GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Escherichia coli BW25113

Align Purine/cytidine ABC transporter ATP-binding 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 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Keio:18115
          Length = 510

 Score =  310 bits (793), Expect = 1e-88
 Identities = 183/501 (36%), Positives = 292/501 (58%), Gaps = 19/501 (3%)

Query: 7   IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66
           I M  + K FG   A   VNL +  GEIHALLGENGAGKSTLM +LSG+ EP++G + + 
Sbjct: 6   ISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTITIN 65

Query: 67  GKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTK---GINL-DLKTAKKK 122
               N      AA LGIG+++Q   ++D  TV EN+ +G  +TK   G+N+ D +  + +
Sbjct: 66  NISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWREMRVR 125

Query: 123 ILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELM 182
              +  R GL V+ D  + ++S+  +Q +EI KTL   A ++I DEPT+ LT  E+  L 
Sbjct: 126 AAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDYLF 185

Query: 183 QIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRS 242
            IM  L KEG +I+ I+HKL EIR + DR TV++ G S+ +  + D +N ++  LMVGR 
Sbjct: 186 LIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMVGRE 245

Query: 243 V----SFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQ 298
           +    + + E  +    + V E++++    SR   KV+ +S  V  GEI+G AG+ G+G+
Sbjct: 246 LQNRFNAMKENVSNLAHETVFEVRNVT---SRDRKKVRDISFSVCRGEILGFAGLVGSGR 302

Query: 299 TELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENI 358
           TEL+  + G+ K   G I+L+ KDI+ + P    ++ + ++ E R  +G     ++A+N+
Sbjct: 303 TELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIAQNM 362

Query: 359 ALQTY-----YKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAI 413
           A+        YK  M  +  +D  +   + REL+    ++      + + LSGGNQQK +
Sbjct: 363 AISRSLKDGGYKGAMGLFHEVDEQRTAENQRELLA---LKCHSVNQNITELSGGNQQKVL 419

Query: 414 IAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRI 473
           I++ +   P+++I  +PTRG+DVGA   I+K + Q  D+GK +L++S EL EI+ V DRI
Sbjct: 420 ISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITVCDRI 479

Query: 474 AVIHDGQIQGIVSPETTTKQE 494
           AV  +G++  I++      +E
Sbjct: 480 AVFCEGRLTQILTNRDDMSEE 500


Lambda     K      H
   0.315    0.135    0.365 

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: 642
Number of extensions: 30
Number of successful extensions: 8
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: 506
Length of database: 510
Length adjustment: 34
Effective length of query: 472
Effective length of database: 476
Effective search space:   224672
Effective search space used:   224672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 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