GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfoscipio geothermicus DSM 3669

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_092483295.1 BM299_RS09255 TRAP transporter large permease

Query= SwissProt::O07838
         (440 letters)



>NCBI__GCF_900115975.1:WP_092483295.1
          Length = 429

 Score =  372 bits (955), Expect = e-107
 Identities = 178/435 (40%), Positives = 286/435 (65%), Gaps = 14/435 (3%)

Query: 3   ALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIPFF 62
           ALI+  +L+ L+L G PI+ SL +  +  L +   +P+  V  +LFT  + F ++A+PFF
Sbjct: 4   ALILLLVLLLLLLVGFPIAFSLAMAAVAALLSKGTIPLTVVPQRLFTATDSFILLAVPFF 63

Query: 63  ILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSVI 122
           +LAG  + HGG+++R++NFA+ ++G   GGL L  + + A FAA+SGSS AT  AIG V+
Sbjct: 64  VLAGELMQHGGISRRLVNFASDLLGWISGGLALVSIASAAFFAAISGSSAATTAAIGGVM 123

Query: 123 LPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSASVG 182
            P M  +G+   F A V    G LG++IPPSI +++Y V T               AS+G
Sbjct: 124 YPEMRQRGYKPDFTAVVQAVGGTLGVVIPPSIPLIIYGVITG--------------ASIG 169

Query: 183 ELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQRWTAFREAAWGLMLIVVVIG 242
           +LF+AG++PGL+ A       W  A K GY  ++++SL++ W +FREA+WGL++ V+++G
Sbjct: 170 DLFLAGIIPGLLGAAVYMAVAWKMAGKLGYKTMQRSSLKKTWHSFREASWGLLMPVIILG 229

Query: 243 GIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNAVLF 302
           GIY G+FTPTEAA ++ VYA  +  F+YK+L  ++   +L+ S   SAM++ +I  A LF
Sbjct: 230 GIYGGVFTPTEAAVVAVVYALLVGFFIYKELNWKNFYSMLVKSGLTSAMIMLLIATASLF 289

Query: 303 SFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFPVAV 362
           +++M  E IPQA+   +++   S  +FL++VN++ L AG F++  +I+L++ PI FP+A+
Sbjct: 290 TWIMTIENIPQAITGAILSMTESKLVFLLLVNMVFLIAGMFLDTVAIILLLIPIFFPIAL 349

Query: 363 RLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLAFLV 422
           +LG+DPVHFG++ V N+ VG   PP G+ L+V+SG++ + + +L  AV P+LL     ++
Sbjct: 350 QLGVDPVHFGVIAVFNLAVGQMTPPFGVCLFVSSGVSGVSLEKLFKAVLPYLLAAFILIL 409

Query: 423 LVTYVPAISLALPNL 437
           L+TYVP++SL +  L
Sbjct: 410 LLTYVPSLSLGILEL 424


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: 616
Number of extensions: 36
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: 429
Length adjustment: 32
Effective length of query: 408
Effective length of database: 397
Effective search space:   161976
Effective search space used:   161976
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 Apr 09 2024. 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