GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ectP in Dietzia timorensis ID05-A0528

Align Ectoine/glycine betaine/proline transporter EctP (characterized)
to candidate WP_075844956.1 BJL86_RS10330 BCCT family transporter

Query= SwissProt::Q79VE0
         (615 letters)



>NCBI__GCF_001659785.1:WP_075844956.1
          Length = 725

 Score =  319 bits (818), Expect = 2e-91
 Identities = 172/504 (34%), Positives = 283/504 (56%), Gaps = 18/504 (3%)

Query: 25  IFSISVGFIVVFVIATIALGEKARTTFSAIAGWLLENLGWMYIGGVSLVFIFLMGIFASR 84
           +F+ +   IV FV+      + A T       W+  N GW YI   ++V +F++ +  SR
Sbjct: 36  VFAGTSVIIVAFVLWAAIWPDAASTAIFGAMDWVATNFGWYYILTATIVVVFVIVVAFSR 95

Query: 85  YGRVKLGDDDDDPEHTLIVWFCMLFAGGVGAVLMFWGVAEPINHAFNVPMANEESMSEAA 144
            GR K+G D   P+  L  W  MLFA G+G  LMF+G++ P  +    P     +MS+ A
Sbjct: 96  VGRTKMGPDHSRPKFNLFTWAAMLFAAGIGVDLMFFGISGPATNYLTPPDVG--AMSDEA 153

Query: 145 IVQAFAYTFYHFGIHMWVIMALPGLSLGYFIYKRKLPPRLSSVFSPILGKHIYSTPGKLI 204
              A  +T +H+GI  W + AL G++ G F Y+  LP  + S  +PI GK I+   G  +
Sbjct: 154 ARMAPIWTIFHYGIPGWAMYALMGMAFGLFAYRYHLPLSIRSALAPIFGKRIHGAAGHTV 213

Query: 205 DVLAIVGTTFGIAVSVGLGVLQINAGMNKLWSTPQVSWVQLLIILIITAVACISVASGLD 264
           ++ A +GT FGI+VS+G+GV+ +N G+++L+  P    VQ+ ++ +   +   S  SG+D
Sbjct: 214 EIAATIGTIFGISVSLGIGVVFLNYGLSELFGVPNSLSVQIALMALAVFITIASTVSGVD 273

Query: 265 KGIKLLSNINIAMAVALMFFILFTGPTLTLLRFLVESFGIYASWMPNLMFWTDSFQ---- 320
           KGI+ LS +N+ +A+ L  ++LF+G T  +L  LV++ G + S  P++M  T ++     
Sbjct: 274 KGIRRLSELNVILAIVLALWVLFSGQTAHMLDALVQNIGDFFSRFPSMMMNTFAYSTGTA 333

Query: 321 DNPG--WQGKWTVFYWAWTICWSPYVGMFVARISRGRTVREFIGGVLALPAIFGVVWFSI 378
           D P   W+  WT+F+WAW I W+P+V +F+ARISRGRT+R+F+ GVL +P  F ++W SI
Sbjct: 334 DYPAEQWKADWTLFFWAWWIAWAPFVSLFLARISRGRTLRQFVIGVLLIPFSFILMWVSI 393

Query: 379 FGRAGIEVELSNPGFLTQPTVVEGDVPAALFNVLQEYPLTGIVSAFALVIIVIFFITSID 438
           FG A +     +  FL Q   +     +  F +L++YP +    + A++  + F++TS D
Sbjct: 394 FGNAALSF-FDDQEFLNQAVELP---ESGFFTLLEQYPGSTFTISIAVLTGMFFYVTSAD 449

Query: 439 SAALVNDMFA---TGAENQTPTSYRVMWACTIGAVAGSLLIISPSSGIATLQEVVIIVAF 495
           S +LV        T  ++  P   R++WA   GA+   +L I    G+ TLQ   ++V  
Sbjct: 450 SGSLVMANMTSKPTMNDSDGPPWLRIVWAVITGALTLVMLFI---DGVYTLQAATVMVGL 506

Query: 496 PFFLVQFVMMFSLLKGMSEDAAAV 519
           P  ++ +++MFSL K +  +   +
Sbjct: 507 PLSILIYLVMFSLWKVLKTEQLGI 530


Lambda     K      H
   0.324    0.140    0.434 

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: 1120
Number of extensions: 58
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: 615
Length of database: 725
Length adjustment: 38
Effective length of query: 577
Effective length of database: 687
Effective search space:   396399
Effective search space used:   396399
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 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