GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Sphingomonas koreensis DSMZ 15582

Align proline porter II (characterized)
to candidate Ga0059261_2720 Ga0059261_2720 Arabinose efflux permease

Query= CharProtDB::CH_024324
         (500 letters)



>FitnessBrowser__Korea:Ga0059261_2720
          Length = 558

 Score =  214 bits (546), Expect = 5e-60
 Identities = 121/325 (37%), Positives = 177/325 (54%), Gaps = 16/325 (4%)

Query: 24  RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83
           RK I A+SLG   EW+DF +YG +A  +   FF G + +   + AL  F+  F +RP G 
Sbjct: 13  RKVIIASSLGTVFEWYDFYLYGLLATVISAKFFSGVNETTAFILALGAFAAGFAVRPFGA 72

Query: 84  LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143
           L FG LGD  GR+    +T+ +M +STF +G++PSY +IG+ API+L+  ++ QG ++GG
Sbjct: 73  LVFGRLGDVVGRKYTFLVTMGLMGLSTFAVGILPSYASIGVAAPIILVALRLVQGLALGG 132

Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203
           EY GA+ +VAE++P+ KRG   SW+   +  G      VV+ I T +GEA F DWGWR+P
Sbjct: 133 EYGGAATYVAEHAPEGKRGLFTSWIQTTATLGLFAALLVVIGIRTAIGEAAFADWGWRLP 192

Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263
           F +++ L  + L++R  L E+P FQ+     E+G         K  F E A   WR+L T
Sbjct: 193 FLVSILLLAVSLWIRLQLAESPVFQK---MKEEGTTS------KAPFTE-AFGQWRNLRT 242

Query: 264 ----CIGLVIATNVTYYMLLTYMPSYLSHNLHY-SEDHGVLIIIAIMIGMLFVQPVMGLL 318
                +G V    V +Y    Y   +L   L        +LI IA+ +   F   + G L
Sbjct: 243 VLIVLLGAVAGQAVVWYTGQFYALFFLEKTLKVDGATANILIAIALALATPFF-VIFGAL 301

Query: 319 SDRFGRRPFVLLGSVALFVLAIPAF 343
           SDR GR+  +L G     +   P F
Sbjct: 302 SDRIGRKKIILTGCALAAISYFPTF 326



 Score = 48.5 bits (114), Expect = 6e-10
 Identities = 31/94 (32%), Positives = 55/94 (58%), Gaps = 2/94 (2%)

Query: 353 LIFAGLLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLV 411
           LI A L  L +++    G +A+ L  +FPT IRY+A++  ++I +    G  PT+A  +V
Sbjct: 458 LIVALLFWLVLLVTAVYGPIAALLVEIFPTRIRYTAMSLPYHIGNGWFGGFLPTIAFAMV 517

Query: 412 ESSQNLMMPAYYLMVVAVVGLITGVT-MKETANR 444
            ++ ++    +Y ++VAV+ LI G+  + ET  R
Sbjct: 518 AATGDIYYGLWYPIIVAVLTLILGLLFLPETFRR 551


Lambda     K      H
   0.327    0.142    0.429 

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: 745
Number of extensions: 42
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 500
Length of database: 558
Length adjustment: 35
Effective length of query: 465
Effective length of database: 523
Effective search space:   243195
Effective search space used:   243195
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.

Links

Downloads

Related tools

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