GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntT in Pseudomonas putida KT2440

Align High-affinity gluconate transporter; Gluconate permease; Gnt-I system (characterized)
to candidate PP_0652 PP_0652 Gluconate transporter

Query= SwissProt::P39835
         (438 letters)



>FitnessBrowser__Putida:PP_0652
          Length = 461

 Score =  322 bits (825), Expect = 2e-92
 Identities = 165/449 (36%), Positives = 274/449 (61%), Gaps = 13/449 (2%)

Query: 3   LVIVAIGVILLLLLMIRFKMNGFIALVLVALAVGLMQGMPLDKVIGSIKAGVGGTLGSLA 62
           L  +A  ++L+ L++ R KM+  +AL++V++ VG    M    ++  +  G G TLG++ 
Sbjct: 10  LTALASVLVLVALIVSRLKMHPLLALLVVSIGVGFATHMAPGSIVSHLLTGAGKTLGAVG 69

Query: 63  LIMGFGAMLGKMLADCGGAQRIATTLIAKFGKKHIQWAVVLTGFTVGFALFYEVGFVLML 122
           +++  GAMLGK+LAD G  +++A  ++ +   + I WA++L  F +G  +F+EVG V+ML
Sbjct: 70  VVIALGAMLGKILADAGVTEQVADVILKRTPDRMIPWAMMLVAFVIGIPMFFEVGLVIML 129

Query: 123 PLVFTIAASANIPL-------LYVGVPMAAALSVTHGFLPPHPGPTAIATIFNADMGKTL 175
           PL+F++A              +YVGVP+ +AL+  HG +PPHPGP     +    +G T+
Sbjct: 130 PLIFSVARKLESKARFKGSAYVYVGVPVISALAAMHGMVPPHPGPLTAIAVLKTSVGPTM 189

Query: 176 LYGTILAIPTVILAGPVYA-----RVLKGIDKPIPEGLYSAKTFSEEEMPSFGVSVWTSL 230
           LYG + AIP +IL GP+Y      R+    D+ + +    A+    +  P   V +  +L
Sbjct: 190 LYGFLAAIPAMILGGPLYGMFISPRMNTRPDQALLDQFTLAEKADGQPRPGVMVGMLAAL 249

Query: 231 VPVVLMAMRAIAEMILPKGHAFLPVAEFLGDPVMATLIAVLIAMFTFGLNRGRSMDQIND 290
           +P +LM + A+AEM+LPKG+A L +A FLG+P++A L+ VL A  +  L RG   +Q+ D
Sbjct: 250 LPAILMLVHAVAEMLLPKGNALLEMASFLGNPLIAMLLGVLFAGASLVLARGGDAEQLRD 309

Query: 291 TLVSSIKIIAMMLLIIGGGGAFKQVLVDSGVDKYIASMMHETNISPLLMAWSIAAVLRIA 350
            L  S+K IA +++II GGGAF+++L  + V   I  +  ++   PL++ W IA +L ++
Sbjct: 310 ALGKSLKPIASIIMIIAGGGAFQEMLTSAKVGDAIVHLTQQSAFPPLILGWLIAMLLSVS 369

Query: 351 LGSATVAAITAGGIAAPLI-ATTGVSPELMVIAVGSGSVIFSHVNDPGFWLFKEYFNLTI 409
            GSATV  + A G+ APL  A   ++  L+ +++G GS+ F++ N  GFW+ KE F +T+
Sbjct: 370 TGSATVGIVGAAGLLAPLAGADPSLNLPLLALSIGCGSLFFNYANHAGFWMVKESFGMTM 429

Query: 410 GETIKSWSMLETIISVCGLVGCLLLNMVI 438
           GE  K+ S++++I++V GL+  L+LN  I
Sbjct: 430 GEATKTISVVQSIVAVVGLMVVLMLNAAI 458


Lambda     K      H
   0.327    0.142    0.417 

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: 525
Number of extensions: 25
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: 438
Length of database: 461
Length adjustment: 33
Effective length of query: 405
Effective length of database: 428
Effective search space:   173340
Effective search space used:   173340
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: 51 (24.3 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