GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ectP in Rhodococcus qingshengii djl-6-2

Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate WP_050655916.1 C1M55_RS03105 BCCT family transporter

Query= SwissProt::Q87PP5
         (562 letters)



>NCBI__GCF_002893965.1:WP_050655916.1
          Length = 617

 Score =  390 bits (1002), Expect = e-113
 Identities = 204/504 (40%), Positives = 322/504 (63%), Gaps = 13/504 (2%)

Query: 64  DIHNPVFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLLFAV 123
           ++  PVF I A +V+F LI+  ++   TA DA   + N I +    +++ S   F++FA+
Sbjct: 10  ELRKPVF-IPASIVIFALIAFAVIYAGTAADAFETLNNVISDGVGWWYILSATGFVIFAL 68

Query: 124 GLLFSPLGKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGTPLN 183
               S +G IRLG  +  P+   +SW +MLF+AGMGIGL+F+ VAEP +++ +    P+ 
Sbjct: 69  YCGISRIGNIRLGRDDEQPEFGMLSWFAMLFSAGMGIGLVFYGVAEPLSHYVN---PPVA 125

Query: 184 AE-AYSADAKS-LAMGATMFHWGVHGWSIYALVALALAFFAFNKGLPLSLRAAFYPIFGD 241
            + A S DA +  AM  T+FHWG+H W+IY +V L LA+  + KG PLS+R    P+ G 
Sbjct: 126 GQIAGSTDAAANQAMELTLFHWGLHAWAIYVVVGLGLAYMTYRKGRPLSIRWLLEPLLGR 185

Query: 242 -RAWGWLGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVFGLNGGIGTQMVVIAFVTF 300
            R  G +GH ID++A++ TLFG+ATSLG G QQ ++G++++  +       + +I  VT 
Sbjct: 186 ARIEGKIGHAIDVVAIVGTLFGVATSLGFGVQQISAGLDYLGWVETDNWLVITIIVIVTG 245

Query: 301 IAVLSVVRGIDGGVKLLSNVNMIVAFALLIFITFITFDT-AMGSLVDTTMAYIQNIIPL- 358
           +A  SVV G+  G+K LSN+NM++A AL +F+  +      M S V     Y+Q +  L 
Sbjct: 246 MATFSVVSGVTKGLKWLSNINMMLAAALALFVLILGPTLFLMQSWVQNLGGYVQALPELM 305

Query: 359 --SNPHGREDETWMHGWTVFYWAWWVSWSPFVGMFIARVSKGRTVREFLFAVIVIPTLVT 416
             ++P    ++ W   WT+FYW WW+SW+PFVGMFIAR+S+GRT+REF+F V++ PTLV 
Sbjct: 306 LRTSPFA--EDGWQGAWTIFYWGWWMSWAPFVGMFIARISRGRTIREFVFGVLLAPTLVG 363

Query: 417 LVWMSVFGGIALDQVVNKVGELGANGLTDISLTLFHVYDVLPYSSVISILSIVLILVFFI 476
            +W ++FG   + +  N+   L A+G  D + +LF + D LP  ++ S+L+IV+I+ FF+
Sbjct: 364 SLWFTIFGNSGILRQRNEGTMLDASGAVDTNTSLFTLLDGLPLGTISSVLAIVVIVFFFV 423

Query: 477 TSSDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWVGGKEALQALQSGVVATG 536
           TS+DSGS+VID +  GG ++     R++W  + G+ AAV+L VGG  +L ALQ+  +AT 
Sbjct: 424 TSADSGSIVIDILATGGSLETSKITRVYWTFLSGAAAAVLLIVGGSGSLTALQTVAIATA 483

Query: 537 LPFTFVLLLMCVSLVKGLRTELSA 560
           +PF+ +++L C+S++K  R E+++
Sbjct: 484 VPFSVIMVLACLSMLKAFRYEVAS 507


Lambda     K      H
   0.327    0.141    0.445 

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: 985
Number of extensions: 52
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: 562
Length of database: 617
Length adjustment: 37
Effective length of query: 525
Effective length of database: 580
Effective search space:   304500
Effective search space used:   304500
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 (21.7 bits)
S2: 53 (25.0 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