GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Halopiger salifodinae KCY07-B2

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_049989147.1 LT39_RS03805 TRAP transporter large permease

Query= uniprot:I7DRS6
         (467 letters)



>NCBI__GCF_000784335.1:WP_049989147.1
          Length = 431

 Score =  241 bits (616), Expect = 3e-68
 Identities = 144/463 (31%), Positives = 240/463 (51%), Gaps = 39/463 (8%)

Query: 1   MDVVLLFSMVIGLL---LIGVPIAVALGLSSTLFLLIYSDS-SLASVAGTLFEAFEGHFT 56
           MDVVL+   ++ LL   LIGVP+A ALGL+S + +L    S S   VA TL    +  F 
Sbjct: 1   MDVVLIALFILVLLALYLIGVPVAFALGLTSLILMLTPMVSYSPELVAQTLVSGADS-FV 59

Query: 57  LLAIPFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATV 116
           LLAIP F+L   +M + G+   I  F+   +G + GG+A   + A +LF+ ++G++ A  
Sbjct: 60  LLAIPLFLLTGLYMNSFGLTSIIFDFAEEMIGPIRGGIAHVNILASILFSGMTGTAAADA 119

Query: 117 VAIGSIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGV 176
             +G+I    M+  GY K ++A V  ++  +G +IPPS+ +++Y    +VS+G +F+AG+
Sbjct: 120 AGLGAIEYEAMQDAGYEKGYSAAVTGSSAIIGPIIPPSVPLIMYGILAQVSIGVLFIAGI 179

Query: 177 IPGLMAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIF 236
           +PGL+ G  L++     A      +G W    ++  S   A+  L    +I+GG+ GG F
Sbjct: 180 VPGLIMGATLLMLCTYYAHSHGYERGTWWSLPDIWESFKTAAPALGTPVLIIGGLLGGFF 239

Query: 237 TPTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFH 296
           T TEA AVA  Y  FV    Y  +          + G F+                    
Sbjct: 240 TATEAGAVALFYTLFVGYVFYGGV----------ENGDFV-------------------- 269

Query: 297 ADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNV 356
                  +E    T  L F++A+A +   ++   Q+P  +A A++     P + L+++  
Sbjct: 270 ----ETTYEGVVTTAALTFIVASATLYGFLVRRAQLPDALAEAVIGVTGDPTLLLLMIVG 325

Query: 357 ILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVT 416
           +LLI G  ME    + I+ P+  P+    GIDPIH GI+M++ + IG++TPP G+ LF+ 
Sbjct: 326 VLLIVGLMMETIAAITILTPVFLPVIDVAGIDPIHFGIVMILTLMIGLLTPPFGIILFIL 385

Query: 417 SGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAV 459
             V  + +  ++R+ +PF   L + L+++  +P ++  LP  V
Sbjct: 386 EKVTDVGLERIMRSMVPFYIPLLIILLLVVVLPGLTLWLPKFV 428


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: 618
Number of extensions: 28
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 467
Length of database: 431
Length adjustment: 33
Effective length of query: 434
Effective length of database: 398
Effective search space:   172732
Effective search space used:   172732
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