GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfoscipio geothermicus DSM 3669

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_092484450.1 BM299_RS11930 TRAP transporter large permease

Query= uniprot:I7DRS6
         (467 letters)



>NCBI__GCF_900115975.1:WP_092484450.1
          Length = 425

 Score =  301 bits (772), Expect = 2e-86
 Identities = 169/453 (37%), Positives = 259/453 (57%), Gaps = 35/453 (7%)

Query: 4   VLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFF 63
           ++LF+    L+LIGVP+A +LGLSS   LL      L      LF   +  F L+AIPFF
Sbjct: 3   LILFASFFVLVLIGVPVAFSLGLSSIAALLYQGQIPLIVSVQRLFTGTDS-FPLMAIPFF 61

Query: 64  ILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIV 123
           ++A + M TGG++RR++ F+ A VGH  GGLA     A MLFAA+SGS  AT  AIG ++
Sbjct: 62  MMAGALMNTGGISRRLVDFASAVVGHKTGGLAYVTAMASMLFAAVSGSGAATTAAIGGMM 121

Query: 124 IAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAG 183
           I  + + GY KEFA+ +  ++G+LG++IPPSI  V++     VS+  +FLAG++PG++  
Sbjct: 122 IPALIKKGYGKEFASALQASSGSLGVVIPPSIPFVLFGFMSGVSIAELFLAGIVPGVLIA 181

Query: 184 LMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAAA 243
           ++LMV  Y M K       E + + E+      A   LL+  IILGGI+ G FTPTEAA 
Sbjct: 182 VLLMVVSYFMVKNGPSTLEERVPFKEMVRRFFAALPALLMPAIILGGIFSGQFTPTEAAV 241

Query: 244 VASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHAL 303
           +A VY F V  FVYR++                                    A+   A+
Sbjct: 242 IAVVYGFIVGIFVYRELN----------------------------------LANIMEAM 267

Query: 304 FEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQ 363
            +A      +L ++A A     ++  E +PQ+IA  M S      +FL++V V LLI G 
Sbjct: 268 KDAVISNAVVLMLLAFASTFSWIMASELIPQKIAALMSSIAPNQFIFLLLVTVFLLIIGT 327

Query: 364 FMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMP 423
           F+E +  L+++ P++ P+A    ++ +H G++MVVN+ IGM+TPP+G+ LFV S ++ +P
Sbjct: 328 FLETTPALILLVPILVPVAQTFDVNLVHFGVLMVVNLAIGMVTPPLGITLFVASNISKVP 387

Query: 424 MMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456
           +  + RA +PF+  +   L+++T++P IS  +P
Sbjct: 388 LANLFRAIVPFILCMIAALLVLTFVPQISLFVP 420


Lambda     K      H
   0.329    0.144    0.421 

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: 596
Number of extensions: 32
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: 467
Length of database: 425
Length adjustment: 32
Effective length of query: 435
Effective length of database: 393
Effective search space:   170955
Effective search space used:   170955
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