFATLLQVLDSTIRL-ATPLLLACLAGLFSERAGIFDIGLEGKMLVAAFLSAAM----A 55

Query: 61  GMFGSMTPWLSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFY 120
            + GS+  W+ +  G     LFS++H +A++  R + ++SG  LN +A  L V + Q ++
Sbjct: 56  AITGSV--WIGLFAGVFAALLFSAIHGLASITFRGNQLISGVALNFLAAGLTVLIAQSWF 113

Query: 121 QQGQININ-------EQIGYWNVPLLSNIPVIGKIFFTQTSLPGFLAIVVAILA----WY 169
            QG    +       E I       L N+P++G I++   S    L + VA+LA    WY
Sbjct: 114 SQGGRTPSLIGGARFEPITLPFAEALQNVPILGPIYYELISGHTIL-VYVALLAVPATWY 172

Query: 170 VLFKTRFGLRLRSVGENPQAADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSV 229
           +LF+TRFGLRLR+VGENP A DT GI+V   R+A V + G+L G+ GA  A  +S  F  
Sbjct: 173 ILFRTRFGLRLRAVGENPAAVDTAGISVVGLRYAAVAICGLLCGLAGAYLATGLSAGFVK 232

Query: 230 STIAGQGFISLAAMIFGKWNPIGAMLSSLLFGLFTSLAVVGGQIPGIK-EIPSSFLQMAP 288
              AG+G+I+LAA+IF KW P  A+++ LLFG   ++A     I  +   IP   +Q  P
Sbjct: 233 DMTAGRGYIALAALIFAKWRPWYALMACLLFGFLEAIANRFQNIEILSIPIPVQLMQALP 292

Query: 289 YVFTIIVLALFLGKAIAPKADGVNYIKSK 317
           Y+ T+++LA F+GKAI P+A G  Y+K +
Sbjct: 293 YILTVVILAGFVGKAIPPRAGGEPYVKER 321


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: 250
Number of extensions: 12
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: 321
Length adjustment: 28
Effective length of query: 289
Effective length of database: 293
Effective search space:    84677
Effective search space used:    84677
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 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