GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Dechlorosoma suillum PS

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate Dsui_3153 Dsui_3153 TRAP transporter, DctM subunit

Query= SwissProt::O07838
         (440 letters)



>FitnessBrowser__PS:Dsui_3153
          Length = 427

 Score =  677 bits (1746), Expect = 0.0
 Identities = 344/440 (78%), Positives = 385/440 (87%), Gaps = 14/440 (3%)

Query: 1   MSALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIP 60
           M+A IIFGLL+ALMLTGMPISISLGLTVLTFLFTMTQVPI++VALKLFTGIEKFEIMAIP
Sbjct: 1   MNAAIIFGLLLALMLTGMPISISLGLTVLTFLFTMTQVPIESVALKLFTGIEKFEIMAIP 60

Query: 61  FFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGS 120
           FFILAGNFLTHGGVA+RMINFA+AMVGH++GGLGLAGV+ACALFAAVSGSSPATVVAIGS
Sbjct: 61  FFILAGNFLTHGGVARRMINFASAMVGHFYGGLGLAGVLACALFAAVSGSSPATVVAIGS 120

Query: 121 VILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSAS 180
           ++LPAMV  GFP +FGAGVITTSGALGILIPPSIVMVMY+VAT+               S
Sbjct: 121 ILLPAMVRAGFPNRFGAGVITTSGALGILIPPSIVMVMYSVATN--------------TS 166

Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVV 240
           VG LFMAGV+PGL+LA  L   TW RA+KF YPR+ KAS  +RW AFR++ WGLMLIV+V
Sbjct: 167 VGALFMAGVIPGLLLAFTLGMVTWYRAKKFDYPRMPKASWGERWVAFRKSVWGLMLIVIV 226

Query: 241 IGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAV 300
           +GGIY G+FTPTEAAAMSAVYAF ++VFVYKD+ L+ +P+VLL SANMSAMLLYIITNAV
Sbjct: 227 MGGIYTGMFTPTEAAAMSAVYAFIVAVFVYKDMGLKQIPKVLLDSANMSAMLLYIITNAV 286

Query: 301 LFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPV 360
           LFSFLM +E IPQ L EW+++ GL    FL+ VN+LLL AGNFMEPSSIVLIMAPILFPV
Sbjct: 287 LFSFLMTNENIPQLLAEWLLDKGLGPIAFLLAVNVLLLVAGNFMEPSSIVLIMAPILFPV 346

Query: 361 AVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAF 420
           AV+LGIDPVHFGI+IVVNMEVGMCHPPVGLNLYVASGITKMGITELT+AVWPWLL+ML F
Sbjct: 347 AVKLGIDPVHFGILIVVNMEVGMCHPPVGLNLYVASGITKMGITELTIAVWPWLLSMLCF 406

Query: 421 LVLVTYVPAISLALPNLLGM 440
           L LVTY P +SL LP  LGM
Sbjct: 407 LGLVTYWPTLSLWLPRTLGM 426


Lambda     K      H
   0.329    0.142    0.431 

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: 774
Number of extensions: 33
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: 440
Length of database: 427
Length adjustment: 32
Effective length of query: 408
Effective length of database: 395
Effective search space:   161160
Effective search space used:   161160
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