GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Dinoroseobacter shibae DFL-12

Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 3608435 Dshi_1832 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= SwissProt::O07838
         (440 letters)



>FitnessBrowser__Dino:3608435
          Length = 446

 Score =  301 bits (772), Expect = 2e-86
 Identities = 155/440 (35%), Positives = 260/440 (59%), Gaps = 5/440 (1%)

Query: 4   LIIFGLLIALMLTGMPISISLGLTVLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIPFFI 63
           LI+FG  + L+L G PI+++LG++ L     + + PI  V +  FT +  F +MA+P FI
Sbjct: 7   LILFGGFLTLLLIGAPITVALGVSTLISFLYLGENPIKFVQIA-FTSVGSFPLMALPAFI 65

Query: 64  LAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSVIL 123
           LAG  +   G+++R+IN A +  G + GG+  A V AC  F A+SGS PAT  A+G +++
Sbjct: 66  LAGALMEASGLSRRLINVAESFAGPFTGGMSAATVFACLFFGAISGSGPATTAAVGMLMI 125

Query: 124 PAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSS---AS 180
           PAM+ +G+ + + + +  +SG LGI+IPPSI ++++ +A  GM       +   +    S
Sbjct: 126 PAMIQRGYGRSYSSAITASSGGLGIVIPPSIPLIIFGIAALGMPAPPEAVEKFGTFQTVS 185

Query: 181 VGELFMAGVVPGLMLAGFLAFTTWNRARKFGYP-RLEKASLRQRWTAFREAAWGLMLIVV 239
           + +LF+AG +P  ++AG L    +  A+K GY    E  S RQ W       W LM  +V
Sbjct: 186 IPKLFIAGFMPAFLIAGSLLLMNYILAKKHGYKGSAEGWSARQIWCELYRGFWALMAPLV 245

Query: 240 VIGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLLYIITNA 299
           ++GGIY+G FTPTEAA ++  Y   +   +Y++L+ + +   L ++  ++  +L I+  A
Sbjct: 246 ILGGIYSGFFTPTEAAIVAIFYTLVVGTVIYRELSWQKLFTALETTTWLTGRVLLIMFTA 305

Query: 300 VLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIMAPILFP 359
            +F  L+    IP  +   M++   + ++   +V + LL  G FME  + +LI+ P++ P
Sbjct: 306 TVFGRLLVENQIPAVIANGMLSITDNIYIIWTLVILFLLFVGMFMETLATILILVPVMLP 365

Query: 360 VAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPWLLTMLA 419
           VA  +GIDP+HFG+++V  + +G   PP+G NL++ASGI+ + I  ++VA  P+      
Sbjct: 366 VAYSVGIDPIHFGVVMVCCLGIGFQTPPLGENLFIASGISNISIERISVAALPFAFINTV 425

Query: 420 FLVLVTYVPAISLALPNLLG 439
            + ++ +VP I+L LP LLG
Sbjct: 426 AIFIIAFVPEITLWLPRLLG 445


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: 647
Number of extensions: 39
Number of successful extensions: 5
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: 446
Length adjustment: 32
Effective length of query: 408
Effective length of database: 414
Effective search space:   168912
Effective search space used:   168912
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