GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Desulfovibrio vulgaris Hildenborough

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate 206131 DVU0705 TRAP dicarboxylate transporter, putative

Query= uniprot:I7DRS6
         (467 letters)



>MicrobesOnline__882:206131
          Length = 427

 Score =  240 bits (613), Expect = 6e-68
 Identities = 146/455 (32%), Positives = 237/455 (52%), Gaps = 38/455 (8%)

Query: 4   VLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFF 63
           +LLF +   ++ IGVP+A A+GLS+T+ +   +   L SV  +++      + LLAIP F
Sbjct: 3   ILLFGLFAVMMFIGVPLATAMGLSATVAIAA-AKLGLLSVPISVYTGV-AKYPLLAIPMF 60

Query: 64  ILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIV 123
           I A       GVA R++ F++A VG L GGLAIA +  CM+   +SGS PA   A+  ++
Sbjct: 61  IFAGMVFERSGVALRLVNFTVALVGPLRGGLAIASIMVCMVLGGISGSGPADAAAVAMVM 120

Query: 124 IAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAV-EVSVGRMFLAGVIPGLMA 182
           I GM   GY K F+AG+I  AG+  ILIPPSI  ++Y+  V + SV  +F AG+IPG +A
Sbjct: 121 IPGMAAAGYPKAFSAGLIAAAGSTAILIPPSIAFILYSVLVPQASVPALFAAGLIPGFLA 180

Query: 183 GLMLMVTIYVMAKVKNLP-KGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEA 241
           G+ L++  + ++        G+    G +  +   A  GLL   IILGGI  G FTPTEA
Sbjct: 181 GIALIIPAWALSVRHGFGLVGDDASCGSILIAFKEAIWGLLAPVIILGGIRSGYFTPTEA 240

Query: 242 AAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRH 301
           A  A  Y  FV  FVYR                 LT+                       
Sbjct: 241 AVAAVFYGLFVGFFVYRT----------------LTL------------------RGIYE 266

Query: 302 ALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIG 361
            L E+ +++  ++ +IA + +     +     + +  A++       M L+ V ++L+I 
Sbjct: 267 LLVESAEVSAVVMMIIALSSVFAWAGSTLGAFEAMGNALIGISTSETMTLLAVVLVLIIA 326

Query: 362 GQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAG 421
           G F++   +L I  P++ P+    G + +  G+IM + + IG  TPP+ LNL VT+ +A 
Sbjct: 327 GMFLDGVSILFIFIPILLPVMTHFGWNAVWFGVIMTMCLAIGQFTPPLALNLMVTTRIAD 386

Query: 422 MPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456
           + +   V   L F+  + + ++++ ++P ++T++P
Sbjct: 387 IGIEETVPWVLWFVLAMTIAMLLVVFVPQLATLVP 421


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: 646
Number of extensions: 43
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 467
Length of database: 427
Length adjustment: 33
Effective length of query: 434
Effective length of database: 394
Effective search space:   170996
Effective search space used:   170996
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