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_092484450.1 BM299_RS11930 TRAP transporter large permease

Query= SwissProt::Q9HU16
         (427 letters)



>NCBI__GCF_900115975.1:WP_092484450.1
          Length = 425

 Score =  345 bits (885), Expect = 2e-99
 Identities = 167/418 (39%), Positives = 275/418 (65%)

Query: 4   LFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIPFFL 63
           L LF   F+L+ IGVP+A SLGLS    +L      +     +LF  ++ + L+AIPFF+
Sbjct: 3   LILFASFFVLVLIGVPVAFSLGLSSIAALLYQGQIPLIVSVQRLFTGTDSFPLMAIPFFM 62

Query: 64  LSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIAI 123
           ++GA M TGG++RRL+DFA+A VGH  GGLA    +A MLFAA+SGS  AT AA+G + I
Sbjct: 63  MAGALMNTGGISRRLVDFASAVVGHKTGGLAYVTAMASMLFAAVSGSGAATTAAIGGMMI 122

Query: 124 AGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLGL 183
             +++ GY + F + +  ++G+LG++IPPSI  V++   +  S+ +LF+AG+VPG+L+ +
Sbjct: 123 PALIKKGYGKEFASALQASSGSLGVVIPPSIPFVLFGFMSGVSIAELFLAGIVPGVLIAV 182

Query: 184 ILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEAAAV 243
           +LMVV Y + +        RV  +E +     AL  LL+  IILGGI+SG FTPTEAA +
Sbjct: 183 LLMVVSYFMVKNGPSTLEERVPFKEMVRRFFAALPALLMPAIILGGIFSGQFTPTEAAVI 242

Query: 244 AAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQSIAS 303
           A VY   V +FVYR++ L+   + + ++     +++ ++A A  F+ ++ +E IPQ IA+
Sbjct: 243 AVVYGFIVGIFVYRELNLANIMEAMKDAVISNAVVLMLLAFASTFSWIMASELIPQKIAA 302

Query: 304 WVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGIIMVV 363
            ++ +  + ++FLL+V + LLI G F+E +  +++L PI  P+A    ++ +H G++MVV
Sbjct: 303 LMSSIAPNQFIFLLLVTVFLLIIGTFLETTPALILLVPILVPVAQTFDVNLVHFGVLMVV 362

Query: 364 NMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLALP 421
           N+ IG++TPP+G+ LFV S ++ +PL    RA +P+++ ++  L+++T++P +SL +P
Sbjct: 363 NLAIGMVTPPLGITLFVASNISKVPLANLFRAIVPFILCMIAALLVLTFVPQISLFVP 420


Lambda     K      H
   0.330    0.144    0.425 

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: 512
Number of extensions: 23
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: 427
Length of database: 425
Length adjustment: 32
Effective length of query: 395
Effective length of database: 393
Effective search space:   155235
Effective search space used:   155235
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 (21.9 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