GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntB in Dechlorosoma suillum PS

Align Large component of TRAP-type D-gluconate transporter (characterized)
to candidate Dsui_3153 Dsui_3153 TRAP transporter, DctM subunit

Query= reanno::azobra:AZOBR_RS15920
         (426 letters)



>FitnessBrowser__PS:Dsui_3153
          Length = 427

 Score =  308 bits (788), Expect = 3e-88
 Identities = 155/417 (37%), Positives = 257/417 (61%), Gaps = 2/417 (0%)

Query: 1   MALAVFLSSLFGLMLLGMPIAFALMLTGVALMVHLDFFDAQLVAQNMLSGADNYPLMAVP 60
           M  A+    L  LML GMPI+ +L LT +  +  +     + VA  + +G + + +MA+P
Sbjct: 1   MNAAIIFGLLLALMLTGMPISISLGLTVLTFLFTMTQVPIESVALKLFTGIEKFEIMAIP 60

Query: 61  FFILAGELMNAGGISQRIINLAVSLVGHIRGGLGYVTIGASVMLASLSGSAIADTAALAT 120
           FFILAG  +  GG+++R+IN A ++VGH  GGLG   + A  + A++SGS+ A   A+ +
Sbjct: 61  FFILAGNFLTHGGVARRMINFASAMVGHFYGGLGLAGVLACALFAAVSGSSPATVVAIGS 120

Query: 121 LLIPMMRDNGYPVPRSAGLIASGGIIAPIIPPSMPFIIFGVTTNTSISGLFMAGIVPGLL 180
           +L+P M   G+P    AG+I + G +  +IPPS+  +++ V TNTS+  LFMAG++PGLL
Sbjct: 121 ILLPAMVRAGFPNRFGAGVITTSGALGILIPPSIVMVMYSVATNTSVGALFMAGVIPGLL 180

Query: 181 MGAGL-VITWMFVVRGMTVKLQPKASWGERRTALVEGVWALALPVIIIGGLRGGIFTPTE 239
           +   L ++TW +  +       PKASWGER  A  + VW L L VI++GG+  G+FTPTE
Sbjct: 181 LAFTLGMVTW-YRAKKFDYPRMPKASWGERWVAFRKSVWGLMLIVIVMGGIYTGMFTPTE 239

Query: 240 AAVVAAVYSLVVALFVYRQVTLKDLVPLLVQAARTTSTVMFLCAAALVSSYMVTLADLPQ 299
           AA ++AVY+ +VA+FVY+ + LK +  +L+ +A  ++ ++++   A++ S+++T  ++PQ
Sbjct: 240 AAAMSAVYAFIVAVFVYKDMGLKQIPKVLLDSANMSAMLLYIITNAVLFSFLMTNENIPQ 299

Query: 300 QMNEMLAPLLHEPKLLMVAITLLLLAVGTVMDLTPTILVLGPVLTPLAAAAGIDPTYFGV 359
            + E L      P   ++A+ +LLL  G  M+ +  +L++ P+L P+A   GIDP +FG+
Sbjct: 300 LLAEWLLDKGLGPIAFLLAVNVLLLVAGNFMEPSSIVLIMAPILFPVAVKLGIDPVHFGI 359

Query: 360 MFVLTGTLGLIHPPVCTVLNVVCGVARISLESATRGIWPFLLTYLLLLCLLIAVPEI 416
           + V+   +G+ HPPV   L V  G+ ++ +   T  +WP+LL+ L  L L+   P +
Sbjct: 360 LIVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVWPWLLSMLCFLGLVTYWPTL 416


Lambda     K      H
   0.328    0.142    0.420 

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: 399
Number of extensions: 19
Number of successful extensions: 2
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: 426
Length of database: 427
Length adjustment: 32
Effective length of query: 394
Effective length of database: 395
Effective search space:   155630
Effective search space used:   155630
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 (21.8 bits)
S2: 51 (24.3 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