GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfoscipio geothermicus DSM 3669

Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_092483295.1 BM299_RS09255 TRAP transporter large permease

Query= uniprot:Q88NP0
         (426 letters)



>NCBI__GCF_900115975.1:WP_092483295.1
          Length = 429

 Score =  339 bits (869), Expect = 1e-97
 Identities = 174/418 (41%), Positives = 271/418 (64%), Gaps = 3/418 (0%)

Query: 3   AFILLGSFIVLILIGMPVAYALGLSALIGAWWID-IPLQAMMIQVASGVNKFSLLAIPFF 61
           A ILL   ++L+L+G P+A++L ++A+        IPL  +  ++ +  + F LLA+PFF
Sbjct: 4   ALILLLVLLLLLLVGFPIAFSLAMAAVAALLSKGTIPLTVVPQRLFTATDSFILLAVPFF 63

Query: 62  VLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVL 121
           VLAG +M  GG+SRRLV FA  L+G++ GGL+LV+I ++ FF AISGSS A TA++G V+
Sbjct: 64  VLAGELMQHGGISRRLVNFASDLLGWISGGLALVSIASAAFFAAISGSSAATTAAIGGVM 123

Query: 122 IPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLL 181
            PEM ++GY  +F+  V   G    ++ PPS   ++Y +  G   SI  LF+AGI+PGLL
Sbjct: 124 YPEMRQRGYKPDFTAVVQAVGGTLGVVIPPSIPLIIYGVITGA--SIGDLFLAGIIPGLL 181

Query: 182 LSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATES 241
            +AV M +    A K  Y   +   L++      EA WGL+  VIILGGI  GVFT TE+
Sbjct: 182 GAAVYMAVAWKMAGKLGYKTMQRSSLKKTWHSFREASWGLLMPVIILGGIYGGVFTPTEA 241

Query: 242 AAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSK 301
           A VAVV++  V  FIY++  W++   ++ ++  T +++M+LI  A+ F ++MT+  IP  
Sbjct: 242 AVVAVVYALLVGFFIYKELNWKNFYSMLVKSGLTSAMIMLLIATASLFTWIMTIENIPQA 301

Query: 302 ITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMI 361
           IT A L++++++ V L+ +N + ++ G  +D   +IL+L PI  P+   +GVDPVHFG+I
Sbjct: 302 ITGAILSMTESKLVFLLLVNMVFLIAGMFLDTVAIILLLIPIFFPIALQLGVDPVHFGVI 361

Query: 362 MLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISL 419
            + NL +G +TPP G  LFV S +  VS+E   KA++P+ LA F++++ +TY+P++SL
Sbjct: 362 AVFNLAVGQMTPPFGVCLFVSSGVSGVSLEKLFKAVLPYLLAAFILILLLTYVPSLSL 419


Lambda     K      H
   0.329    0.142    0.418 

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: 561
Number of extensions: 30
Number of successful extensions: 3
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: 429
Length adjustment: 32
Effective length of query: 394
Effective length of database: 397
Effective search space:   156418
Effective search space used:   156418
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