GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deh in Pseudomonas putida KT2440

Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate PP_2914 PP_2914 osmosensory proline/betaine/H+ permease

Query= TCDB::M1Q159
         (468 letters)



>lcl|FitnessBrowser__Putida:PP_2914 PP_2914 osmosensory
           proline/betaine/H+ permease
          Length = 500

 Score =  238 bits (607), Expect = 3e-67
 Identities = 152/458 (33%), Positives = 241/458 (52%), Gaps = 34/458 (7%)

Query: 15  KVIFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAI 74
           K I A++ G  +EW+DF ++G +A  L   F+    P   +IA L TF+V FL+RP G +
Sbjct: 26  KAITAAALGNAMEWFDFGVYGFVAYALGKVFFPNADPSVQMIAALATFSVPFLIRPLGGL 85

Query: 75  VFGRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQ 134
            FG +GD  GR+     TI IM   TF IGL+P+   +G WA I+L+  ++ QG ++GG+
Sbjct: 86  FFGALGDRFGRQKILAATIVIMSLSTFAIGLIPSYASIGIWAPILLLLAKMAQGFSVGGE 145

Query: 135 YGGAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPF 194
           Y GA+ FVAE+AP  KRGF  SW+   +  G ++  GV+++    LGE  F +WGWRLPF
Sbjct: 146 YTGASIFVAEYAPDRKRGFLGSWLDFGSIAGFVLGAGVVVLISTVLGEEKFLDWGWRLPF 205

Query: 195 MASILLVILSLWIRRALKESPLFQQ------LKDTKAVSKNPLKESFANPYNLRW-VLIA 247
             ++ L I+ L++R AL+E+P FQQ        D + ++  P K SF       W  L+ 
Sbjct: 206 FLALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLASGP-KVSFKEVATQHWRSLVT 264

Query: 248 LFGATMGQGVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFF-VFFGSLSDRI 306
             G  +   V +Y    Y   YL    +    D  +++  A+++ M F     G LSD+ 
Sbjct: 265 CIGVVIATNVTYYMLLTYMPSYLSHNLHYS-EDHGVLIIIAIMVGMLFVQPIIGLLSDKF 323

Query: 307 GRKKVMLSGMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLL---VFIQVI 363
           GR+  ++ G +          GL+A   P         A++  N  +LGL+   + I  +
Sbjct: 324 GRRPFIIVGSV----------GLLALAIP---------AFMLINSGVLGLIFAGLLIIAV 364

Query: 364 YVTMVYGPIAAFLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLW 423
            +    G +A+ L  +FPT IRY++++  ++I + +  GL P +   L+  T + +   +
Sbjct: 365 LLNFFIGVMASTLPAMFPTHIRYSALASAFNI-SVLIAGLTPTLAAWLVETTNDLYMPAY 423

Query: 424 WPMAIAGICLVVGFLLIKETNKVDISDASTSISVKHEA 461
           + M IA + LV G L +KET    +  A+ + S   EA
Sbjct: 424 YLMVIAAVGLVTG-LTMKETANKPLRGAAPAASDIEEA 460


Lambda     K      H
   0.328    0.144    0.450 

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: 727
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: 468
Length of database: 500
Length adjustment: 34
Effective length of query: 434
Effective length of database: 466
Effective search space:   202244
Effective search space used:   202244
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: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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