GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupB in Burkholderia phytofirmans PsJN

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 BPHYT_RS26075 BPHYT_RS26075 ABC transporter permease

Query= TCDB::A2RKA6
         (364 letters)



>FitnessBrowser__BFirm:BPHYT_RS26075
          Length = 363

 Score =  122 bits (305), Expect = 2e-32
 Identities = 101/328 (30%), Positives = 163/328 (49%), Gaps = 9/328 (2%)

Query: 12  LIAIVFGFLLGAIIMLAFGYNPIWGYEDLFISALGSARSIGETLQTMGPLILTALSFAVA 71
           L+AIV    L AI+ +  G + +  + D    A GS  +IG ++       L    F +A
Sbjct: 30  LVAIVAAMALIAIVHVPLG-DAMAAFAD---GAWGSPYAIGASINRSLVFALVGSGFVLA 85

Query: 72  MKVGLFNIGMSGQALAGWISSMWFALSFPDIPRLLMIPLVV-IIGMVF-GAFMGFIPGIL 129
            +  L N+G  GQ   G I++   +L        L +P VV ++G    GA  G IPG L
Sbjct: 86  NRAQLTNVGGEGQIAMGGIAATAVSLYGHVAHLPLGLPFVVPMLGAALAGAAWGAIPGWL 145

Query: 130 RALLGTSEVITTIMLNYIMLFFSTFMIHSMFQKNILMDNTTDQTKLISANASFRTNWMSS 189
           +A  GT+EVI+T++L +I ++F  + + S       M N     + +    S R   ++S
Sbjct: 146 KARAGTNEVISTLLLTFIAVWFLYWCVQSEALLRQPMSNAATLPESLDIPDSTRLPLLAS 205

Query: 190 LTDNSTLNIGLIIAIIALVIMAIIFTKTTLGFEIKAVGLNPDASEYAGISAKRTLILSMV 249
            + ++ L+IGL I ++  + +A++   +  G  ++AVGLN  A+  AG+    T++ ++ 
Sbjct: 206 -SSSTGLHIGLPITVVLCIAVALVLVYSRFGMHLRAVGLNALAARRAGMPITSTIVGALA 264

Query: 250 VAGALAGLGGVVYGFGYMQNFVSQSASLDIGFYGMAVALLGGNSPIGILFAALLFSVLQT 309
           +AGAL GL G +   G  Q  +    S   GF G+ V LL   S  G+  AALLF  L++
Sbjct: 265 LAGALGGLAGALMLQG-DQYSLKAGFSSGYGFDGLVVGLLARGSITGVCAAALLFGFLRS 323

Query: 310 GAPGMTN-DGIPPEIVKVVTAAIIFFIA 336
           G   M     +P  +V VV   +I  +A
Sbjct: 324 GGINMEMVASVPSALVLVVQGIVIVALA 351


Lambda     K      H
   0.327    0.141    0.404 

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: 316
Number of extensions: 21
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: 364
Length of database: 363
Length adjustment: 29
Effective length of query: 335
Effective length of database: 334
Effective search space:   111890
Effective search space used:   111890
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 (21.7 bits)
S2: 49 (23.5 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