GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Azospirillum thiophilum BV-S

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_045582020.1 AL072_RS00100 TRAP transporter large permease subunit

Query= uniprot:I7DRS6
         (467 letters)



>NCBI__GCF_001305595.1:WP_045582020.1
          Length = 432

 Score =  389 bits (1000), Expect = e-113
 Identities = 207/461 (44%), Positives = 295/461 (63%), Gaps = 40/461 (8%)

Query: 1   MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60
           M+  ++F +++ L+L G+PI+++LGL+   FL   +   + +VA  LF   E  F ++AI
Sbjct: 1   MNAAIIFGLLLALMLTGMPISISLGLTVLSFLFFMTTVPIDAVALKLFTGIE-KFEIMAI 59

Query: 61  PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120
           PFFILA +F+T GGVARR+I F+ A VGH  GGL +AGV AC LFAA+SGSSPATVVAIG
Sbjct: 60  PFFILAGNFLTHGGVARRMINFATAMVGHWHGGLGLAGVMACALFAAVSGSSPATVVAIG 119

Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVE-----VSVGRMFLAG 175
           SI++  M   G+ K F AG++  +G LGILIPPSIVMV+Y  A        S+G+MF+AG
Sbjct: 120 SIILPAMVAQGFPKHFGAGIVTTSGALGILIPPSIVMVMYCVATTGHPQAPSIGQMFIAG 179

Query: 176 VIPGLMAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGI 235
           V+PGLM  L L  T +  A+    P+     + +   +   +  GLLLI +++GGIY GI
Sbjct: 180 VVPGLMLALFLGFTTWNRARRFGYPRLPKASFAQRLHALRESFWGLLLIVVVMGGIYSGI 239

Query: 236 FTPTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFF 295
           FTPTEAAA+A+VYAF VA FVY+DM PL   PK                           
Sbjct: 240 FTPTEAAAMAAVYAFVVAVFVYKDM-PLSRVPK--------------------------- 271

Query: 296 HADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVN 355
                  L ++  ++  LL++I NA++   ++T EQ+PQ +A  +L    G  +FL+VVN
Sbjct: 272 ------VLLDSASMSAMLLYIITNAVLFSFLMTSEQIPQNMAAWILDQNMGVWVFLLVVN 325

Query: 356 VILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFV 415
           +ILL  G FMEPS +++I+AP++FP+A++LGIDP+H GI+++VNME+GM  PPVGLNL+V
Sbjct: 326 IILLAAGNFMEPSSIVLIMAPILFPVAMKLGIDPVHFGILIIVNMEVGMCHPPVGLNLYV 385

Query: 416 TSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456
            SG+  M +  +  A  P+L  + +FL ++TY+P I+   P
Sbjct: 386 ASGITKMGITELTVAVWPWLLTMLIFLGLVTYVPAITLWFP 426


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: 630
Number of extensions: 30
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: 467
Length of database: 432
Length adjustment: 33
Effective length of query: 434
Effective length of database: 399
Effective search space:   173166
Effective search space used:   173166
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 24 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