GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Pseudomonas putida KT2440

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate PP_2761 PP_2761 putative Ribose ABC transporter, permease protein

Query= SwissProt::P39328
         (341 letters)



>FitnessBrowser__Putida:PP_2761
          Length = 328

 Score =  132 bits (333), Expect = 9e-36
 Identities = 101/302 (33%), Positives = 158/302 (52%), Gaps = 11/302 (3%)

Query: 22  MPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGG 81
           MP L A   VLL  +L AP F  V    G L      +LN    +A++AIGMT  IA GG
Sbjct: 26  MPTLFAA--VLLFFALKAPGFLTV----GNLSSL---LLNNFVLLAIVAIGMTYAIAAGG 76

Query: 82  IDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATL 141
           IDLSVG  +  +  T   +  AGF L + +   L  G LAGL+N  L+A L+I PF+ATL
Sbjct: 77  IDLSVGTALDFSALTFVLLLNAGFGLYVAIPGGLLAGSLAGLFNAGLIAGLRISPFLATL 136

Query: 142 ILMVAGRGVAQLIT-AGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTA 200
             +  G  V +L++  GQ +   +   S   +  +L +P P+++  L  +++ ++  +  
Sbjct: 137 GTLFIGSSVQKLLSEGGQPIYLEAQVRSGLATERMLGVPLPLLLVALLALVYGVVLARGR 196

Query: 201 LGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWL 260
           LG  I  +G     A+ +G+  R I  L ++ S   +A+AGI++ A +  A A  +G   
Sbjct: 197 LGREIIVLGSQPLVARYSGLAQRRIAALVFIASAFASALAGILLPATV-NAYAPMSGNAF 255

Query: 261 ELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCV 320
            ++AI AV IG    +  R N+  +++G L +     G+LL G+     QV   V++L V
Sbjct: 256 LMNAIGAVFIGATLSLHNRVNVPGTLLGVLFLNVTANGLLLIGWNFFWQQVATGVLILSV 315

Query: 321 LI 322
           L+
Sbjct: 316 LL 317


Lambda     K      H
   0.327    0.142    0.416 

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: 295
Number of extensions: 28
Number of successful extensions: 2
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: 341
Length of database: 328
Length adjustment: 28
Effective length of query: 313
Effective length of database: 300
Effective search space:    93900
Effective search space used:    93900
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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