GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Brucella microti CCM 4915

Align Ectoine/proline transporter ProP (characterized)
to candidate WP_004684138.1 BMI_RS07815 MFS transporter

Query= SwissProt::Q79VC4
         (504 letters)



>NCBI__GCF_000022745.1:WP_004684138.1
          Length = 450

 Score =  187 bits (474), Expect = 9e-52
 Identities = 134/425 (31%), Positives = 213/425 (50%), Gaps = 25/425 (5%)

Query: 36  TVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFG-FAVSYLVRPLGGLVLGP 94
           + +G  +E+YDF I+ +    +  +F      +W +L   FG FA  YLVRP+GG+VL  
Sbjct: 26  SALGGALEFYDFIIFVFFASVIGHLFFPPDMPDWLVLIQTFGIFAAGYLVRPVGGIVLAH 85

Query: 95  LGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGGEYAGA 154
            GDK GR++V   ++ +M++ST  +  LPT A++G  A +LL + +M+QG + GGE  GA
Sbjct: 86  FGDKFGRKRVFAFSVFLMSISTLAMAALPTYATLGVGAPILLIVFRMLQGAAIGGEVPGA 145

Query: 155 TTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASVVAITTWVTTHFYGATAMEDFGWRIPF 214
            T+VAE  P  R G    FL  G  LG   G+ +     W+ T       +  + WRIPF
Sbjct: 146 WTFVAEHVPANRVGMACGFLCSGLTLGIMIGSLIATAINWIFT----PEELSAYAWRIPF 201

Query: 215 LTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHWRPLLI 274
                 G++AVYLR  + ETP F    +  N+ + KD      +L L  V+R+H   ++I
Sbjct: 202 FIGGIFGLLAVYLRRWLAETPIF---TEMKNSRLLKD------KLPLGTVLRNHMHGVVI 252

Query: 275 GIAIVAATNTAGYALTSYM-PVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMWSDRV 333
            + ++    +AG  +T+ M   +L++  G     + A T    + +       G   DR+
Sbjct: 253 SV-LLTWILSAGIVVTTLMTATFLQKLYGYTPLQSLAATSFGTLFLMFGTVSAGAIVDRI 311

Query: 334 GRKPVYATAVAATLILMVPAFLIMNTGTIG-AVLIAL-SMVAIPTGLYVALSASALPALF 391
           G    +A    A +   V  F+      +   VL AL +++ +  G+ V  +   +   F
Sbjct: 312 GSGRFFA---VAGIFFGVATFVFYTYAAVSLPVLFALYAVMGLSVGM-VGAAPYVMVRAF 367

Query: 392 PTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAI-AGVALLFM 450
           P   RFSG+  SYN+S ++FGG TP+I   LL      +  A Y++F + +  G+ L  M
Sbjct: 368 PAPVRFSGLSFSYNVSYAVFGGLTPVIVTSLLAVN--PMAHAWYLVFIAVLTCGLGLYLM 425

Query: 451 TESSQ 455
             S Q
Sbjct: 426 ARSDQ 430


Lambda     K      H
   0.322    0.138    0.407 

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: 629
Number of extensions: 51
Number of successful extensions: 4
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: 504
Length of database: 450
Length adjustment: 33
Effective length of query: 471
Effective length of database: 417
Effective search space:   196407
Effective search space used:   196407
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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